Waters | Nonlinear Dynamics

Progenesis QI for proteomics

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


Annual publications citing the use of Progenesis QI and Progenesis QI.P

Progenesis QI for proteomics software references


Abdulwahab RA, Alaiya A, Shinwari Z, Allaith AAA, Giha HA (2019) LCMS/MS proteomic analysis revealed novel associations of 37 proteins with T2DM and notable upregulation of immunoglobulins. Int J Mol Med 43:2118-2132

Abdulwahab RA, Allaith AAA, Shinwari Z, Alaiya A, Giha HA (2019) Association of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) with T2DM. Gene 706:43-51

Al-Majdoub ZM, Al Feteisi H, Achour B, Warwood S, Neuhoff S, Rostami-Hodjegan A, Barber J (2019) Proteomic Quantification of Human Blood-Brain Barrier SLC and ABC Transporters in Healthy Individuals and Dementia Patients. Mol Pharm 16:1220-1233

Almeida FA, Vale EM, Reis RS, Santa-Catarina C, Silveira V (2019) LED lamps enhance somatic embryo maturation in association with the differential accumulation of proteins in the Carica papaya L. 'Golden' embryogenic callus. Plant Physiol Biochem 143:109-118

Al-Mutairy EA, Imtiaz FA, Khalid M, Al Qattan S, Saleh S, Mahmoud LM, Al-Saif MM, et al. (2019) An atypical pulmonary fibrosis is associated with co-inheritance of mutations in the calcium binding protein genes S100A3 and S100A13. Eur Respir J 54 (in press)

Aloui C, Barlier C, Claverol S, Fagan J, Awounou D, Tavernier E, Guyotat D, Hamzeh-Cognasse H, Cognasse F, Garraud O, Laradi S (2019) Differential protein expression of blood platelet components associated with adverse transfusion reactions. J Proteomics 194:25-36

Araujo-Gomes N, Romero-Gavilan F, Zhang Y, Martinez-Ramos C, Elortza F, Azkargorta M, Martin de Llano JJ, Gurruchaga M, Goni I, van den Beucken J, Suay J (2019) Complement proteins regulating macrophage polarisation on biomaterials. Colloids Surf B Biointerfaces 181:125-133

Arffman RK, Saraswat M, Joenvaara S, Khatun M, Agarwal R, Tohmola T, Sundstrom-Poromaa I, Renkonen R, Piltonen TT (2019) Thromboinflammatory changes in plasma proteome of pregnant women with PCOS detected by quantitative label-free proteomics. Sci Rep 9:17578

Bagi Z, Couch Y, Broskova Z, Perez-Balderas F, Yeo T, Davis S, Fischer R, Sibson NR, Davis BG, Anthony DC (2019) Extracellular vesicle integrins act as a nexus for platelet adhesion in cerebral microvessels. Sci Rep 9:15847

Banfi C, Brioschi M, Karjalainen MK, Huusko JM, Gianazza E, Agostoni P (2019) Immature surfactant protein-B impairs the antioxidant capacity of HDL. Int J Cardiol 285:53-58

Banova Vulic R, Zduriencikova M, Tyciakova S, Benada O, Dubrovcakova M, Lakota J, Skultety L (2019) Silencing of carbonic anhydrase I enhances the malignant potential of exosomes secreted by prostatic tumour cells. J Cell Mol Med 23:3641-3655

Bardell D, Milner PI, Goljanek-Whysall K, Peffers MJ (2019) Differences in plasma and peritoneal fluid proteomes identifies potential biomarkers associated with survival following strangulating small intestinal disease. Equine Vet J 51:727-732

Barjaktarovic Z, Merl-Pham J, Braga-Tanaka I, Tanaka S, Hauck SM, Saran A, Mancuso M, Atkinson MJ, Tapio S, Azimzadeh O (2019) Hyperacetylation of Cardiac Mitochondrial Proteins Is Associated with Metabolic Impairment and Sirtuin Downregulation after Chronic Total Body Irradiation of ApoE (-/-) Mice. Int J Mol Sci 20 (in press)

Baud A, Little D, Wen TQ, Heywood WE, Gissen P, Mills K (2019) An Optimized Method for the Proteomic Analysis of Low Volumes of Cell Culture Media and the Secretome: The Application and the Demonstration of Altered Protein Expression in iPSC-Derived Neuronal Cell Lines from Parkinson's Disease Patients. J Proteome Res 18:1198-1207

Bazile J, Picard B, Chambon C, Valais A, Bonnet M (2019) Pathways and biomarkers of marbling and carcass fat deposition in bovine revealed by a combination of gel-based and gel-free proteomic analyses. Meat Sci 156:146-155

Beker MC, Caglayan B, Caglayan AB, Kelestemur T, Yalcin E, Caglayan A, Kilic U, Baykal AT, Reiter RJ, Kilic E (2019) Interaction of melatonin and Bmal1 in the regulation of PI3K/AKT pathway components and cellular survival. Sci Rep 9:19082

Belchi-Navarro S, Almagro L, Bru-Martinez R, Pedreno MA (2019) Changes in the secretome of Vitis vinifera cv. Monastrell cell cultures treated with cyclodextrins and methyl jasmonate. Plant Physiol Biochem 135:520-527

Bell M, Blais JM (2019) "-Omics" workflow for paleolimnological and geological archives: A review. Sci Total Environ 672:438-455

Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV (2019) Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics. BMC Bioinformatics 20:102

Beyer JA, Szollossi A, Byles E, Fischer R, Armitage JP (2019) Mechanism of Signalling and Adaptation through the Rhodobacter sphaeroides Cytoplasmic Chemoreceptor Cluster. Int J Mol Sci 20 (in press)

Bharucha T, Gangadharan B, Kumar A, de Lamballerie X, Newton PN, Winterberg M, Dubot-Peres A, Zitzmann N (2019) Mass spectrometry-based proteomic techniques to identify cerebrospinal fluid biomarkers for diagnosing suspected central nervous system infections. A systematic review. J Infect 79:407-418

Bi B, Choi HP, Hyeon SJ, Sun S, Su N, Liu Y, Lee J, Kowall NW, McKee AC, Yang JH, Ryu H (2019) Quantitative Proteomic Analysis Reveals Impaired Axonal Guidance Signaling in Human Postmortem Brain Tissues of Chronic Traumatic Encephalopathy. Exp Neurobiol 28:362-375

Biswal AK, McConnell EW, Werth EG, Lo SF, Yu SM, Hicks LM, Jones AM (2019) The Nucleotide-Dependent Interactome of Rice Heterotrimeric G-Protein alpha -Subunit. Proteomics 19:e1800385

Blank-Landeshammer B, Teichert I, Marker R, Nowrousian M, Kuck U, Sickmann A (2019) Combination of Proteogenomics with Peptide De Novo Sequencing Identifies New Genes and Hidden Posttranscriptional Modifications. MBio 10 (in press)

Boccard J, Tonoli D, Strajhar P, Jeanneret F, Odermatt A, Rudaz S (2019) Removal of batch effects using stratified subsampling of metabolomic data for in vitro endocrine disruptors screening. Talanta 195:77-86

Bonnet J, Garcia C, Leger T, Couquet MP, Vignoles P, Vatunga G, Ndung'u J, Boudot C, Bisser S, Courtioux B (2019) Proteome characterization in various biological fluids of Trypanosoma brucei gambiense-infected subjects. J Proteomics 196:150-161

Bouillier C, Cosentino G, Leger T, Rincheval V, Richard CA, Desquesnes A, Sitterlin D, Blouquit-Laye S, Eleouet JF, Gault E, Rameix-Welti MA (2019) The Interactome analysis of the Respiratory Syncytial Virus protein M2-1 suggests a new role in viral mRNA metabolism post-transcription. Sci Rep 9:15258

Bowazolo C, Tse SPK, Beauchemin M, Lo SC, Rivoal J, Morse D (2019) Label-free MS/MS analyses of the dinoflagellate Lingulodinium identifies rhythmic proteins facilitating adaptation to a diurnal LD cycle. Sci Total Environ:135430

Brandao-Teles C, de Almeida V, Cassoli JS, Martins-de-Souza D (2019) Oligodendrocytes: Potential of Discovering New Treatment Targets. Front Pharmacol 10:186

Brault ML, Petit JD, Immel F, Nicolas WJ, Glavier M, Brocard L, Gaston A, Fouche M, Hawkins TJ, Crowet JM, Grison MS, Germain V, Rocher M, Kraner M, Alva V, Claverol S, Paterlini A, Helariutta Y, Deleu M, Lins L, Tilsner J, Bayer EM (2019) Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata. EMBO Rep 20:e47182

Breton J, Legrand R, Achamrah N, Chan P, do Rego JL, do Rego JC, Coeffier M, Dechelotte P, Fetissov SO (2019) Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production. Nutrition 67-68:110557

Brunoro GVF, Carvalho PC, Barbosa VC, Pagnoncelli D, De Moura Gallo CV, Perales J, Zahedi RP, Valente RH, Neves-Ferreira A (2019) Differential proteomic comparison of breast cancer secretome using a quantitative paired analysis workflow. BMC Cancer 19:365

Burlina S, Banfi C, Brioschi M, Visentin S, Dalfra MG, Traldi P, Lapolla A (2019) Is the placental proteome impaired in well-controlled gestational diabetes? J Mass Spectrom 54:359-365

Calderon-Rodriguez SI, Sanabria-Salas MC, Umana-Perez A (2019) A comparative proteomic study of plasma in Colombian childhood acute lymphoblastic leukemia. PLoS One 14:e0221509

Canals R, Hammarlof DL, Kroger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD (2019) Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580. PLoS Biol 17:e3000059

Cao TH, Jones DJL, Voors AA, Quinn PA, Sandhu JK, Chan DCS, Parry HM, Mohan M, Mordi IR, Sama IE, Anker SD, Cleland JG, Dickstein K, Filippatos G, Hillege HL, Metra M, Ponikowski P, Samani NJ, Van Veldhuisen DJ, Zannad F, Lang CC, Ng LL (2019) Plasma proteomic approach in patients with heart failure: insights into pathogenesis of disease progression and potential novel treatment targets. Eur J Heart Fail (in press)

Chan BD, Wong WY, Lee MM, Cho WC, Yee BK, Kwan YW, Tai WC (2019) Exosomes in Inflammation and Inflammatory Disease. Proteomics 19:e1800149

Chang YT, Chang MC, Tsai YJ, Ferng C, Shih HC, Kuo YP, Chen CH, Tsai IL (2019) Method development of immunoglobulin G purification from micro-volumