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Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.

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Progenesis QI for proteomics is the new name for Progenesis LC-MS

Progenesis QI for proteomics software references

2017

Abreu TF, Sumitomo BN, Nishiyama MY, Jr., Oliveira UC, Souza GH, Kitano ES, Zelanis A, Serrano SM, Junqueira-de-Azevedo I, Silva PI, Jr., Tashima AK (2017) Peptidomics of Acanthoscurria gomesiana spider venom reveals new toxins with potential antimicrobial activity. J Proteomics 151:232-242

Al Shweiki MR, Monchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W (2017) Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance. J Proteome Res 16:1410-1424

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Boukpessi T, Hoac B, Coyac BR, Leger T, Garcia C, Wicart P, Whyte MP, Glorieux FH, Linglart A, Chaussain C, McKee MD (2017) Osteopontin and the dento-osseous pathobiology of X-linked hypophosphatemia. Bone 95:151-161

Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Brehelin C (2017) Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions. Front Plant Sci 8:894

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Bromilow SN, Gethings LA, Langridge JI, Shewry PR, Buckley M, Bromley MJ, Mills EN (2017) Comprehensive Proteomic Profiling of Wheat Gluten Using a Combination of Data-Independent and Data-Dependent Acquisition. Front Plant Sci 7:2020

Casanovas A, Pinto-Llorente R, Carrascal M, Abian J (2017) Large-Scale Filter-Aided Sample Preparation Method for the Analysis of the Ubiquitinome. Anal Chem 89:3840-3846

Cases O, Obry A, Ben-Yacoub S, Augustin S, Joseph A, Toutirais G, Simonutti M, Christ A, Cosette P, Kozyraki R (2017) Impaired vitreous composition and retinal pigment epithelium function in the FoxG1::LRP2 myopic mice. Biochim Biophys Acta 1863:1242-1254

Chang L, Ni J, Beretov J, Wasinger VC, Hao J, Bucci J, Malouf D, Gillatt D, Graham PH, Li Y (2017) Identification of protein biomarkers and signaling pathways associated with prostate cancer radioresistance using label-free LC-MS/MS proteomic approach. Sci Rep 7:41834

Chen H, Zhang Q, Qiao L, Fan X, Zhang W, Zhao W, Chen JJ (2017) Cdc6 contributes to abrogating the G1 checkpoint under hypoxic conditions in HPV E7 expressing cells. Sci Rep 7:2927

Clamens T, Rosay T, Crepin A, Grandjean T, Kentache T, Hardouin J, Bortolotti P, Neidig A, Mooij M, Hillion M, Vieillard J, Cosette P, Overhage J, O'Gara F, Bouffartigues E, Dufour A, Chevalier S, Guery B, Cornelis P, Feuilloley MG, Lesouhaitier O (2017) The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence. Sci Rep 7:41178

Correia S, Hebraud M, Chafsey I, Chambon C, Viala D, Saenz Y, Capelo JL, Poeta P, Igrejas G (2017) Comparative subproteomic analysis of clinically acquired fluoroquinolone resistance and ciprofloxacin stress in Salmonella Typhimurium DT104B. Proteomics Clin Appl 11 (In press)

Crouzet M, Claverol S, Lomenech AM, Le Senechal C, Costaglioli P, Barthe C, Garbay B, Bonneu M, Vilain S (2017) Pseudomonas aeruginosa cells attached to a surface display a typical proteome early as 20 minutes of incubation. PLoS One 12:e0180341

Dai P, Wang Q, Wang W, Jing R, Wang F, Azadzoi KM, Yang JH, Yan Z (2017) Unraveling Molecular Differences of Gastric Cancer by Label-Free Quantitative Proteomics Analysis. Int J Mol Sci 17 (In press)

Davidson R, Gardner S, Jupp O, Bullough A, Butters S, Watts L, Donell S, Traka M, Saha S, Mithen R, Peffers M, Clegg P, Bao Y, Cassidy A, Clark I (2017) Isothiocyanates are detected in human synovial fluid following broccoli consumption and can affect the tissues of the knee joint. Sci Rep 7:3398

Demircan T, Keskin I, Dumlu SN, Ayturk N, Avsaroglu ME, Akgun E, Ozturk G, Baykal AT (2017) Detailed tail proteomic analysis of axolotl (Ambystoma mexicanum) using an mRNA-seq reference database. Proteomics 17 (In press)

Dezonne RS, Sartore RC, Nascimento JM, Saia-Cereda VM, Romao LF, Alves-Leon SV, de Souza JM, Martins-de-Souza D, Rehen SK, Gomes FC (2017) Derivation of Functional Human Astrocytes from Cerebral Organoids. Sci Rep 7:45091

Dominguez-Martin MA, Gomez-Baena G, Diez J, Lopez-Grueso MJ, Beynon RJ, Garcia-Fernandez JM (2017) Quantitative Proteomics Shows Extensive Remodeling Induced by Nitrogen Limitation in Prochlorococcusmarinus SS120. mSystems 2 (In press)

Dozio V, Sanchez JC (2017) Characterisation of extracellular vesicle-subsets derived from brain endothelial cells and analysis of their protein cargo modulation after TNF exposure. J Extracell Vesicles 6:1302705

Du Z, Chen Y, Li X (2017) Quantitative proteomic analyses of the microbial degradation of estrone under various background nitrogen and carbon conditions. Water Res 123:361-368

Eastlake K, Heywood WE, Tracey-White D, Aquino E, Bliss E, Vasta GR, Mills K, Khaw PT, Moosajee M, Limb GA (2017) Comparison of proteomic profiles in the zebrafish retina during experimental degeneration and regeneration. Sci Rep 7:44601

Fisunov GY, Evsyutina DV, Garanina IA, Arzamasov AA, Butenko IO, Altukhov IA, Nikitina AS, Govorun VM (2017) Ribosome profiling reveals an adaptation strategy of reduced bacterium to acute stress. Biochimie 132:66-74

Furrer R, Eisele PS, Schmidt A, Beer M, Handschin C (2017) Paracrine cross-talk between skeletal muscle and macrophages in exercise by PGC-1alpha-controlled BNP. Sci Rep 7:40789

Garcez PP, Nascimento JM, de Vasconcelos JM, Madeiro da Costa R, Delvecchio R, Trindade P, Loiola EC, Higa LM, Cassoli JS, Vitoria G, Sequeira PC, Sochacki J, Aguiar RS, Fuzii HT, de Filippis AM, da Silva Goncalves Vianez Junior JL, Tanuri A, Martins-de-Souza D, Rehen SK (2017) Zika virus disrupts molecular fingerprinting of human neurospheres. Sci Rep 7:40780

Gardiner M, Bournazos AM, Maturana-Martinez C, Zhong L, Egan S (2017) Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. Front Microbiol 8:1203

Glass LN, Swapna G, Chavadi SS, Tufariello JM, Mi K, Drumm JE, Lam TT, Zhu G, Zhan C, Vilcheze C, Arcos J, Chen Y, Bi L, Mehta S, Porcelli SA, Almo SC, Yeh SR, Jacobs WR, Jr., Torrelles JB, Chan J (2017) Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (APC) transporter Rv1747 to regulate mycobacterial growth. PLoS Pathog 13:e1006515

Gombar R, Pitcher TE, Lewis JA, Auld J, Vacratsis PO (2017) Proteomic characterization of seminal plasma from alternative reproductive tactics of Chinook salmon (Oncorhynchus tswatchysha). J Proteomics 157:1-9

Gomez-Baena G, Bennett RJ, Martinez-Rodriguez C, Wnek M, Laing G, Hickey G, McLean L, Beynon RJ, Carrol ED (2017) Quantitative Proteomics of Cerebrospinal Fluid in Paediatric Pneumococcal Meningitis. Sci Rep 7:7042

Goss R, Greifenhagen A, Bergner J, Volke D, Hoffmann R, Wilhelm C, Schaller-Laudel S (2017) Direct isolation of a functional violaxanthin cycle domain from thylakoid membranes of higher plants. Planta 245:793-806

Govaert E, Van Steendam K, Willems S, Vossaert L, Dhaenens M, Deforce D (2017) Comparison of fractionation proteomics for local SWATH library building. Proteomics (In press)

Grosserueschkamp F, Bracht T, Diehl HC, Kuepper C, Ahrens M, Kallenbach-Thieltges A, Mosig A, Eisenacher M, Marcus K, Behrens T, Bruning T, Theegarten D, Sitek B, Gerwert K (2017) Spatial and molecular resolution of diffuse malignant mesothelioma heterogeneity by integrating label-free FTIR imaging, laser capture microdissection and proteomics. Sci Rep 7:44829

Guerreiro JF, Mira NP, Santos AXS, Riezman H, Sa-Correia I (2017) Membrane Phosphoproteomics of Yeast Early Response to Acetic Acid: Role of Hrk1 Kinase and Lipid Biosynthetic Pathways, in Particular Sphingolipids. Front Microbiol 8:1302

Guo Z, Cheng J, Sun H, Sun W (2017) A qualitative and quantitative evaluation of the peptide characteristics of microwave- and ultrasound-assisted digestion in discovery and targeted proteomic analyses. Rapid Commun Mass Spectrom 31:1353-1362

Hakimi O, Ternette N, Murphy R, Kessler BM, Carr A (2017) A quantitative label-free analysis of the extracellular proteome of human supraspinatus tendon reveals damage to the pericellular and elastic fibre niches in torn and aged tissue. PLoS One 12:e0177656

Hanhart P, Thiess M, Amari K, Bajdzienko K, Giavalisco P, Heinlein M, Kehr J (2017) Bioinformatic and expression analysis of the Brassica napus L. cyclophilins. Sci Rep 7:1514

Hendgen-Cotta UB, Esfeld S, Coman C, Ahrends R, Klein-Hitpass L, Flogel U, Rassaf T, Totzeck M (2017) A novel physiological role for cardiac myoglobin in lipid metabolism. Sci Rep 7:43219

Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P (2017) Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 16:2339-2358

Hmmier A, O'Brien ME, Lynch V, Clynes M, Morgan R, Dowling P (2017) Proteomic analysis of bronchoalveolar lavage fluid (BALF) from lung cancer patients using label-free mass spectrometry. BBA Clin 7:97-104

Ibanez MI, Cabello P, Luque-Almagro VM, Saez LP, Olaya A, Sanchez de Medina V, Luque de Castro MD, Moreno-Vivian C, Roldan MD (2017) Quantitative proteomic analysis of Pseudomonas pseudoalcaligenes CECT5344 in response to industrial cyanide-containing wastewaters using Liquid Chromatography-Mass Spectrometry/Mass Spectrometry (LC-MS/MS). PLoS One 12:e0172908

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Kalsch J, Pott LL, Takeda A, Kumamoto H, Mollmann D, Canbay A, Sitek B, Baba HA (2017) Bathing in carbon dioxide-enriched water alters protein expression in keratinocytes of skin tissue in rats. Int J Biometeorol 61:739-746

Keck M, Androsova G, Gualtieri F, Walker A, von Ruden EL, Russmann V, Deeg CA, Hauck SM, Krause R, Potschka H (2017) A systems level analysis of epileptogenesis-associated proteome alterations. Neurobiol Dis 105:164-178

Kimura Y, Yanagimachi M, Ino Y, Aketagawa M, Matsuo M, Okayama A, Shimizu H, Oba K, Morioka I, Imagawa T, Kaneko T, Yokota S, Hirano H, Mori M (2017) Identification of candidate diagnostic serum biomarkers for Kawasaki disease using proteomic analysis. Sci Rep 7:43732

Klingeborn M, Dismuke WM, Skiba NP, Kelly U, Stamer WD, Bowes Rickman C (2017) Directional Exosome Proteomes Reflect Polarity-Specific Functions in Retinal Pigmented Epithelium Monolayers. Sci Rep 7:4901

Kuusela P, Saraswat M, Joenvaara S, Kaartinen J, Jarvinen A, Renkonen R (2017) Changes in plasma protein levels as an early indication of a bloodstream infection. PLoS One 12:e0172987

Labisch T, Buchkremer S, Phan V, Kollipara L, Gatz C, Lentz C, Nolte K, Vervoorts J, Coraspe JA, Sickmann A, Carr S, Zahedi RP, Weis J, Roos A (2017) Tracking Effects of SIL1 Increase: Taking a Closer Look Beyond the Consequences of Elevated Expression Level. Mol Neurobiol (In press)

Lee R, Fischer R, Charles PD, Adlam D, Valli A, Di Gleria K, Kharbanda RK, Choudhury RP, Antoniades C, Kessler BM, Channon KM (2017) A novel workflow combining plaque imaging, plaque and plasma proteomics identifies biomarkers of human coronary atherosclerotic plaque disruption. Clin Proteomics 14:22

Li SY, Oyala PH, Britt RD, Weintraub ST, Hunsicker-Wang LM (2017) Reactive sites and course of reduction in the Rieske protein. J Biol Inorg Chem 22:545-557

Liljedahl L, Norlin J, McGuire JN, James P (2017) Effects of insulin and the glucagon-like peptide 1 receptor agonist liraglutide on the kidney proteome in db/db mice. Physiol Rep 5

Lin F, Williams BJ, Thangella PAV, Ladak A, Schepmoes AA, Olivos HJ, Zhao K, Callister SJ, Bartley LE (2017) Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode. Front Plant Sci 8:1134

Lindner S, Gruhle K, Schmidt R, Garamus VM, Ramsbeck D, Hause G, Meister A, Sinz A, Drescher S (2017) Azide-Modified Membrane Lipids: Synthesis, Properties, and Reactivity. Langmuir 33:4960-4973

Liu X, Guo Z, Sun H, Li W, Sun W (2017) Comprehensive Map and Functional Annotation of Human Pituitary and Thyroid Proteome. J Proteome Res (In press)

Lopes-Rodrigues V, Di Luca A, Mleczko J, Meleady P, Henry M, Pesic M, Cabrera D, van Liempd S, Lima RT, O'Connor R, Falcon-Perez JM, Vasconcelos MH (2017) Identification of the metabolic alterations associated with the multidrug resistant phenotype in cancer and their intercellular transfer mediated by extracellular vesicles. Sci Rep 7:44541

Maddala R, Skiba NP, Rao PV (2017) Vertebrate Lonesome Kinase Regulated Extracellular Matrix Protein Phosphorylation, Cell Shape, and Adhesion in Trabecular Meshwork Cells. J Cell Physiol 232:2447-2460

Megger DA, Rosowski K, Radunsky C, Kosters J, Sitek B, Muller J (2017) Structurally related hydrazone-based metal complexes with different antitumor activities variably induce apoptotic cell death. Dalton Trans 46:4759-4767

Mezni A, Khazri A, Khazri O, Limam F, Cosette P, Aouani E (2017) Neuroprotective Activity of Grape Seed and Skin Extract Against Lithium Exposure Using Proteomic Research. Mol Neurobiol 54:2720-2730

Migani D, Smales CM, Bracewell DG (2017) Effects of lysosomal biotherapeutic recombinant protein expression on cell stress and protease and general host cell protein release in Chinese hamster ovary cells. Biotechnol Prog 33:666-676

Miikkulainen P, Hogel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM (2017) HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma. Cancer Metab 5:5

Mossina A, Lukas C, Merl-Pham J, Uhl FE, Mutze K, Schamberger A, Staab-Weijnitz C, Jia J, Yildirim AO, Konigshoff M, Hauck SM, Eickelberg O, Meiners S (2017) Cigarette smoke alters the secretome of lung epithelial cells. Proteomics 17 (In press)

Moussa E, Huang H, Ahras M, Lall A, Thezenas ML, Fischer R, Kessler BM, Pain A, Billker O, Casals-Pascual C (2017) Proteomic profiling of the brain of mice with experimental cerebral malaria. J Proteomics (In press)

Mulvihill ED, Moloney NM, Owens RA, Dolan SK, Russell L, Doyle S (2017) Functional Investigation of Iron-Responsive Microsomal Proteins, including MirC, in Aspergillus fumigatus. Front Microbiol 8:418

Nawrot R, Lippmann R, Matros A, Musidlak O, Nowicki G, Mock HP (2017) Proteomic comparison of Chelidonium majus L. latex in different phases of plant development. Plant Physiol Biochem 112:312-325

Neves GW, Curty NA, Kubitschek-Barreira PH, Fontaine T, Souza GH, Cunha ML, Goldman GH, Beauvais A, Latge JP, Lopes-Bezerra LM (2017) Modifications to the composition of the hyphal outer layer of Aspergillus fumigatus modulates HUVEC proteins related to inflammatory and stress responses. J Proteomics 151:83-96

Niksirat H, Andersson L, Golpour A, Chupani L, James P (2017) Quantification of egg proteome changes during fertilization in sterlet Acipenser ruthenus. Biochem Biophys Res Commun 490:189-193

Paban V, Loriod B, Villard C, Buee L, Blum D, Pietropaolo S, Cho YH, Gory-Faure S, Mansour E, Gharbi A, Alescio-Lautier B (2017) Omics analysis of mouse brain models of human diseases. Gene 600:90-100

Passamani LZ, Barbosa RR, Reis RS, Heringer AS, Rangel PL, Santa-Catarina C, Grativol C, Veiga CFM, Souza-Filho GA, Silveira V (2017) Salt stress induces changes in the proteomic profile of micropropagated sugarcane shoots. PLoS One 12:e0176076

Petushkova NA, Zgoda VG, Pyatnitskiy MA, Larina OV, Teryaeva NB, Potapov AA, Lisitsa AV (2017) Post-translational modifications of FDA-approved plasma biomarkers in glioblastoma samples. PLoS One 12:e0177427

Porte B, Chatelain C, Hardouin J, Derambure C, Zerdoumi Y, Hauchecorne M, Dupre N, Bekri S, Gonzalez B, Marret S, Cosette P, Leroux P (2017) Proteomic and transcriptomic study of brain microvessels in neonatal and adult mice. PLoS One 12:e0171048

Potu H, Peterson LF, Kandarpa M, Pal A, Sun H, Durham A, Harms PW, Hollenhorst PC, Eskiocak U, Talpaz M, Donato NJ (2017) Usp9x regulates Ets-1 ubiquitination and stability to control NRAS expression and tumorigenicity in melanoma. Nat Commun 8:14449

Procopio N, Chamberlain AT, Buckley M (2017) Intra- and Interskeletal Proteome Variations in Fresh and Buried Bones. J Proteome Res 16:2016-2029

Quesada-Calvo F, Massot C, Bertrand V, Longuespee R, Bletard N, Somja J, Mazzucchelli G, Smargiasso N, Baiwir D, De Pauw-Gillet MC, Delvenne P, Malaise M, Coimbra Marques C, Polus M, De Pauw E, Meuwis MA, Louis E (2017) OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics 14:9

Salah A, Yoshifuji H, Ito S, Kitagori K, Kiso K, Yamada N, Nakajima T, Haga H, Tsuruyama T, Miyagawa-Hayashino A (2017) High Expression of Galectin-3 in Patients with IgG4-Related Disease: A Proteomic Approach. Patholog Res Int 2017:9312142

Saraswat M, Joenvaara S, Seppanen H, Mustonen H, Haglund C, Renkonen R (2017) Comparative proteomic profiling of the serum differentiates pancreatic cancer from chronic pancreatitis. Cancer Med 6:1738-1751

Saraswat M, Makitie A, Agarwal R, Joenvaara S, Renkonen S (2017) Oral squamous cell carcinoma patients can be differentiated from healthy individuals with label-free serum proteomics. Br J Cancer 117:376-384

Sarver DC, Kharaz YA, Sugg KB, Gumucio JP, Comerford E, Mendias CL (2017) Sex differences in tendon structure and function. J Orthop Res (In press)

Sebastiana M, Martins J, Figueiredo A, Monteiro F, Sardans J, Penuelas J, Silva A, Roepstorff P, Pais MS, Coelho AV (2017) Oak protein profile alterations upon root colonization by an ectomycorrhizal fungus. Mycorrhiza 27:109-128

Shevchenko A, Yang Y, Knaust A, Verbavatz JM, Mai H, Wang B, Wang C (2017) Open sesame: Identification of sesame oil and oil soot ink in organic deposits of Tang Dynasty lamps from Astana necropolis in China. PLoS One 12:e0158636

Smine S, Obry A, Kadri S, Hardouin J, Freret M, Amri M, Jouenne T, Limam F, Cosette P, Aouani E (2017) Brain proteomic modifications associated to protective effect of grape extract in a murine model of obesity. Biochim Biophys Acta 1865:578-588

Soares EA, Werth EG, Madronero LJ, Ventura JA, Rodrigues SP, Hicks LM, Fernandes PM (2017) Label-free quantitative proteomic analysis of pre-flowering PMeV-infected Carica papaya L. J Proteomics 151:275-283

Sollanek KJ, Burniston JG, Kavazis AN, Morton AB, Wiggs MP, Ahn B, Smuder AJ, Powers SK (2017) Global Proteome Changes in the Rat Diaphragm Induced by Endurance Exercise Training. PLoS One 12:e0171007

Soman KV, Stafford SJ, Pazdrak K, Wu Z, Luo X, White WI, Wiktorowicz JE, Calhoun WJ, Kurosky A (2017) Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study. J Proteome Res 16:2663-2679

Subramanian V, Seemann I, Merl-Pham J, Hauck SM, Stewart FA, Atkinson MJ, Tapio S, Azimzadeh O (2017) Role of TGF Beta and PPAR Alpha Signaling Pathways in Radiation Response of Locally Exposed Heart: Integrated Global Transcriptomics and Proteomics Analysis. J Proteome Res 16:307-318

Sydor S, Sowa JP, Megger DA, Schlattjan M, Jafoui S, Wingerter L, Carpinteiro A, Baba HA, Bechmann LP, Sitek B, Gerken G, Gulbins E, Canbay A (2017) Acid sphingomyelinase deficiency in Western diet-fed mice protects against adipocyte hypertrophy and diet-induced liver steatosis. Mol Metab 6:416-427

Taleb RSZ, Moez P, Younan D, Eisenacher M, Tenbusch M, Sitek B, Bracht T (2017) Quantitative proteome analysis of plasma microparticles for the characterization of HCV-induced hepatic cirrhosis and hepatocellular carcinoma. Proteomics Clin Appl (In press)

Ting KR, Henry M, Meiller J, Larkin A, Clynes M, Meleady P, Bazou D, Dowling P, O'Gorman P (2017) Novel panel of protein biomarkers to predict response to bortezomib-containing induction regimens in multiple myeloma patients. BBA Clin 8:28-34

Valikangas T, Suomi T, Elo LL (2017) A comprehensive evaluation of popular proteomics software workflows for label-free proteome quantification and imputation. Brief Bioinform (In press)

von Toerne C, Laimighofer M, Achenbach P, Beyerlein A, de Las Heras Gala T, Krumsiek J, Theis FJ, Ziegler AG, Hauck SM (2017) Peptide serum markers in islet autoantibody-positive children. Diabetologia 60:287-295

Wadsworth C, Procopio N, Anderung C, Carretero JM, Iriarte E, Valdiosera C, Elburg R, Penkman K, Buckley M (2017) Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites. J Proteomics 158:1-8

Werth EG, McConnell EW, Gilbert TS, Couso Lianez I, Perez CA, Manley CK, Graves LM, Umen JG, Hicks LM (2017) Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics. Plant J 89:416-426

Witzke KE, Rosowski K, Muller C, Ahrens M, Eisenacher M, Megger DA, Knobloch J, Koch A, Bracht T, Sitek B (2017) Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins. J Proteome Res 16:137-146

Willems S, Bouyssie D, David M, Locard-Paulet M, Mechtler K, Schwammle V, Uszkoreit J, Vaudel M, Dorfer V (2017) Proceedings of the EuBIC Winter School 2017. J Proteomics 161:78-80

Wu CY, Hsu WL, Tsai MH, Liang JL, Lu JH, Yen CJ, Yu HS, Noda M, Lu CY, Chen CH, Yan SJ, Yoshioka T (2017) Hydrogen gas protects IP3Rs by reducing disulfide bridges in human keratinocytes under oxidative stress. Sci Rep 7:3606

Yadetie F, Oveland E, Doskeland A, Berven F, Goksoyr A, Karlsen OA (2017) Quantitative proteomics analysis reveals perturbation of lipid metabolic pathways in the liver of Atlantic cod (Gadus morhua) treated with PCB 153. Aquat Toxicol 185:19-28

Yang K, Adin C, Shen Q, Lee LJ, Yu L, Fadda P, Samogyi A, Ham K, Xu L, Gilor C, Ziouzenkova O (2017) Aldehyde dehydrogenase 1 a1 regulates energy metabolism in adipocytes from different species. Xenotransplantation (In press)

Yang X, Feng L, Zhao L, Liu X, Hassani D, Huang D (2017) Effect of glycine nitrogen on lettuce growth under soilless culture: a metabolomics approach to identify the main changes occurred in plant primary and secondary metabolism. J Sci Food Agric (In press)

Yuan ET, Ino Y, Kawaguchi M, Kimura Y, Hirano H, Kinoshita-Kikuta E, Kinoshita E, Koike T (2017) A Phos-tag-based micropipette-tip method for rapid and selective enrichment of phosphopeptides. Electrophoresis (In press)

Zhang Y, Beard KFM, Swart C, Bergmann S, Krahnert I, Nikoloski Z, Graf A, Ratcliffe RG, Sweetlove LJ, Fernie AR, Obata T (2017) Protein-protein interactions and metabolite channelling in the plant tricarboxylic acid cycle. Nat Commun 8:15212

Zhao M, Li M, Yang Y, Guo Z, Sun Y, Shao C, Sun W, Gao Y (2017) A comprehensive analysis and annotation of human normal urinary proteome. Sci Rep 7:3024

Zhou X, Xing X, Hou J, Liu J (2017) Quantitative proteomics analysis of proteins involved in alkane uptake comparing the profiling of Pseudomonas aeruginosa SJTD-1 in response to n-octadecane and n-hexadecane. PLoS One 12:e0179842


2016

Acioglu C, Mirabelli E, Baykal AT, Ni L, Ratnayake A, Heary RF, Elkabes S (2016) Toll like receptor 9 antagonism modulates spinal cord neuronal function and survival: Direct versus astrocyte-mediated mechanisms. Brain Behav Immun 56:310-324

Ademowo OS, Hernandez B, Collins E, Rooney C, Fearon U, van Kuijk AW, Tak PP, Gerlag DM, FitzGerald O, Pennington SR (2016) Discovery and confirmation of a protein biomarker panel with potential to predict response to biological therapy in psoriatic arthritis. Ann Rheum Dis 75:234-241

Ahrne E, Glatter T, Vigano C, Schubert C, Nigg EA, Schmidt A (2016) Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments. J Proteome Res 15:2537-2547

Akhtar MZ, Huang H, Kaisar M, Lo Faro ML, Rebolledo R, Morten K, Heather LC, Dona A, Leuvenink HG, Fuggle SV, Kessler BM, Pugh CW, Ploeg RJ (2016) Using an Integrated -Omics Approach to Identify Key Cellular Processes That Are Disturbed in the Kidney After Brain Death. Am J Transplant 16:1421-1440

Almeida AM, Nanni P, Ferreira AM, Fortes C, Grossmann J, Bessa RJ, Costa P (2016) The longissimus thoracis muscle proteome in Alentejana bulls as affected by growth path. J Proteomics 152:206-215

Angi M, Kalirai H, Prendergast S, Simpson D, Hammond DE, Madigan MC, Beynon RJ, Coupland SE (2016) In-depth proteomic profiling of the uveal melanoma secretome. Oncotarget 7:49623-49635

Annibal A, Riemer T, Jovanovic O, Westphal D, Griesser E, Pohl EE, Schiller J, Hoffmann R, Fedorova M (2016) Structural, biological and biophysical properties of glycated and glycoxidized phosphatidylethanolamines. Free Radic Biol Med 95:293-307

Armstrong SD, Xia D, Bah GS, Krishna R, Ngangyung HF, LaCourse EJ, McSorley HJ, Kengne-Ouafo JA, Chounna-Ndongmo PW, Wanji S, Enyong PA, Taylor DW, Blaxter ML, Wastling JM, Tanya VN, Makepeace BL (2016) Stage-specific Proteomes from Onchocerca ochengi, Sister Species of the Human River Blindness Parasite, Uncover Adaptations to a Nodular Lifestyle. Mol Cell Proteomics 15:2554-2575

Bauer M, Cubizolles F, Schmidt A, Nigg EA (2016) Quantitative analysis of human centrosome architecture by targeted proteomics and fluorescence imaging. Embo J 35:2152-2166

Bespyatykh J, Shitikov E, Butenko I, Altukhov I, Alexeev D, Mokrousov I, Dogonadze M, Zhuravlev V, Yablonsky P, Ilina E, Govorun V (2016) Proteome analysis of the Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 6:28985

Betz BB, Jenks SJ, Cronshaw AD, Lamont DJ, Cairns C, Manning JR, Goddard J, Webb DJ, Mullins JJ, Hughes J, McLachlan S, Strachan MW, Price JF, Conway BR (2016) Urinary peptidomics in a rodent model of diabetic nephropathy highlights epidermal growth factor as a biomarker for renal deterioration in patients with type 2 diabetes. Kidney Int 89:1125-1135

Bivol LM, Iversen BM, Hultstrom M, Wallace PW, Reed RK, Wiig H, Tenstad O (2016) Unilateral renal ischaemia in rats induces a rapid secretion of inflammatory markers to renal lymph and increased capillary permeability. J Physiol 594:1709-1726

Blein-Nicolas M, Zivy M (2016) Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics. Biochim Biophys Acta 1864:883-895

Bonde MT, Pedersen M, Klausen MS, Jensen SI, Wulff T, Harrison S, Nielsen AT, Herrgard MJ, Sommer MO (2016) Predictable tuning of protein expression in bacteria. Nat Methods 13:233-236

Borgdorff H, Armstrong SD, Tytgat HL, Xia D, Ndayisaba GF, Wastling JM, van de Wijgert JH (2016) Unique Insights in the Cervicovaginal Lactobacillus iners and L. crispatus Proteomes and Their Associations with Microbiota Dysbiosis. PLoS One 11:e0150767

Branson OE, Freitas MA (2016) Tag-Count Analysis of Large-Scale Proteomic Data. J Proteome Res 15:4742-4746

Brauers E, Roos A, Kollipara L, Zahedi RP, Beckmann A, Mohanadas N, Bauer H, Hausler M, Thoma S, Kress W, Senderek J, Weis J (2016) The Caveolin-3 G56S sequence variant of unknown significance: Muscle biopsy findings and functional cell biological analysis. Proteomics Clin Appl (In press)

Broeckx V, Boonen K, Pringels L, Sagaert X, Prenen H, Landuyt B, Schoofs L, Maes E (2016) Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues. Mol Biosyst 12:553-565

Broering R, Trippler M, Werner M, Real CI, Megger DA, Bracht T, Schweinsberg V, Sitek B, Eisenacher M, Meyer HE, Baba HA, Weber F, Hoffmann AC, Gerken G, Schlaak JF (2016) Hepatic expression of proteasome subunit alpha type-6 is upregulated during viral hepatitis and putatively regulates the expression of ISG15 ubiquitin-like modifier, a proviral host gene in hepatitis C virus infection. J Viral Hepat 23:375-386

Buts K, Hertog ML, Ho QT, America AH, Cordewener J, Vercammen J, Carpentier SC, Nicolai B (2016) Influence of pre-harvest calcium, potassium and triazole application on the proteome of apple at harvest. J Sci Food Agric 96:4984-4993

Cappelle K, Smagghe G, Dhaenens M, Meeus I (2016) Israeli Acute Paralysis Virus Infection Leads to an Enhanced RNA Interference Response and Not Its Suppression in the Bumblebee Bombus terrestris. Viruses 8 of apple at harvest. J Sci Food Agric 96:4984-4993

Carella P, Merl-Pham J, Wilson DC, Dey S, Hauck SM, Vlot AC, Cameron RK (2016) Comparative Proteomics Analysis of Phloem Exudates Collected during the Induction of Systemic Acquired Resistance. Plant Physiol 171:1495-1510

Casadei N, Sood P, Ulrich T, Fallier-Becker P, Kieper N, Helling S, May C, Glaab E, Chen J, Nuber S, Marcus K, Rapaport D, Ott T, Riess O, Kruger R, Fitzgerald JC (2016) Mitochondrial defects and neurodegeneration in mice overexpressing wild-type or G399S mutant HtrA2. Hum Mol Genet 25:459-471

Cevik O, Baykal AT, Sener A (2016) Platelets Proteomic Profiles of Acute Ischemic Stroke Patients. PLoS One 11:e0158287

Chen F, Spiessens C, D'Hooghe T, Peeraer K, Carpentier S (2016) Follicular fluid biomarkers for human in vitro fertilization outcome: Proof of principle. Proteome Sci 14:17

Cholet C, Claverol S, Claisse O, Rabot A, Osowsky A, Dumot V, Ferrari G, Geny L (2016) Tartaric acid pathways in Vitis vinifera L. (cv. Ugni blanc): a comparative study of two vintages with contrasted climatic conditions. BMC Plant Biol 16:144

Ciregia F, Kollipara L, Giusti L, Zahedi RP, Giacomelli C, Mazzoni MR, Giannaccini G, Scarpellini P, Urbani A, Sickmann A, Lucacchini A, Bazzichi L (2016) Bottom-up proteomics suggests an association between differential expression of mitochondrial proteins and chronic fatigue syndrome. Transl Psychiatry 6:e904

Colak D, Alaiya AA, Kaya N, Muiya NP, AlHarazi O, Shinwari Z, Andres E, Dzimiri N (2016) Integrated Left Ventricular Global Transcriptome and Proteome Profiling in Human End-Stage Dilated Cardiomyopathy. PLoS One 11:e0162669

Correia S, Hebraud M, Chafsey I, Chambon C, Viala D, Torres C, de Toro M, Capelo JL, Poeta P, Igrejas G (2016) Impacts of experimentally induced and clinically acquired quinolone resistance on the membrane and intracellular subproteomes of Salmonella Typhimurium DT104B. J Proteomics 145:46-59

Coskun A, Baykal AT, Kazan D, Akgoz M, Senal MO, Berber I, Titiz I, Bilsel G, Kilercik H, Karaosmanoglu K, Cicek M, Yurtsever I, Yazici C (2016) Proteomic Analysis of Kidney Preservation Solutions Prior to Renal Transplantation. PLoS One 11:e0168755

Cowan E, Kumar P, Burch KJ, Grieve DJ, Green BD, Graham SF (2016) Treatment of lean and diet-induced obesity (DIO) mice with a novel stable obestatin analogue alters plasma metabolite levels as detected by untargeted LC-MS metabolomics. Metabolomics 12:124

Del Boccio P, Rossi C, di Ioia M, Cicalini I, Sacchetta P, Pieragostino D (2016) Integration of metabolomics and proteomics in multiple sclerosis: From biomarkers discovery to personalized medicine. Proteomics Clin Appl 10:470-484

Demarchi B, Hall S, Roncal-Herrero T, Freeman CL, Woolley J, Crisp MK, Wilson J, et al. (2016) Protein sequences bound to mineral surfaces persist into deep time. Elife 5

Denis S, Sayd T, Georges A, Chambon C, Chalancon S, Sante-Lhoutellier V, Blanquet-Diot S (2016) Digestion of cooked meat proteins is slightly affected by age as assessed using the dynamic gastrointestinal TIM model and mass spectrometry. Food Funct 7:2682-2691

Dhawi F, Datta R, Ramakrishna W (2016) Proteomics provides insights into biological pathways altered by plant growth promoting bacteria and arbuscular mycorrhiza in sorghum grown in marginal soil. Biochim Biophys Acta 1865:243-251

Dionisio G, Kryger P, Steenberg T (2016) Label-Free Differential Proteomics and Quantification of Exoenzymes from Isolates of the Entomopathogenic Fungus Beauveria bassiana. Insects 7 (in press)

Distler U, Kuharev J, Navarro P, Tenzer S (2016) Label-free quantification in ion mobility-enhanced data-independent acquisition proteomics. Nat Protoc 11:795-812

Dong S, Liu L, Wu W, Armstrong SD, Xia D, Nan H, Hiscox JA, Chen H (2016) Determination of the interactome of non-structural protein12 from highly pathogenic porcine reproductive and respiratory syndrome virus with host cellular proteins using high throughput proteomics and identification of HSP70 as a cellular factor for virus replication. J Proteomics 146:58-69

Dowle AA, Wilson J, Thomas JR (2016) Comparing the Diagnostic Classification Accuracy of iTRAQ, Peak-Area, Spectral-Counting, and emPAI Methods for Relative Quantification in Expression Proteomics. J Proteome Res 15:3550-3562

Downs ML, Baumert JL, Taylor SL, Mills EN (2016) Mass spectrometric analysis of allergens in roasted walnuts. J Proteomics 142:62-69

Dudekula K, Le Bihan T (2016) Data from quantitative label free proteomics analysis of rat spleen. Data Brief 8:494-500

Duressa TF, Boonen K, Huybrechts R (2016) A quantitative peptidomics approach to unravel immunological functions of angiotensin converting enzyme in Locusta migratoria. Gen Comp Endocrinol 235:120-129

Fascellaro G, Petrera A, Lai ZW, Nanni P, Grossmann J, Burger S, Biniossek ML, Gomez-Auli A, Schilling O, Imkamp F (2016) Comprehensive Proteomic Analysis of Nitrogen-Starved Mycobacterium smegmatis Deltapup Reveals the Impact of Pupylation on Nitrogen Stress Response. J Proteome Res 15:2812-2825

Frolov A, Bilova T, Paudel G, Berger R, Balcke GU, Birkemeyer C, Wessjohann LA (2016) Early responses of mature Arabidopsis thaliana plants to reduced water potential in the agar-based polyethylene glycol infusion drought model. J Plant Physiol 208:70-83

Gasser V, Baco E, Cunrath O, August PS, Perraud Q, Zill N, Schleberger C, Schmidt A, Paulen A, Bumann D, Mislin GL, Schalk IJ (2016) Catechol siderophores repress the pyochelin pathway and activate the enterobactin pathway in Pseudomonas aeruginosa: an opportunity for siderophore-antibiotic conjugates development. Environ Microbiol 18:819-832

Geiger R, Rieckmann JC, Wolf T, Basso C, Feng Y, Fuhrer T, Kogadeeva M, Picotti P, Meissner F, Mann M, Zamboni N, Sallusto F, Lanzavecchia A (2016) L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity. Cell 167:829-842 e813

Gergondey R, Garcia C, Serre V, Camadro JM, Auchere F (2016) The adaptive metabolic response involves specific protein glutathionylation during the filamentation process in the pathogen Candida albicans. Biochim Biophys Acta 1862:1309-1323

Govaert E, Van Steendam K, Scheerlinck E, Vossaert L, Meert P, Stella M, Willems S, De Clerck L, Dhaenens M, Deforce D (2016) Extracting histones for the specific purpose of label-free MS. Proteomics 16:2937-2944

Grandl G, Muller S, Moest H, Moser C, Wollscheid B, Wolfrum C (2016) Depot specific differences in the adipogenic potential of precursors are mediated by collagenous extracellular matrix and Flotillin 2 dependent signaling. Mol Metab 5:937-947

Grosche A, Hauser A, Lepper MF, Mayo R, von Toerne C, Merl-Pham J, Hauck SM (2016) The Proteome of Native Adult Muller Glial Cells From Murine Retina. Mol Cell Proteomics 15:462-480

Grouneva I, Muth-Pawlak D, Battchikova N, Aro EM (2016) Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana. J Proteome Res 15:1649-1658

Gu H, Ren JM, Jia X, Levy T, Rikova K, Yang V, Lee KA, Stokes MP, Silva JC (2016) Quantitative Profiling of Post-translational Modifications by Immunoaffinity Enrichment and LC-MS/MS in Cancer Serum without Immunodepletion. Mol Cell Proteomics 15:692-702

Gutierrez-Carbonell E, Takahashi D, Luthje S, Gonzalez-Reyes JA, Mongrand S, Contreras-Moreira B, Abadia A, Uemura M, Abadia J, Lopez-Millan AF (2016) A Shotgun Proteomic Approach Reveals That Fe Deficiency Causes Marked Changes in the Protein Profiles of Plasma Membrane and Detergent-Resistant Microdomain Preparations from Beta vulgaris Roots. J Proteome Res 15:2510-2524

Hammond DE, Claydon AJ, Simpson DM, Edward D, Stockley P, Hurst JL, Beynon RJ (2016) Proteome Dynamics: Tissue Variation in the Kinetics of Proteostasis in Intact Animals. Mol Cell Proteomics 15:1204-1219

Heinz A, Huertas AC, Schrader CU, Pankau R, Gosch A, Schmelzer CE (2016) Elastins from patients with Williams-Beuren syndrome and healthy individuals differ on the molecular level. Am J Med Genet A 170:1832-1842

Heinzelmann K, Noskovicova N, Merl-Pham J, Preissler G, Winter H, Lindner M, Hatz R, Hauck SM, Behr J, Eickelberg O (2016) Surface proteome analysis identifies platelet derived growth factor receptor-alpha as a critical mediator of transforming growth factor-beta-induced collagen secretion. Int J Biochem Cell Biol 74:44-59

Henderson MX, Wirak GS, Zhang YQ, Dai F, Ginsberg SD, Dolzhanskaya N, Staropoli JF, Nijssen PC, Lam TT, Roth AF, Davis NG, Dawson G, Velinov M, Chandra SS (2016) Neuronal ceroid lipofuscinosis with DNAJC5/CSPalpha mutation has PPT1 pathology and exhibit aberrant protein palmitoylation. Acta Neuropathol 131:621-637

Hernandez-Castellano LE, Ferreira AM, Nanni P, Grossmann J, Arguello A, Capote J, Cai G, Lippolis J, Castro N, de Almeida AM (2016) The goat (Capra hircus) mammary gland secretory tissue proteome as influenced by weight loss: A study using label free proteomics. J Proteomics 145:60-69

Hoehenwarter W, Monchgesang S, Neumann S, Majovsky P, Abel S, Muller J (2016) Comparative expression profiling reveals a role of the root apoplast in local phosphate response. BMC Plant Biol 16:106

Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ (2016) Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). Philos Trans A Math Phys Eng Sci 374

Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ (2016) Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition. J Cell Biol 212:349-364

Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, et al. (2016) The genomic basis of parasitism in the Strongyloides clade of nematodes. Nat Genet 48:299-307

Ino Y, Arakawa N, Ishiguro H, Uemura H, Kubota Y, Hirano H, Toda T (2016) Phosphoproteome analysis demonstrates the potential role of THRAP3 phosphorylation in androgen-independent prostate cancer cell growth. Proteomics 16:1069-1078

Johnson PE, Sayers RL, Gethings LA, Balasundaram A, Marsh JT, Langridge JI, Mills EN (2016) Quantitative Proteomic Profiling of Peanut Allergens in Food Ingredients Used for Oral Food Challenges. Anal Chem 88:5689-5695

Kahne T, Richter S, Kolodziej A, Smalla KH, Pielot R, Engler A, Ohl FW, Dieterich DC, Seidenbecher C, Tischmeyer W, Naumann M, Gundelfinger ED (2016) Proteome rearrangements after auditory learning: high-resolution profiling of synapse-enriched protein fractions from mouse brain. J Neurochem 138:124-138

Kaisar M, van Dullemen LF, Thezenas ML, Charles PD, Ploeg RJ, Kessler BM (2016) Plasma Biomarker Profile Alterations during Variable Blood Storage. Clin Chem 62:1272-1274

Kaisar M, van Dullemen LF, Thezenas ML, Zeeshan Akhtar M, Huang H, Rendel S, Charles PD, Fischer R, Ploeg RJ, Kessler BM (2016) Plasma degradome affected by variable storage of human blood. Clin Proteomics 13:26

Kanonidis EI, Roy MM, Deighton RF, Le Bihan T (2016) Protein Co-Expression Analysis as a Strategy to Complement a Standard Quantitative Proteomics Approach: Case of a Glioblastoma Multiforme Study. PLoS One 11:e0161828

Kelly PS, McSweeney S, Coleman O, Carillo S, Henry M, Chandran D, Kellett A, Bones J, Clynes M, Meleady P, Barron N (2016) Process-relevant concentrations of the leachable bDtBPP impact negatively on CHO cell production characteristics. Biotechnol Prog 32:1547-1558

Kharaz YA, Tew SR, Peffers M, Canty-Laird EG, Comerford E (2016) Proteomic differences between native and tissue-engineered tendon and ligament. Proteomics 16:1547-1556

Klobucar M, Sedic M, Gehrig P, Grossmann J, Bilic M, Kovac-Bilic L, Pavelic K, Kraljevic Pavelic S (2016) Basement membrane protein ladinin-1 and the MIF-CD44-beta1 integrin signaling axis are implicated in laryngeal cancer metastasis. Biochim Biophys Acta 1862:1938-1954

Kohtala S, Theilmann W, Suomi T, Wigren HK, Porkka-Heiskanen T, Elo LL, Rokka A, Rantamaki T (2016) Brief Isoflurane Anesthesia Produces Prominent Phosphoproteomic Changes in the Adult Mouse Hippocampus. ACS Chem Neurosci 7:749-756

Konig T, Troder SE, Bakka K, Korwitz A, Richter-Dennerlein R, Lampe PA, Patron M, Muhlmeister M, Guerrero-Castillo S, Brandt U, Decker T, Lauria I, Paggio A, Rizzuto R, Rugarli EI, De Stefani D, Langer T (2016) The m-AAA Protease Associated with Neurodegeneration Limits MCU Activity in Mitochondria. Mol Cell 64:148-162

Kras KA, Willis WT, Barker N, Czyzyk T, Langlais PR, Katsanos CS (2016) Subsarcolemmal mitochondria isolated with the proteolytic enzyme nagarse exhibit greater protein specific activities and functional coupling. Biochem Biophys Rep 6:101-107

Kumar Y, Zhang L, Panigrahi P, Dholakia BB, Dewangan V, Chavan SG, Kunjir SM, Wu X, Li N, Rajmohanan PR, Kadoo NY, Giri AP, Tang H, Gupta VS (2016) Fusarium oxysporum mediates systems metabolic reprogramming of chickpea roots as revealed by a combination of proteomics and metabolomics. Plant Biotechnol J 14:1589-1603

Lachen-Montes M, Gonzalez-Morales A, de Morentin XM, Perez-Valderrama E, Ausin K, Zelaya MV, Serna A, Aso E, Ferrer I, Fernandez-Irigoyen J, Santamaria E (2016) An early dysregulation of FAK and MEK/ERK signaling pathways precedes the beta-amyloid deposition in the olfactory bulb of APP/PS1 mouse model of Alzheimer's disease. J Proteomics 148:149-158

Lereim RR, Oveland E, Xiao Y, Torkildsen O, Wergeland S, Myhr KM, Sun SC, Berven FS (2016) The Brain Proteome of the Ubiquitin Ligase Peli1 Knock-Out Mouse during Experimental Autoimmune Encephalomyelitis. J Proteomics Bioinform 9:209-219

Leroy C, Ramos P, Cornille K, Bonenfant D, Fritsch C, Voshol H, Bentires-Alj M (2016) Activation of IGF1R/p110beta/AKT/mTOR confers resistance to alpha-specific PI3K inhibition. Breast Cancer Res 18:41

Le-Trilling VT, Megger DA, Katschinski B, Landsberg CD, Ruckborn MU, Tao S, Krawczyk A, Bayer W, Drexler I, Tenbusch M, Sitek B, Trilling M (2016) Broad and potent antiviral activity of the NAE inhibitor MLN4924. Sci Rep 6:19977

Li X, Gao Y (2016) Potential urinary aging markers of 20-month-old rats. PeerJ 4:e2058

Liljedahl L, Pedersen MH, Norlin J, McGuire JN, James P (2016) N-glycosylation proteome enrichment analysis in kidney reveals differences between diabetic mouse models. Clin Proteomics 13:22

Limonier F, Van Steendam K, Waeterloos G, Brusselmans K, Sneyers M, Deforce D (2016) An application of mass spectrometry for quality control of biologicals: Highly sensitive profiling of plasma residuals in human plasma-derived immunoglobulin. J Proteomics 152:312-320

Lin CY, Chen CY, Yu CH, Yu IS, Lin SR, Wu JT, Lin YH, Kuo PL, Wu JC, Lin SW (2016) Human X-linked Intellectual Disability Factor CUL4B Is Required for Post-meiotic Sperm Development and Male Fertility. Sci Rep 6:20227

Lin PC, Yang YF, Tyan YC, Hsiao ES, Chu PC, Lee CT, Lee JC, Chen YM, Liao PC (2016) Identification of Phosphorylated Cyclin-Dependent Kinase 1 Associated with Colorectal Cancer Survival Using Label-Free Quantitative Analyses. PLoS One 11:e0158844

Liu F, Bai X, Yang FQ, Zhang XJ, Hu Y, Li P, Wan JB (2016) Discriminating from species of Curcumae Radix (Yujin) by a UHPLC/Q-TOFMS-based metabolomics approach. Chin Med 11:21

Lochmatter C, Fischer R, Charles PD, Yu Z, Powrie F, Kessler BM (2016) Integrative Phosphoproteomics Links IL-23R Signaling with Metabolic Adaptation in Lymphocytes. Sci Rep 6:24491

Lockman KA, Htun V, Sinha R, Treskes P, Nelson LJ, Martin SF, Rogers SM, Le Bihan T, Hayes PC, Plevris JN (2016) Proteomic profiling of cellular steatosis with concomitant oxidative stress in vitro. Lipids Health Dis 15:114

Lohr K, Pachl F, Moghaddas Gholami A, Geillinger KE, Daniel H, Kuster B, Klingenspor M (2016) Reduced mitochondrial mass and function add to age-related susceptibility toward diet-induced fatty liver in C57BL/6J mice. Physiol Rep 4 (In press)

Ly A, Merl-Pham J, Priller M, Gruhn F, Senninger N, Ueffing M, Hauck SM (2016) Proteomic Profiling Suggests Central Role Of STAT Signaling during Retinal Degeneration in the rd10 Mouse Model. J Proteome Res 15:1350-1359

McClure-Begley TD, Esterlis I, Stone KL, Lam TT, Grady SR, Colangelo CM, Lindstrom JM, Marks MJ, Picciotto MR (2016) Evaluation of the Nicotinic Acetylcholine Receptor-Associated Proteome at Baseline and Following Nicotine Exposure in Human and Mouse Cortex. eNeuro 3

McConnell JC, O'Connell OV, Brennan K, Weiping L, Howe M, Joseph L, Knight D, O'Cualain R, Lim Y, Leek A, Waddington R, Rogan J, Astley SM, Gandhi A, Kirwan CC, Sherratt MJ, Streuli CH (2016) Increased peri-ductal collagen micro-organization may contribute to raised mammographic density. Breast Cancer Res 18:5

Moloney NM, Owens RA, Meleady P, Henry M, Dolan SK, Mulvihill E, Clynes M, Doyle S (2016) The iron-responsive microsomal proteome of Aspergillus fumigatus. J Proteomics 136:99-111

Moskovets EV, Ivanov AR (2016) Comparative studies of peak intensities and chromatographic separation of proteolytic digests, PTMs, and intact proteins obtained by nanoLC-ESI MS analysis at room and elevated temperatures. Anal Bioanal Chem 408:3953-3968

Mulay A, Akram KM, Williams D, Armes H, Russell C, Hood D, Armstrong S, Stewart JP, Brown SD, Bingle L, Bingle CD (2016) An in vitro model of murine middle ear epithelium. Dis Model Mech 9:1405-1417

Murphy S, Dowling P, Zweyer M, Mundegar RR, Henry M, Meleady P, Swandulla D, Ohlendieck K (2016) Proteomic analysis of dystrophin deficiency and associated changes in the aged mdx-4cv heart model of dystrophinopathy-related cardiomyopathy. J Proteomics 145:24-36

Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B (2016) Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation. Biochim Biophys Acta 1864:1579-1585

Nakamura H, Yamashita N, Kimura A, Kimura Y, Hirano H, Makihara H, Kawamoto Y, Jitsuki-Takahashi A, Yonezaki K, Takase K, Miyazaki T, Nakamura F, Tanaka F, Goshima Y (2016) Comprehensive behavioral study and proteomic analyses of CRMP2-deficient mice. Genes Cells 21:1059-1079

Nassar AF, Williams BJ, Yaworksy DC, Patel V, Rusling JF (2016) Rapid label-free profiling of oral cancer biomarker proteins using nano-UPLC-Q-TOF ion mobility mass spectrometry. Proteomics Clin Appl 10:280-289

Okayama A, Kimura Y, Miyagi Y, Oshima T, Oshita F, Ito H, Nakayama H, Nagashima T, Rino Y, Masuda M, Ryo A, Hirano H (2016) Relationship between phosphorylation of sperm-specific antigen and prognosis of lung adenocarcinoma. J Proteomics 139:60-66

Opsahl JA, Vaudel M, Guldbrandsen A, Aasebo E, Van Pesch V, Franciotta D, Myhr KM, Barsnes H, Berle M, Torkildsen O, Kroksveen AC, Berven FS (2016) Label-free analysis of human cerebrospinal fluid addressing various normalization strategies and revealing protein groups affected by multiple sclerosis. Proteomics 16:1154-1165

Palfi A, Hokamp K, Hauck SM, Vencken S, Millington-Ward S, Chadderton N, Carrigan M, Kortvely E, Greene CM, Kenna PF, Farrar GJ (2016) microRNA regulatory circuits in a mouse model of inherited retinal degeneration. Sci Rep 6:31431

Paudel G, Bilova T, Schmidt R, Greifenhagen U, Berger R, Tarakhovskaya E, Stockhardt S, Balcke GU, Humbeck K, Brandt W, Sinz A, Vogt T, Birkemeyer C, Wessjohann L, Frolov A (2016) Osmotic stress is accompanied by protein glycation in Arabidopsis thaliana. J Exp Bot 67:6283-6295

Peters M, Guidato PM, Peters K, Megger DA, Sitek B, Classen B, Heise EM, Bufe A (2016) Allergy-Protective Arabinogalactan Modulates Human Dendritic Cells via C-Type Lectins and Inhibition of NF-kappaB. J Immunol 196:1626-1635

Pu Z, Ino Y, Kimura Y, Tago A, Shimizu M, Natsume S, Sano Y, Fujimoto R, Kaneko K, Shea DJ, Fukai E, Fuji S, Hirano H, Okazaki K (2016) Changes in the Proteome of Xylem Sap in Brassica oleracea in Response to Fusarium oxysporum Stress. Front Plant Sci 7:31

Rabbani N, Ashour A, Thornalley PJ (2016) Mass spectrometric determination of early and advanced glycation in biology. Glycoconj J 33:553-568

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Veit J, Sachsenberg T, Chernev A, Aicheler F, Urlaub H, Kohlbacher O (2016) LFQProfiler and RNP(xl): Open-Source Tools for Label-Free Quantification and Protein-RNA Cross-Linking Integrated into Proteome Discoverer. J Proteome Res 15:3441-3448

Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L (2016) Fast and Reliable Quantitative Peptidomics with labelpepmatch. J Proteome Res 15:1080-1089

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Akhtar MZ, Huang H, Kaisar M, Lo Faro ML, Robolledo R, Morten K, Heather LC, Dona A, Leuvenink HG, Fuggle SV, Kessler BM, Pugh CW, Ploeg RJ (2015) Using an integrated -omics approach to identify key cellular processes that are disturbed in the kidney following brain death. Am J Transplant (In press)

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Antberg_L (2015) Pathway-centric analysis of the DNA damageresponse to chemotherapeutic agents in two breast cell lines. eupa open proteomics (In press)

Bao K, Bostanci N, Selevsek N, Thurnheer T, Belibasakis GN (2015) Quantitative Proteomics Reveal Distinct Protein Regulations Caused by Aggregatibacter actinomycetemcomitans within Subgingival Biofilms. PLoS One 10:e0119222

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Bi Z, Merl-Pham J, Uehlein N, Zimmer I, Muhlhans S, Aichler M, Walch AK, Kaldenhoff R, Palme K, Schnitzler JP, Block K (2015) RNAi-mediated downregulation of poplar plasma membrane intrinsic proteins (PIPs) changes plasma membrane proteome composition and affects leaf physiology. J Proteomics 128:321-332

Birse K, Arnold KB, Novak RM, McCorrister S, Shaw S, Westmacott GR, Ball TB, Lauffenburger DA, Burgener A (2015) Molecular Signatures of Immune Activation and Epithelial Barrier Remodeling Are Enhanced during the Luteal Phase of the Menstrual Cycle: Implications for HIV Susceptibility. J Virol 89:8793-8805

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Bostanci N, Bao K, Wahlander A, Grossmann J, Thurnheer T, Belibasakis GN (2015) Secretome of gingival epithelium in response to subgingival biofilms. Mol Oral Microbiol 30:323-335

Bracht T, Schweinsberg V, Trippler M, Kohl M, Ahrens M, Padden J, Naboulsi W, Barkovits K, Megger DA, Eisenacher M, Borchers CH, Schlaak JF, Hoffmann AC, Weber F, Baba HA, Meyer HE, Sitek B (2015) Analysis of disease-associated protein expression using quantitative proteomics-fibulin-5 is expressed in association with hepatic fibrosis. J Proteome Res 14:2278-2286

Burch TC, Isaac G, Booher CL, Rhim JS, Rainville P, Langridge J, Baker A, Nyalwidhe JO (2015) Comparative Metabolomic and Lipidomic Analysis of Phenotype Stratified Prostate Cells. PLoS One 10:e0134206

Burch TC, Morris MA, Campbell-Thompson M, Pugliese A, Nadler JL, Nyalwidhe JO (2015) Proteomic Analysis of Disease Stratified Human Pancreas Tissue Indicates Unique Signature of Type 1 Diabetes. PLoS One 10:e0135663

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Casadei N, Sood P, Ulrich T, Kieper N, Helling S, May C, Glaab E, Chen J, Nuber S, Marcus K, Rapaport D, Ott T, Riess O, Kruger R, Fitzgerald JC (2015) Mitochondrial defects and neurodegeneration in mice overexpressing wild-type or G399S mutant HtrA2. Hum Mol Genet (In press)

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Castelli LM, Talavera D, Kershaw CJ, Mohammad-Qureshi SS, Costello JL, Rowe W, Sims PF, Grant CM, Hubbard SJ, Ashe MP, Pavitt GD (2015) The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation. PLoS Genet 11:e1005233

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Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR (2015) YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-based Proteomics Research. Genomics Proteomics Bioinformatics 13:25-35

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Dowling P, Hughes DJ, Larkin AM, Meiller J, Henry M, Meleady P, Lynch V, Pardini B, Naccarati A, Levy M, Vodicka P, Neary P, Clynes M (2015) Elevated levels of 14-3-3 proteins, serotonin, gamma enolase and pyruvate kinase identified in clinical samples from patients diagnosed with colorectal cancer. Clin Chim Acta 441:133-141

Espino JA, Mali VS, Jones LM (2015) In Cell Footprinting Coupled with Mass Spectrometry for the Structural Analysis of Proteins in Live Cells. Anal Chem 87:7971-7978

Fesenko IA, Arapidi GP, Skripnikov AY, Alexeev DG, Kostryukova ES, Manolov AI, Altukhov IA, Khazigaleeva RA, Seredina AV, Kovalchuk SI, Ziganshin RH, Zgoda VG, Novikova SE, Semashko TA, Slizhikova DK, Ptushenko VV, Gorbachev AY, Govorun VM, Ivanov VT (2015) Specific pools of endogenous peptides are present in gametophore, protonema, and protoplast cells of the moss Physcomitrella patens. BMC Plant Biol 15:87

Finamore F, Priego-Capote F, Nolli S, Zufferey A, Fontana P, Sanchez JC (2015) Characterisation of the influences of aspirin-acetylation and glycation on human plasma proteins. J Proteomics 114:125-135

Foe IT, Child MA, Majmudar JD, Krishnamurthy S, van der Linden WA, Ward GE, Martin BR, Bogyo M (2015) Global Analysis of Palmitoylated Proteins in Toxoplasma gondii. Cell Host Microbe 18:501-511

Garelli A, Heredia F, Casimiro AP, Macedo A, Nunes C, Garcez M, Dias AR, Volonte YA, Uhlmann T, Caparros E, Koyama T, Gontijo AM (2015) Dilp8 requires the neuronal relaxin receptor Lgr3 to couple growth to developmental timing. Nat Commun 6:8732

Gentzel M, Schille C, Rauschenberger V, Schambony A (2015) Distinct functionality of dishevelled isoforms on Ca2+/calmodulin-dependent protein kinase 2 (CamKII) in Xenopus gastrulation. Mol Biol Cell 26:966-977

Glatter T, Ahrne E, Schmidt A (2015) Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells. J Proteome Res 14:4472-4485

Glibert P, Meert P, Van Steendam K, Van Nieuwerburgh F, De Coninck D, Martens L, Dhaenens M, Deforce D (2015) Phospho-iTRAQ: assessing isobaric labels for the large-scale study of phosphopeptide stoichiometry. J Proteome Res 14:839-849

Gomez-Sanchez JA, Carty L, Iruarrizaga-Lejarreta M, Palomo-Irigoyen M, Varela-Rey M, Griffith M, Hantke J, Macias-Camara N, Azkargorta M, Aurrekoetxea I, De Juan VG, Jefferies HB, Aspichueta P, Elortza F, Aransay AM, Martinez-Chantar ML, Baas F, Mato JM, Mirsky R, Woodhoo A, Jessen KR (2015) Schwann cell autophagy, myelinophagy, initiates myelin clearance from injured nerves. J Cell Biol 210:153-168

Graessel A, Hauck SM, von Toerne C, Kloppmann E, Goldberg T, Koppensteiner H, Schindler M, Knapp B, Krause L, Dietz K, Schmidt-Weber CB, Suttner K (2015) A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. Mol Cell Proteomics 14:2085-2102

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ (2015) Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst. Nat Commun 6:7838

Grison MS, Brocard L, Fouillen L, Nicolas W, Wewer V, Dormann P, Nacir H, Benitez-Alfonso Y, Claverol S, Germain V, Boutte Y, Mongrand S, Bayer EM (2015) Specific membrane lipid composition is important for plasmodesmata function in Arabidopsis. Plant Cell 27:1228-1250

Grosche A, Hauser A, Lepper MF, Mayo R, von Toerne C, Merl-Pham J, Hauck SM (2015) The proteome of native adult Muller glial cells from murine retina. Mol Cell Proteomics (in press)

Harrington TD, Mohamed A, Tran VN, Biria S, Gargouri M, Park JJ, Gang DR, Beyenal H (2015) Neutral red-mediated microbial electrosynthesis by Escherichia coli, Klebsiella pneumoniae, and Zymomonas mobilis. Bioresour Technol 195:57-65

Haslene-Hox H, Oveland E, Woie K, Salvesen HB, Tenstad O, Wiig H (2015) Distribution volumes of macromolecules in human ovarian and endometrial cancers--effects of extracellular matrix structure. Am J Physiol Heart Circ Physiol 308:H18-28

Heywood WE, Camuzeaux S, Doykov I, Patel N, Preece RL, Footitt E, Cleary M, Clayton P, Grunewald S, Abulhoul L, Chakrapani A, Sebire NJ, Hindmarsh P, de Koning TJ, Heales S, Burke D, Gissen P, Mills K (2015) Proteomic Discovery and Development of a Multiplexed Targeted MRM-LC-MS/MS Assay for Urine Biomarkers of Extracellular Matrix Disruption in Mucopolysaccharidoses I, II, and VI. Anal Chem 87:12238-12244

Heywood WE, Galimberti D, Bliss E, Sirka E, Paterson RW, Magdalinou NK, Carecchio M, Reid E, Heslegrave A, Fenoglio C, Scarpini E, Schott JM, Fox NC, Hardy J, Bahtia K, Heales S, Sebire NJ, Zetterburg H, Mills K (2015) Identification of novel CSF biomarkers for neurodegeneration and their validation by a high-throughput multiplexed targeted proteomic assay. Mol Neurodegener 10:64

Hofener M, Pachl F, Kuster B, Sewald N (2015) Inhibitor-based affinity probes for the investigation of JAK signaling pathways. Proteomics 15:3066-3074

Holland A, Dowling P, Meleady P, Henry M, Zweyer M, Mundegar RR, Swandulla D, Ohlendieck K (2015) Label-free mass spectrometric analysis of the mdx-4cv diaphragm identifies the matricellular protein periostin as a potential factor involved in dystrophinopathy-related fibrosis. Proteomics 15:2318-2331

Hyder CL, Kemppainen K, Isoniemi KO, Imanishi SY, Goto H, Inagaki M, Fazeli E, Eriksson JE, Tornquist K (2015) Sphingolipids inhibit vimentin-dependent cell migration. J Cell Sci 128:2057-2069

Ikoma-Seki K, Nakamura K, Morishita S, Ono T, Sugiyama K, Nishino H, Hirano H, Murakoshi M (2015) Role of LRP1 and ERK and cAMP Signaling Pathways in Lactoferrin-Induced Lipolysis in Mature Rat Adipocytes. PLoS One 10:e0141378

Inagaki T, Iwasaki S, Matsumura Y, Kawamura T, Tanaka T, Abe Y, Yamasaki A, Tsurutani Y, Yoshida A, Chikaoka Y, Nakamura K, Magoori K, Nakaki R, Osborne TF, Fukami K, Aburatani H, Kodama T, Sakai J (2015) The FBXL10/KDM2B scaffolding protein associates with novel polycomb repressive complex-1 to regulate adipogenesis. J Biol Chem 290:4163-4177

Ittig SJ, Schmutz C, Kasper CA, Amstutz M, Schmidt A, Sauteur L, Vigano MA, Low SH, Affolter M, Cornelis GR, Nigg EA, Arrieumerlou C (2015) A bacterial type III secretion-based protein delivery tool for broad applications in cell biology. J Cell Biol 211:913-931

Jaafar SN, Coelho AV, Sheehan D (2015) Redox proteomic analysis of mytilus edulis gills: effects of the pharmaceutical diclofenac on a non-target organism. Drug Test Anal 7:957-966

Jackson AP, Goyard S, Xia D, Foth BJ, Sanders M, Wastling JM, Minoprio P, Berriman M (2015) Global Gene Expression Profiling through the Complete Life Cycle of Trypanosoma vivax. PLoS Negl Trop Dis 9:e0003975

Jeong EH, Vaidya B, Cho SY, Park MA, Kaewintajuk K, Kim SR, Oh MJ, Choi JS, Kwon J, Kim D (2015) Identification of regulators of the early stage of viral hemorrhagic septicemia virus infection during curcumin treatment. Fish Shellfish Immunol 45:184-193

Kauko O, Laajala TD, Jumppanen M, Hintsanen P, Suni V, Haapaniemi P, Corthals G, Aittokallio T, Westermarck J, Imanishi SY (2015) Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling. Sci Rep 5:13099

Kellett-Clarke H, Stegmann M, Barclay AN, Metcalfe C (2015) CD44 Binding to Hyaluronic Acid Is Redox Regulated by a Labile Disulfide Bond in the Hyaluronic Acid Binding Site. PLoS One 10:e0138137

Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM (2015) The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response. PLoS Genet 11:e1004903

Kershaw CJ, Costello JL, Talavera D, Rowe W, Castelli LM, Sims PF, Grant CM, Ashe MP, Hubbard SJ, Pavitt GD (2015) Integrated multi-omics analyses reveal the pleiotropic nature of the control of gene expression by Puf3p. Sci Rep 5:15518

Kimura A, Kurata Y, Nakabayashi J, Kagawa H, Hirano H (2015) N-Myristoylation of the Rpt2 subunit of the yeast 26S proteasome is implicated in the subcellular compartment-specific protein quality control system. J Proteomics 130:33-41

Koeck DE, Koellmeier T, Zverlov VV, Liebl W, Schwarz WH (2015) Differences in biomass degradation between newly isolated environmental strains of Clostridium thermocellum and heterogeneity in the size of the cellulosomal scaffoldin. Syst Appl Microbiol 38:424-432

Kraljevic Pavelic S, Klobucar M, Sedic M, Micek V, Gehrig P, Grossman J, Pavelic K, Vojnikovic B (2015) UV-induced retinal proteome changes in the rat model of age-related macular degeneration. Biochim Biophys Acta 1852:1833-1845

Kulej K, Avgousti DC, Weitzman MD, Garcia BA (2015) Characterization of histone post-translational modifications during virus infection using mass spectrometry-based proteomics. Methods 90:8-20

Kurbasic E, Sjostrom M, Krogh M, Folkesson E, Grabau D, Hansson K, Ryden L, Waldemarson S, James P, Nimeus E (2015) Changes in glycoprotein expression between primary breast tumour and synchronous lymph node metastases or asynchronous distant metastases. Clin Proteomics 12:13

Law KP, Han TL, Tong C, Baker PN (2015) Mass spectrometry-based proteomics for pre-eclampsia and preterm birth. Int J Mol Sci 16:10952-10985

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Schira J, Falkenberg H, Hendricks M, Waldera-Lupa DM, Kogler G, Meyer HE, Muller HW, Stuhler K (2015) Characterization of Regenerative Phenotype of Unrestricted Somatic Stem Cells (USSC) from Human Umbilical Cord Blood (hUCB) by Functional Secretome Analysis. Mol Cell Proteomics 14:2630-2643

Schmidt A, Kochanowski K, Vedelaar S, Ahrne E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold R, Heinemann M (2015) The quantitative and condition-dependent Escherichia coli proteome. Nat Biotechnol 34:104-110

Shearer JJ, Wold EA, Umbaugh CS, Lichti CF, Nilsson CL, Figueiredo ML (2015) Inorganic Arsenic Related Changes in the Stromal Tumor Microenvironment in a Prostate Cancer Cell-Conditioned Media Model. Environ Health Perspect (In press)

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Ternette N, Block PD, Sanchez-Bernabeu A, Borthwick N, Pappalardo E, Abdul-Jawad S, Ondondo B, Charles PD, Dorrell L, Kessler BM, Hanke T (2015) Early Kinetics of the HLA Class I-Associated Peptidome of MVA.HIVconsv-Infected Cells. J Virol 89:5760-5771

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Wojdyla K, Williamson J, Roepstorff P, Rogowska-Wrzesinska A (2015) The SNO/SOH TMT strategy for combinatorial analysis of reversible cysteine oxidations. J Proteomics 113:415-434

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Ye F, Xin Z, Han W, Fan J, Yin B, Wu S, Yang W, Yuan J, Qiang B, Sun W, Peng X (2015) Quantitative Proteomics Analysis of the Hepatitis C Virus Replicon High-Permissive and Low-Permissive Cell Lines. PLoS One 10:e0142082

Yerlikaya A, Okur E, Baykal AT, Acilan C, Boyaci I, Ulukaya E (2015) A proteomic analysis of p53-independent induction of apoptosis by bortezomib in 4T1 breast cancer cell line. J Proteomics 113:315-325

Yeung EN, Treskes P, Martin SF, Manning JR, Dunbar DR, Rogers SM, Le Bihan T, Lockman KA, Morley SD, Hayes PC, Nelson LJ, Plevris JN (2015) Fibrinogen production is enhanced in an in-vitro model of non-alcoholic fatty liver disease: an isolated risk factor for cardiovascular events? Lipids Health Dis 14:86

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Yoo M, Bestel-Corre G, Croux C, Riviere A, Meynial-Salles I, Soucaille P (2015) A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum. MBio 6 (In press)

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Zhang L, Li X, Hill RC, Qiu Y, Zhang W, Hansen KC, Zhao R (2015) Brr2 plays a role in spliceosomal activation in addition to U4/U6 unwinding. Nucleic Acids Res 43:3286-3297

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Zhao F, Elkelish A, Durner J, Lindermayr C, Winkler JB, Rusmall io RF, Behrendt H, Traidl-Hoffmann C, Holzinger A, Kofler W, Braun P, von Toerne C, Hauck SM, Ernst D, Frank U (2015) Common ragweed (Ambrosia artemisiifolia L.): Allergenicity and molecular characterisation of pollen after plant exposure to elevated NO. Plant Cell Environ (in press)

Zhao Z, Wu F, Ding S, Sun L, Liu Z, Ding K, Lu J (2015) Label-free quantitative proteomic analysis reveals potential biomarkers and pathways in renal cell carcinoma. Tumour Biol 36:939-951

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Ademowo OS, Hernandez B, Collins E, Rooney C, Fearon U, van Kuijk AW, Tak PP, Gerlag DM, FitzGerald O, Pennington SR (2014) Discovery and confirmation of a protein biomarker panel with potential to predict response to biological therapy in psoriatic arthritis. Ann Rheum Dis (In press)

Adiguzel Z, Baykal AT, Kacar O, Yilmaz VT, Ulukaya E, Acilan C (2014) Biochemical and Proteomic Analysis of a Potential Anticancer Agent: Palladium(II) Saccharinate Complex of Terpyridine Acting through Double Strand Break Formation. J Proteome Res 13:5240-5249

Al-Moghrabi N, Nofel A, Al-Yousef N, Madkhali S, Bin Amer SM, Alaiya A, Shinwari Z, Al-Tweigeri T, Karakas B, Tulbah A, Aboussekhra A (2014) The molecular significance of methylated BRCA1 promoter in white blood cells of cancer-free females. BMC Cancer 14:830

Ansari D, Andersson R, Bauden MP, Andersson B, Connolly JB, Welinder C, Sasor A, Marko-Varga G (2014) Protein deep sequencing applied to biobank samples from patients with pancreatic cancer. J Cancer Res Clin Oncol

Armstrong SD, Babayan SA, Lhermitte-Vallarino N, Gray N, Xia D, Martin C, Kumar S, Taylor DW, Blaxter ML, Wastling JM, Makepeace BL (2014) Comparative analysis of the secretome from a model filarial nematode (Litomosoides sigmodontis) reveals maximal diversity in gravid female parasites. Mol Cell Proteomics 13:2527-2544

Astarita G, McKenzie JH, Wang B, Strassburg K, Doneanu A, Johnson J, Baker A, Hankemeier T, Murphy J, Vreeken RJ, Langridge J, Kang JX (2014) A protective lipidomic biosignature associated with a balanced omega-6/omega-3 ratio in fat-1 transgenic mice. PLoS One 9:e96221

Atrih A, Mudaliar MA, Zakikhani P, Lamont DJ, Huang JT, Bray SE, Barton G, Fleming S, Nabi G (2014) Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling. Br J Cancer 110:1622-1633

Avanesov AS, Ma S, Pierce KA, Yim SH, Lee BC, Clish CB, Gladyshev VN (2014) Age- and diet-associated metabolome remodeling characterizes the aging process driven by damage accumulation. Elife 3:e02077

Bauer M, Ahrne E, Baron AP, Glatter T, Fava LL, Santamaria A, Nigg EA, Schmidt A (2014) Evaluation of data-dependent and -independent mass spectrometric workflows for sensitive quantification of proteins and phosphorylation sites. J Proteome Res 13:5973-5988

Ben Mlouka MA, Khemiri A, Seyer D, Hardouin J, Chan Tchi Song P, De E, Jouenne T, Cosette P (2014) Characterization of new outer membrane proteins of Pseudomonas aeruginosa using a combinatorial peptide ligand library. Anal Bioanal Chem (In press)

Bonacci T, Audebert S, Camoin L, Baudelet E, Bidaut G, Garcia M, Witzel, II, Perkins ND, Borg JP, Iovanna JL, Soubeyran P (2014) Identification of new mechanisms of cellular response to chemotherapy by tracking changes in post-translational modifications by ubiquitin and ubiquitin-like proteins. J Proteome Res 13:2478-2494

Bracht T, Hagemann S, Loscha M, Megger DA, Padden J, Eisenacher M, Kuhlmann K, Meyer HE, Baba HA, Sitek B (2014) Proteome Analysis of a Hepatocyte-Specific BIRC5 (Survivin)-Knockout Mouse Model during Liver Regeneration. J Proteome Res 13:2771-2782

Brown LM (2014) Quantitative shotgun proteomics with data-independent acquisition and traveling wave ion mobility spectrometry: a versatile tool in the life sciences. Adv Exp Med Biol 806:79-91

Buck AH, Coakley G, Simbari F, McSorley HJ, Quintana JF, Le Bihan T, Kumar S, Abreu-Goodger C, Lear M, Harcus Y, Ceroni A, Babayan SA, Blaxter M, Ivens A, Maizels RM (2014) Exosomes secreted by nematode parasites transfer small RNAs to mammalian cells and modulate innate immunity. Nat Commun 5:5488

Bui-Nguyen TM, Dennis WE, Jackson DA, Stallings JD, Lewis JA (2014) Detection of dichlorvos adducts in a hepatocyte cell line. J Proteome Res 13:3583-3595

Burniston JG, Connolly J, Kainulainen H, Britton SL, Koch LG (2014) Label-free profiling of skeletal muscle using high-definition mass spectrometry. Proteomics 14:2339-2344

Buts K, Michielssens S, Hertog ML, Hayakawa E, Cordewener J, America AH, Nicolai BM, Carpentier SC (2014) Improving the identification rate of data independent label-free quantitative proteomics experiments on non-model crops: A case study on apple fruit. J Proteomics 105:31-45

Chawade A, Sandin M, Teleman J, Malmstrom J, Levander F (2014) Data processing has major impact on the outcome of quantitative label-free LC-MS analysis. J Proteome Res

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Christensen JB, Dionisio G, Poulsen HD, Brinch-Pedersen H (2014) Effect of pH and recombinant barley (Hordeum vulgare L.) endoprotease B2 on degradation of proteins in soaked barley. J Agric Food Chem 62:8562-8570

Claussnitzer M, Dankel SN, Klocke B, Grallert H, Glunk V, Berulava T, Lee H, et al. (2014) Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms. Cell 156:343-358

Colak E, Leslie A, Zausmer K, Khatamzas E, Kubarenko AV, Pichulik T, Klimosch SN, Mayer A, Siggs O, Hector A, Fischer R, Klesser B, Rautanen A, Frank M, Hill AV, Manoury B, Beutler B, Hartl D, Simmons A, Weber AN (2014) RNA and Imidazoquinolines Are Sensed by Distinct TLR7/8 Ectodomain Sites Resulting in Functionally Disparate Signaling Events. J Immunol 192:5963-5973

Coumans JV, Gau D, Poljak A, Wasinger V, Roy P, Moens P (2014) Green fluorescent protein expression triggers proteome changes in breast cancer cells. Exp Cell Res 320:33-45

Cruz DECR, Bernardes DASA, Soares R, Almeida AM, Coelho AV, Marques DASJ, Branquinho C (2014) Differential proteomics of dehydration and rehydration in bryophytes: evidence towards a common desiccation tolerance mechanism. Plant Cell Environ 37:1499-1515

Dagley LF, Croft NP, Isserlin R, Olsen JB, Fong V, Emili A, Purcell AW (2014) Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis. Mol Cell Proteomics 13:679-700

Daou P, Hasan S, Breitsprecher D, Baudelet E, Camoin L, Audebert S, Goode BL, Badache A (2014) Essential and nonredundant roles for Diaphanous formins in cortical microtubule capture and directed cell migration. Mol Biol Cell 25:658-668

Darby AC, Christina Gill A, Armstrong SD, Hartley CS, Xia D, Wastling JM, Makepeace BL (2014) Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress. Isme J 8:925-937

de Costa D, Broodman I, Calame W, Stingl C, Dekker LJ, Vernhout RM, de Koning HJ, Hoogsteden HC, Sillevis Smitt PA, van Klaveren RJ, Luider TM, Vanduijn MM (2014) Peptides from the variable region of specific antibodies are shared among lung cancer patients. PLoS One 9:e96029

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Van Acker R, Leple JC, Aerts D, Storme V, Goeminne G, Ivens B, Legee F, Lapierre C, Piens K, Van Montagu MC, Santoro N, Foster CE, Ralph J, Soetaert W, Pilate G, Boerjan W (2014) Improved saccharification and ethanol yield from field-grown transgenic poplar deficient in cinnamoyl-CoA reductase. Proc Natl Acad Sci U S A 111:845-850

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Vehmas AP, Muth-Pawlak D, Huhtinen K, Saloniemi-Heinonen T, Jaakkola K, Laajala TD, Kaprio H, Suvitie PA, Aittokallio T, Siitari H, Perheentupa A, Poutanen M, Corthals GL (2014) Ovarian Endometriosis Signatures Established through Discovery and Directed Mass Spectrometry Analysis. J Proteome Res 13:4983-4994

Velikova V, Ghirardo A, Vanzo E, Merl J, Hauck SM, Schnitzler JP (2014) Genetic manipulation of isoprene emissions in poplar plants remodels the chloroplast proteome. J Proteome Res 13:2005-2018

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Euler KN, Hauck SM, Ueffing M, Deeg CA. (2013) Bovine neonatal pancytopenia--comparative proteomic characterization of two BVD vaccines and the producer cell surface proteome (MDBK). BMC Vet Res 9:18 (in press)

Fischer R, Bowness P, Kessler BM. (2013) Two birds with one stone: Doing metabolomics with your proteomics kit. Proteomics 13:3371-3386

Franko A, Baris OR, Bergschneider E, von Toerne C, Hauck SM, Aichler M, Walch AK, Wurst W, Wiesner RJ, Johnston IC, de Angelis MH (2013) Efficient isolation of pure and functional mitochondria from mouse tissues using automated tissue disruption and enrichment with anti-TOM22 magnetic beads. PLoS One 8:e82392

Frei AP, Moest H, Novy K, Wollscheid B. (2013) Ligand-based receptor identification on living cells and tissues using TRICEPS. Nat Protoc 8:1321-1336

Freret M, Drouot L, Obry A, Ahmed-Lacheheb S, Dauly C, Adriouch S, Cosette P, Authier FJ, Boyer O. (2013) Overexpression of MHC class I in muscle of lymphocyte-deficient mice causes a severe myopathy with induction of the unfolded protein response. Am J Pathol 183:893-904

Frese CK, Boender AJ, Mohammed S, Heck AJ, Adan RA, Altelaar AF. (2013) Profiling of diet-induced neuropeptide changes in rat brain by quantitative mass spectrometry. Anal Chem 85:4594-4604

Gluck F, Hoogland C, Antinori P, Robin X, Nikitin F, Zufferey A, Pasquarello C, Fetaud V, Dayon L, Muller M, Lisacek F, Geiser L, Hochstrasser D, Sanchez JC, Scherl A. (2013) EasyProt--an easy-to-use graphical platform for proteomics data analysis. J Proteomics 79:146-160

Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B. (2013) Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry. J Proteome Res 12:927-936

Hakenjos JP, Bejai S, Ranftl Q, Behringer C, Vlot AC, Absmanner B, Hammes U, Heinzlmeir S, Kuster B, Schwechheimer C. (2013) ML3 is a NEDD8- and ubiquitin-modified protein. Plant Physiol 163:135-149

Han B, Zhang L, Feng M, Fang Y, Li J (2013) An integrated proteomics reveals pathological mechanism of honeybee (Apis cerena) sacbrood disease. J Proteome Res 12:1881-1897

Haslene-Hox H, Oveland E, Woie K, Salvesen HB, Wiig H, Tenstad O. (2013) Increased WD-repeat containing protein 1 in interstitial fluid from ovarian carcinomas shown by comparative proteomic analysis of malignant and healthy gynecological tissue. Biochim Biophys Acta 1834:2347-2359

Herrmann AG, Deighton RF, Le Bihan T, McCulloch MC, Searcy JL, Kerr LE, McCulloch J. (2013) Adaptive changes in the neuronal proteome: mitochondrial energy production, endoplasmic reticulum stress, and ribosomal dysfunction in the cellular response to metabolic stress. J Cereb Blood Flow Metab 33:673-683

Hirayama M, Kobayashi D, Mizuguchi S, Morikawa T, Nagayama M, Midorikawa U, Wilson MM, Nambu AN, Yoshizawa AC, Kawano S, Araki N. (2013) Integrated proteomics identified novel activation of dynein IC2-GR-COX-1 signaling in neurofibromatosis type I (NF1) disease model cells. Mol Cell Proteomics 12:1377-1394

Holland A, Dowling P, Zweyer M, Swandulla D, Henry M, Clynes M, Ohlendieck K. (2013) Proteomic profiling of cardiomyopathic tissue from the aged mdx model of Duchenne muscular dystrophy reveals a drastic decrease in laminin, nidogen and annexin. Proteomics 13:2312-2323

Ijsselstijn L, Stoop MP, Stingl C, Sillevis Smitt PA, Luider TM, Dekker LJ. (2013) Comparative Study of Targeted and Label-free Mass Spectrometry Methods for Protein Quantification. J Proteome Res (in press)

Kehasse A, Rich CB, Lee A, McComb ME, Costello CE, Trinkaus-Randall V. (2013) Epithelial wounds induce differential phosphorylation changes in response to purinergic and EGF receptor activation. Am J Pathol 183:1841-1852

Kerkela E, Hakkarainen T, Makela T, Raki M, Kambur O, Kilpinen L, Nikkila J, Lehtonen S, Ritamo I, Pernu R, Pietila M, Takalo R, Juvonen T, Bergstrom K, Kalso E, Valmu L, Laitinen S, Lehenkari P, Nystedt J. (2013) Transient proteolytic modification of mesenchymal stromal cells increases lung clearance rate and targeting to injured tissue. Stem Cells Transl Med 2:510-520

Kim PY, Tan O, Diakiw SM, Carter D, Sekerye EO, Wasinger VC, Liu T, Kavallaris M, Norris MD, Haber M, Chesler L, Dolnikov A, Trahair TN, Cheung NK, Marshall GM, Cheung BB. (2013) Identification of plasma Complement C3 as a potential biomarker for neuroblastoma using a quantitative proteomic approach. J Proteomics 96C:1-12

Kohl M, Megger DA, Trippler M, Meckel H, Ahrens M, Bracht T, Weber F, Hoffmann AC, Baba HA, Sitek B, Schlaak JF, Meyer HE, Stephan C, Eisenacher M. (2013) A practical data processing workflow for multi-OMICS projects. Biochim Biophys Acta 1844:52-62

Ku X, Heinzlmeir S, Liu X, Medard G, Kuster B. (2013) A new chemical probe for quantitative proteomic profiling of fibroblast growth factor receptor and its inhibitors. J Proteomics 96C:44-55

Leon IR, Schwammle V, Jensen ON, Sprenger RR. (2013) Quantitative assessment of in-solution digestion efficiency identifies optimal protocols for unbiased protein analysis. Mol Cell Proteomics 12:2992-3005

Lichti CF, Liu H, Shavkunov AS, Mostovenko E, Sulman EP, Ezhilarasan R, Wang Q, Kroes RA, Moskal JC, Fenyo D, Oksuz BA, Conrad CA, Lang FF, Berven FS, Vegvari A, Rezeli M, Marko-Varga G, Hober S, Nilsson CL (2013) Integrated chromosome 19 transcriptomic and proteomic data sets derived from glioma cancer stem-cell lines. J Proteome Res 13:191-199

Lynskey NN, Goulding D, Gierula M, Turner CE, Dougan G, Edwards RJ, Sriskandan S (2013) RocA truncation underpins hyper-encapsulation, carriage longevity and transmissibility of serotype M18 group A streptococci. PLoS Pathog 9:e1003842

Maller O, Hansen KC, Lyons TR, Acerbi I, Weaver VM, Prekeris R, Tan AC, Schedin P. (2013) Collagen architecture in pregnancy-induced protection from breast cancer. J Cell Sci 126:4108-4110

Marcon C, Lamkemeyer T, Malik WA, Ungrue D, Piepho HP, Hochholdinger F. (2013) Heterosis-associated proteome analyses of maize (Zea mays L.) seminal roots by quantitative label-free LC-MS. J Proteomics 93:295-302

McGouran JF, Gaertner SR, Altun M, Kramer HB, Kessler BM. (2013) Deubiquitinating Enzyme Specificity for Ubiquitin Chain Topology Profiled by Di-Ubiquitin Activity Probes. Chem Biol (in press)

Megger DA, Bracht T, Meyer HE, Sitek B. (2013) Label-free quantification in clinical proteomics. Biochim Biophys Acta 1834:1581-1590

Mehlan H, Schmidt F, Weiss S, Schuler J, Fuchs S, Riedel K, Bernhardt J. (2013) Data visualization in environmental proteomics. Proteomics 13:2805-2821

Merl J, Deeg CA, Swadzba ME, Ueffing M, Hauck SM. (2013) Identification of autoantigens in body fluids by combining pull-downs and organic precipitations of intact immune complexes with quantitative label-free mass spectrometry. J Proteome Res 12:5656-5665

Morrissey B, O'Shea C, Armstrong J, Rooney C, Staunton L, Sheehan M, Shannon AM, Pennington SR. (2013) Development of a label-free LC-MS/MS strategy to approach the identification of candidate protein biomarkers of disease recurrence in prostate cancer patients in a clinical trial of combined hormone and radiation therapy. Proteomics Clin Appl 7:316-326

Mutsaers CA, Lamont DJ, Hunter G, Wishart TM, Gillingwater TH. (2013) Label-free proteomics identifies Calreticulin and GRP75/Mortalin as peripherally accessible protein biomarkers for spinal muscular atrophy. Genome Med 5:95

Nahnsen S, Bielow C, Reinert K, Kohlbacher O. (2013) Tools for label-free peptide quantification. Mol Cell Proteomics 12:549-556

Natunen S, Lampinen M, Suila H, Ritamo I, Pitkanen V, Nairn AV, Rabina J, Laitinen S, Moremen KW, Reutter W, Valmu L. (2013) Metabolic glycoengineering of mesenchymal stromal cells with N-propanoylmannosamine. Glycobiology 23:1004-1012

Olsson N, Carlsson P, James P, Hansson K, Waldemarson S, Malmstrom P, Ferno M, Ryden L, Wingren C, Borrebaeck CA. (2013) Grading breast cancer tissues using molecular portraits. Mol Cell Proteomics 12:3612-3623

Orchard S, Binz PA, Jones AR, Vizcaino JA, Deutsch EW, Hermjakob H. (2013) Preparing to work with big data in proteomics - a report on the HUPO-PSI Spring Workshop: April 15-17, 2013, Liverpool, UK. Proteomics 13:2931-2937

Peffers MJ, Beynon RJ, Clegg PD. (2013) Absolute quantification of selected proteins in the human osteoarthritic secretome. Int J Mol Sci 14:20658-20681

Peltoniemi H, Natunen S, Ritamo I, Valmu L, Rabina J. (2013) Novel data analysis tool for semiquantitative LC-MS-MS2 profiling of N-glycans. Glycoconj J 30:159-170

Quebatte M, Dick MS, Kaever V, Schmidt A, Dehio C. (2013) Dual input control: activation of the Bartonella henselae VirB/D4 type IV secretion system by the stringent sigma factor RpoH1 and the BatR/BatS two-component system. Mol Microbiol 90:756-775

Ramasamy P, Murphy CC, Clynes M, Horgan N, Moriarty P, Tiernan D, Beatty S, Kennedy S, Meleady P. (2013) Proteomics in uveal melanoma. Exp Eye Res 118C:1-12

Ritamo I, Rabina J, Natunen S, Valmu L. (2013) Nanoscale reversed-phase liquid chromatography-mass spectrometry of permethylated N-glycans. Anal Bioanal Chem 405:2469-2480

Rodriguez-Suarez E, Whetton AD. (2013) The application of quantification techniques in proteomics for biomedical research. Mass Spectrom Rev 32:1-26

Schmidt W, Rainville LC, McEneff G, Sheehan D, Quinn B. (2013) A proteomic evaluation of the effects of the pharmaceuticals diclofenac and gemfibrozil on marine mussels (Mytilus spp.): evidence for chronic sublethal effects on stress-response proteins. Drug Test Anal (in press)

Schmutz C, Ahrne E, Kasper CA, Tschon T, Sorg I, Dreier RF, Schmidt A, Arrieumerlou C. (2013) Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. Mol Cell Proteomics 12:2952-2968

Skiba NP, Spencer WJ, Salinas RY, Lieu EC, Thompson JW, Arshavsky VY. (2013) Proteomic identification of unique photoreceptor disc components reveals the presence of PRCD, a protein linked to retinal degeneration. J Proteome Res 12:3010-3018

Song W, Mentink RA, Henquet MG, Cordewener JH, van Dijk AD, Bosch D, America AH, van der Krol AR. (2013) N-glycan occupancy of Arabidopsis N-glycoproteins. J Proteomics 93:343-355

Stoop MP, Singh V, Stingl C, Martin R, Khademi M, Olsson T, Hintzen RQ, Luider TM. (2013) Effects of natalizumab treatment on the cerebrospinal fluid proteome of multiple sclerosis patients. J Proteome Res 12:1101-1107

Takahashi D, Kawamura Y, Uemura M. (2013) Changes of detergent-resistant plasma membrane proteins in oat and rye during cold acclimation: association with differential freezing tolerance. J Proteome Res 12:4998-5011

Ternette N, Yang M, Laroyia M, Kitagawa M, O'Flaherty L, Wolhulter K, Igarashi K, Saito K, Kato K, Fischer R, Berquand A, Kessler BM, Lappin T, Frizzell N, Soga T, Adam J, Pollard PJ. (2013) Inhibition of mitochondrial aconitase by succination in fumarate hydratase deficiency. Cell Rep 3:689-700

Trinh HV, Grossmann J, Gehrig P, Roschitzki B, Schlapbach R, Greber UF, Hemmi S. (2013) iTRAQ-Based and Label-Free Proteomics Approaches for Studies of Human Adenovirus Infections. Int J Proteomics 2013:581862

van Ooijen G, Martin SF, Barrios-Llerena ME, Hindle M, Le Bihan T, O'Neill JS, Millar AJ. (2013) Functional analysis of the rodent CK1tau mutation in the circadian clock of a marine unicellular alga. BMC Cell Biol 14:46

von Toerne C, Kahle M, Schafer A, Ispiryan R, Blindert M, Hrabe De Angelis M, Neschen S, Ueffing M, Hauck SM. (2013) Apoe, Mbl2, and Psp plasma protein levels correlate with diabetic phenotype in NZO mice--an optimized rapid workflow for SRM-based quantification. J Proteome Res 12:1331-1343

Vranakis I, Goniotakis I, Psaroulaki A, Sandalakis V, Tselentis Y, Gevaert K, Tsiotis G. (2013) Proteome studies of bacterial antibiotic resistance mechanisms. J Proteomics

Wasinger VC, Zeng M, Yau Y. (2013) Current status and advances in quantitative proteomic mass spectrometry. Int J Proteomics 2013:180605

Weisser H, Nahnsen S, Grossmann J, Nilse L, Quandt A, Brauer H, Sturm M, Kenar E, Kohlbacher O, Aebersold R, Malmstrom L. (2013) An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics. J Proteome Res (in press)

Wrzesinski K, I RL, Kulej K, Sprenger RR, Bjorndal B, Christensen BJ, Berge RK, O NJ, Rogowska-Wrzesinska A. (2013) Proteomics identifies molecular networks affected by tetradecylthioacetic acid and fish oil supplemented diets. J Proteomics 84:61-77

Xue L, Wang P, Wang L, Renzi E, Radivojac P, Tang H, Arnold R, Zhu JK, Tao WA (2013) Quantitative measurement of phosphoproteome response to osmotic stress in arabidopsis based on Library-Assisted eXtracted Ion Chromatogram (LAXIC). Mol Cell Proteomics 12:2354-2369

Zattas D, Adle DJ, Rubenstein EM, Hochstrasser M. (2013) N-terminal acetylation of the yeast Derlin Der1 is essential for Hrd1 ubiquitin-ligase activity toward luminal ER substrates. Mol Biol Cell 24:890-900


2012

Azimzadeh O, Scherthan H, Yentrapalli R, Barjaktarovic Z, Ueffing M, Conrad M, Neff F, Calzada-Wack J, Aubele M, Buske C, Atkinson MJ, Hauck SM, Tapio S. (2012) Label-free protein profiling of formalin-fixed paraffin-embedded (FFPE) heart tissue reveals immediate mitochondrial impairment after ionising radiation. J Proteomics 75:2384-2395

Bantscheff M, Lemeer S, Savitski MM, Kuster B. (2012) Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 404:939-965

Bastiaan-Net S, Chanput W, Hertz A, Zwittink RD, Mes JJ, Wichers HJ. (2012) Biochemical and functional characterization of recombinant fungal immunomodulatory proteins (rFIPs). Int Immunopharmacol 15:167-175

Bleijerveld OB, Wijten P, Cappadona S, McClellan EA, Polat AN, Raijmakers R, Sels JW, Colle L, Grasso S, van den Toorn HW, van Breukelen B, Stubbs A, Pasterkamp G, Heck AJ, Hoefer IE, Scholten A. (2012) Deep proteome profiling of circulating granulocytes reveals bactericidal/permeability-increasing protein as a biomarker for severe atherosclerotic coronary stenosis. J Proteome Res 11:5235-5244

Broodman I, de Costa D, Stingl C, Dekker LJ, VanDuijn MM, Lindemans J, van Klaveren RJ, Luider TM. (2012) Mass spectrometry analyses of kappa and lambda fractions result in increased number of complementarity-determining region identifications. Proteomics 12:183-191

Dechavanne C, Guillonneau F, Chiappetta G, Sago L, Levy P, Salnot V, Guitard E, Ehrenmann F, Broussard C, Chafey P, Le Port A, Vinh J, Mayeux P, Dugoujon JM, Lefranc MP, Migot-Nabias F. (2012) Mass Spectrometry Detection of G3m and IGHG3 Alleles and Follow-Up of Differential Mother and Neonate IgG3. PLoS One 7:e46097

Eisenacher M, Kohl M, Turewicz M, Koch MH, Uszkoreit J, Stephan C. (2012) Search and decoy: the automatic identification of mass spectra. Methods Mol Biol 893:445-488

Fila J, Matros A, Radau S, Zahedi RP, Capkova V, Mock HP, Honys D. (2012) Revealing phosphoproteins playing role in tobacco pollen activated in vitro. Proteomics 12:3229-3250

Filiou MD, Martins-de-Souza D, Guest PC, Bahn S, Turck CW. (2012) To label or not to label: applications of quantitative proteomics in neuroscience research. Proteomics 12:736-747

Fischer R, Trudgian DC, Wright C, Thomas G, Bradbury LA, Brown MA, Bowness P, Kessler BM. (2012) Discovery of candidate serum proteomic and metabolomic biomarkers in ankylosing spondylitis. Mol Cell Proteomics 11:M111 013904

Frei AP, Jeon OY, Kilcher S, Moest H, Henning LM, Jost C, Pluckthun A, Mercer J, Aebersold R, Carreira EM, Wollscheid B. (2012) Direct identification of ligand-receptor interactions on living cells and tissues. Nat Biotechnol 30:997-1001

Glatter T, Ludwig C, Ahrne E, Aebersold R, Heck AJ, Schmidt A. (2012) Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion. J Proteome Res 11:5145-5156

Greer E, Martin AC, Pendle A, Colas I, Jones AM, Moore G, Shaw P. (2012) The Ph1 locus suppresses Cdk2-type activity during premeiosis and meiosis in wheat. Plant Cell 24:152-162

Gundisch S, Hauck S, Sarioglu H, Schott C, Viertler C, Kap M, Schuster T, Reischauer B, Rosenberg R, Verhoef C, Mischinger HJ, Riegman P, Zatloukal K, Becker KF. (2012) Variability of protein and phosphoprotein levels in clinical tissue specimens during the preanalytical phase. J Proteome Res 11:5748-5762

Hauck SM, Hofmaier F, Dietter J, Swadzba ME, Blindert M, Amann B, Behler J, Kremmer E, Ueffing M, Deeg CA. (2012) Label-free LC-MSMS analysis of vitreous from autoimmune uveitis reveals a significant decrease in secreted Wnt signalling inhibitors DKK3 and SFRP2. J Proteomics 75:4545-4554

Hummel M, Cordewener JH, de Groot JC, Smeekens S, America AH, Hanson J. (2012) Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. Proteomics 12:1024-1038

Karhemo PR, Ravela S, Laakso M, Ritamo I, Tatti O, Makinen S, Goodison S, Stenman UH, Holtta E, Hautaniemi S, Valmu L, Lehti K, Laakkonen P. (2012) An optimized isolation of biotinylated cell surface proteins reveals novel players in cancer metastasis. J Proteomics 77:87-100

Kolmeder CA, de Been M, Nikkila J, Ritamo I, Matto J, Valmu L, Salojarvi J, Palva A, Salonen A, de Vos WM. (2012) Comparative metaproteomics and diversity analysis of human intestinal microbiota testifies for its temporal stability and expression of core functions. PLoS One 7:e29913

Krishnan N, Lam TT, Fritz A, Rempinski D, O'Loughlin K, Minderman H, Berezney R, Marzluff WF, Thapar R. (2012) The prolyl isomerase Pin1 targets stem-loop binding protein (SLBP) to dissociate the SLBP-histone mRNA complex linking histone mRNA decay with SLBP ubiquitination. Mol Cell Biol 32:4306-4322

Lemeer S, Hahne H, Pachl F, Kuster B. (2012) Software tools for MS-based quantitative proteomics: a brief overview. Methods Mol Biol 893:489-499

Li B, Takahashi D, Kawamura Y, Uemura M. (2012) Comparison of plasma membrane proteomic changes of Arabidopsis suspension-cultured cells (T87 Line) after cold and ABA treatment in association with freezing tolerance development. Plant Cell Physiol 53:543-554

Maat P, VanDuijn M, Brouwer E, Dekker L, Zeneyedpour L, Luider T, Smitt PS. (2012) Mass spectrometric detection of antigen-specific immunoglobulin peptides in paraneoplastic patient sera. J Autoimmun 38:354-360

Marguerat S, Schmidt A, Codlin S, Chen W, Aebersold R, Bahler J. (2012) Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells. Cell 151:671-683

McDonagh B, Dominguez-Martin MA, Gomez-Baena G, Lopez-Lozano A, Diez J, Barcena JA, Garcia Fernandez JM. (2012) Nitrogen starvation induces extensive changes in the redox proteome of Prochlorococcus sp. strain SS120. Environ Microbiol Rep 4:257-267

Meding S, Balluff B, Elsner M, Schone C, Rauser S, Nitsche U, Maak M, Schafer A, Hauck SM, Ueffing M, Langer R, Hofler H, Friess H, Rosenberg R, Walch A. (2012) Tissue-based proteomics reveals FXYD3, S100A11 and GSTM3 as novel markers for regional lymph node metastasis in colon cancer. J Pathol (In press)

Meleady P, Gallagher M, Clarke C, Henry M, Sanchez N, Barron N, Clynes M. (2012) Impact of miR-7 over-expression on the proteome of Chinese hamster ovary cells. J Biotechnol 160:251-262

Merl J, Ueffing M, Hauck SM, von Toerne C. (2012) Direct comparison of MS-based label-free and SILAC quantitative proteome profiling strategies in primary retinal Muller cells. Proteomics 12:1902-1911

Michaux C, Martini C, Shioya K, Ahmed Lecheheb S, Budin-Verneuil A, Cosette P, Sanguinetti M, Hartke A, Verneuil N, Giard JC. (2012) CspR, a cold shock RNA-binding protein involved in the long-term survival and the virulence of Enterococcus faecalis. J Bacteriol 194:6900-6908

Mustafa DA, Dekker LJ, Stingl C, Kremer A, Stoop M, Sillevis Smitt PA, Kros JM, Luider TM. (2012) A proteome comparison between physiological angiogenesis and angiogenesis in glioblastoma. Mol Cell Proteomics 11:M111 008466

Nesvizhskii AI. (2012) Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments. Proteomics 12:1639-1655

O'Connell K, Prencipe M, O'Neill A, Corcoran C, Rani S, Henry M, Dowling P, Meleady P, O'Driscoll L, Watson W, O'Connor R. (2012) The use of LC-MS to identify differentially expressed proteins in docetaxel-resistant prostate cancer cell lines. Proteomics 12:2115-2126

Peltoniemi H, Natunen S, Ritamo I, Valmu L, Rabina J. (2012) Novel data analysis tool for semiquantitative LC-MS-MS2 profiling of N-glycans. Glycoconj J 30:159-170

Qi D, Brownridge P, Xia D, Mackay K, Gonzalez-Galarza FF, Kenyani J, Harman V, Beynon RJ, Jones AR. (2012) A software toolkit and interface for performing stable isotope labeling and top3 quantification using Progenesis LC-MS. Omics 16:489-495

Rosenling T, Stoop MP, Attali A, van Aken H, Suidgeest E, Christin C, Stingl C, Suits F, Horvatovich P, Hintzen RQ, Tuinstra T, Bischoff R, Luider TM. (2012) Profiling and identification of cerebrospinal fluid proteins in a rat EAE model of multiple sclerosis. J Proteome Res 11:2048-2060

Sitek B, Waldera-Lupa DM, Poschmann G, Meyer HE, Stuhler K. (2012) Application of label-free proteomics for differential analysis of lung carcinoma cell line A549. Methods Mol Biol 893:241-248

Stoop MP, Rosenling T, Attali A, Meesters RJ, Stingl C, Dekker LJ, van Aken H, Suidgeest E, Hintzen RQ, Tuinstra T, van Gool A, Luider TM, Bischoff R. (2012) Minocycline effects on the cerebrospinal fluid proteome of experimental autoimmune encephalomyelitis rats. J Proteome Res 11:4315-4325

Street JM, Barran PE, Mackay CL, Weidt S, Balmforth C, Walsh TS, Chalmers RT, Webb DJ, Dear JW. (2012) Identification and proteomic profiling of exosomes in human cerebrospinal fluid. J Transl Med 10:5

Takahashi D, Kawamura Y, Yamashita T, Uemura M. (2012) Detergent-resistant plasma membrane proteome in oat and rye: similarities and dissimilarities between two monocotyledonous plants. J Proteome Res 11:1654-1665

Tuli L, Tsai TH, Varghese RS, Xiao JF, Cheema A, Ressom HW. (2012) Using a spike-in experiment to evaluate analysis of LC-MS data. Proteome Sci 10:13

Vasilj A, Gentzel M, Ueberham E, Gebhardt R, Shevchenko A. (2012) Tissue proteomics by one-dimensional gel electrophoresis combined with label-free protein quantification. J Proteome Res 11:3680-3689

Wang H, Alvarez S, Hicks LM. (2012) Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii strains of interest for biofuels engineering. J Proteome Res 11:487-501

Zimmer A, Bouley J, Le Mignon M, Pliquet E, Horiot S, Turfkruyer M, Baron-Bodo V, Horak F, Nony E, Louise A, Moussu H, Mascarell L, Moingeon P. (2012) A regulatory dendritic cell signature correlates with the clinical efficacy of allergen-specific sublingual immunotherapy. J Allergy Clin Immunol 129:1020-1030


2011

Altun M, Kramer HB, Willems LI, McDermott JL, Leach CA, Goldenberg SJ, Kumar KG, Konietzny R, Fischer R, Kogan E, Mackeen MM, McGouran J, Khoronenkova SV, Parsons JL, Dianov GL, Nicholson B, Kessler BM. (2011) Activity-based chemical proteomics accelerates inhibitor development for deubiquitylating enzymes. Chem Biol 18:1401-1412

Beck F, Lewandrowski U, Wiltfang M, Feldmann I, Geiger J, Sickmann A, Zahedi RP. (2011) The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides. Proteomics 11:1099-1109

Blanchet L, Smolinska A, Attali A, Stoop MP, Ampt KA, van Aken H, Suidgeest E, Tuinstra T, Wijmenga SS, Luider T, Buydens LM. (2011) Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis. BMC Bioinformatics 12:254

Christin C, Bischoff R, Horvatovich P. (2011) Data processing pipelines for comprehensive profiling of proteomics samples by label-free LC-MS for biomarker discovery. Talanta 83:1209-1224

Dekker LJ, Zeneyedpour L, Brouwer E, van Duijn MM, Sillevis Smitt PA, Luider TM. (2011) An antibody-based biomarker discovery method by mass spectrometry sequencing of complementarity determining regions. Anal Bioanal Chem 399:1081-1091

English JA, Pennington K, Dunn MJ, Cotter DR. (2011) The neuroproteomics of schizophrenia. Biol Psychiatry 69:163-172

Gil GC, Brennan J, Throckmorton DJ, Branda SS, Chirica GS. (2011) Automated analysis of mouse serum peptidome using restricted access media and nanoliquid chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 879:1112-1120

Glatter T, Schittenhelm RB, Rinner O, Roguska K, Wepf A, Junger MA, Kohler K, Jevtov I, Choi H, Schmidt A, Nesvizhskii AI, Stocker H, Hafen E, Aebersold R, Gstaiger M. (2011) Modularity and hormone sensitivity of the Drosophila melanogaster insulin receptor/target of rapamycin interaction proteome. Mol Syst Biol 7:547

Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M. (2011) Time-resolved quantitative proteome analysis of in vivo intestinal development. Mol Cell Proteomics 10:M110 005231

Ijsselstijn L, Dekker LJ, Koudstaal PJ, Hofman A, Sillevis Smitt PA, Breteler MM, Luider TM. (2011) Serum clusterin levels are not increased in presymptomatic Alzheimer's disease. J Proteome Res 10:2006-2010

Ijsselstijn L, Dekker LJ, Stingl C, van der Weiden MM, Hofman A, Kros J, Koudstaal PJ, Sillevis Smitt P, Ikram MA, Breteler MM, Luider T. (2011) Serum Levels of Pregnancy Zone Protein are Elevated in Presymptomatic Alzheimer's Disease. J Proteome Res 10:4902-4910

Le Bihan T, Martin SF, Chirnside ES, van Ooijen G, Barrios-Llerena ME, O'Neill JS, Shliaha PV, Kerr LE, Millar AJ. (2011) Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J Proteomics 74:2060-2070

Levin Y. (2011) The role of statistical power analysis in quantitative proteomics. Proteomics 11:2565-2567

Matros A, Kaspar S, Witzel K, Mock HP. (2011) Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. Phytochemistry 72:963-974

Mutsaers CA, Wishart TM, Lamont DJ, Riessland M, Schreml J, Comley LH, Murray LM, Parson SH, Lochmuller H, Wirth B, Talbot K, Gillingwater TH. (2011) Reversible molecular pathology of skeletal muscle in spinal muscular atrophy. Hum Mol Genet 20:4334-4344

Neilson KA, Ali NA, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Lee A, van Sluyter SC, Haynes PA. (2011) Less label, more free: approaches in label-free quantitative mass spectrometry. Proteomics 11:535-553

Olsson N, Wingren C, Mattsson M, James P, O'Connell D, Nilsson F, Cahill DJ, Borrebaeck CA. (2011) Proteomic analysis and discovery using affinity proteomics and mass spectrometry. Mol Cell Proteomics 10:M110 003962

Prapainop K, Wentworth P, Jr. (2011) A shotgun proteomic study of the protein corona associated with cholesterol and atheronal-B surface-modified quantum dots. Eur J Pharm Biopharm 77:353-359

Reiland S, Finazzi G, Endler A, Willig A, Baerenfaller K, Grossmann J, Gerrits B, Rutishauser D, Gruissem W, Rochaix JD, Baginsky S. (2011) Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF). Proc Natl Acad Sci U S A 108:12955-12960

Sandin M, Krogh M, Hansson K, Levander F. (2011) Generic workflow for quality assessment of quantitative label-free LC-MS analysis. Proteomics 11:1114-1124

Schmidt A, Beck M, Malmstrom J, Lam H, Claassen M, Campbell D, Aebersold R. (2011) Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol 7:510

Titulaer MK, de Costa D, Stingl C, Dekker LJ, Sillevis Smitt PA, Luider TM. (2011) Label-free peptide profiling of Orbitrap full mass spectra. BMC Res Notes 4:21

Trudgian DC, Ridlova G, Fischer R, Mackeen MM, Ternette N, Acuto O, Kessler BM, Thomas B. (2011) Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline. Proteomics 11:2790-2797

Wada K, Ogiwara A, Nagasaka K, Tanaka N, Komatsu Y. (2011) i-RUBY: a novel software for quantitative analysis of highly accurate shotgun-proteomics liquid chromatography/tandem mass spectrometry data obtained without stable-isotope labeling of proteins. Rapid Commun Mass Spectrom 25:960-968

Wiedl T, Arni S, Roschitzki B, Grossmann J, Collaud S, Soltermann A, Hillinger S, Aebersold R, Weder W. (2011) Activity-based proteomics: identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma. J Proteomics 74:1884-1894

Wu Z, Doondeea JB, Gholami AM, Janning MC, Lemeer S, Kramer K, Eccles SA, Gollin SM, Grenman R, Walch A, Feller SM, Kuster B. (2011) Quantitative chemical proteomics reveals new potential drug targets in head and neck cancer. Mol Cell Proteomics 10:M111 011635

Yun BW, Feechan A, Yin M, Saidi NB, Le Bihan T, Yu M, Moore JW, Kang JG, Kwon E, Spoel SH, Pallas JA, Loake GJ. (2011) S-nitrosylation of NADPH oxidase regulates cell death in plant immunity. Nature 478:264-268

Zabron AA, Horneffer-van der Sluis VM, Wadsworth CA, Laird F, Gierula M, Thillainayagam AV, Vlavianos P, Westaby D, Taylor-Robinson SD, Edwards RJ, Khan SA. (2011) Elevated levels of neutrophil gelatinase-associated lipocalin in bile from patients with malignant pancreatobiliary disease. Am J Gastroenterol 106:1711-1717


2010

Abdul-Salam VB, Wharton J, Cupitt J, Berryman M, Edwards RJ, Wilkins MR. (2010) Proteomic analysis of lung tissues from patients with pulmonary arterial hypertension. Circulation 122:2058-2067

Affolter M, Grass L, Vanrobaeys F, Casado B, Kussmann M. (2010) Qualitative and quantitative profiling of the bovine milk fat globule membrane proteome. J Proteomics 73:1079-1088

de Costa D, Broodman I, Vanduijn MM, Stingl C, Dekker LJ, Burgers PC, Hoogsteden HC, Sillevis Smitt PA, van Klaveren RJ, Luider TM. (2010) Sequencing and quantifying IgG fragments and antigen-binding regions by mass spectrometry. J Proteome Res 9:2937-2945

Dicker L, Lin X, Ivanov AR. (2010) Increased power for the analysis of label-free LC-MS/MS proteomics data by combining spectral counts and peptide peak attributes. Mol Cell Proteomics 9:2704-2718

Dowsey AW, English JA, Lisacek F, Morris JS, Yang GZ, Dunn MJ. (2010) Image analysis tools and emerging algorithms for expression proteomics. Proteomics 10:4226-4257

Hauck SM, Dietter J, Kramer RL, Hofmaier F, Zipplies JK, Amann B, Feuchtinger A, Deeg CA, Ueffing M. (2010) Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry. Mol Cell Proteomics 9:2292-2305

Lalmahomed Z, Roest H, Woltman K, Verhoef C, Luider T, IJzermans J (2010) Identification of urinary biomarkers for colorectal liver metastases. Annals of Oncology 21 (supplement 6): vi31–vi121

Levin Y, Bahn S. (2010) Quantification of proteins by label-free LC-MS/MS. Methods Mol Biol 658:217-231

Magdeldin S, Li H, Yoshida Y, Satokata I, Maeda Y, Yokoyama M, Enany S, Zhang Y, Xu B, Fujinaka H, Yaoita E, Yamamoto T. (2010) Differential proteomic shotgun analysis elucidates involvement of water channel aquaporin 8 in presence of alpha-amylase in the colon. J Proteome Res 9:6635-6646

Nanjo Y, Skultety L, Ashraf Y, Komatsu S. (2010) Comparative proteomic analysis of early-stage soybean seedlings responses to flooding by using gel and gel-free techniques. J Proteome Res 9:3989-4002

Stoop MP, Coulier L, Rosenling T, Shi S, Smolinska AM, Buydens L, Ampt K, Stingl C, Dane A, Muilwijk B, Luitwieler RL, Sillevis Smitt PA, Hintzen RQ, Bischoff R, Wijmenga SS, Hankemeier T, van Gool AJ, Luider TM. (2010) Quantitative proteomics and metabolomics analysis of normal human cerebrospinal fluid samples. Mol Cell Proteomics 9:2063-2075

Strassberger V, Fugmann T, Neri D, Roesli C. (2010) Chemical proteomic and bioinformatic strategies for the identification and quantification of vascular antigens in cancer. J Proteomics 73:1954-1973

VanDuijn MM, Dekker LJ, Zeneyedpour L, Smitt PA, Luider TM. (2010) Immune responses are characterized by specific shared immunoglobulin peptides that can be detected by proteomic techniques. J Biol Chem 285:29247-29253

Zhang R, Barton A, Brittenden J, Huang J, Crowther D. (2010) Evaluation for Computational Platforms of LC-MS Based Label-Free Quantitative Proteomics: A Global View. J Proteomics Bioinform 3:260-265


2009

Dakna M, He Z, Yu WC, Mischak H, Kolch W. (2009) Technical, bioinformatical and statistical aspects of liquid chromatography-mass spectrometry (LC-MS) and capillary electrophoresis-mass spectrometry (CE-MS) based clinical proteomics: a critical assessment. J Chromatogr B Analyt Technol Biomed Life Sci 877:1250-1258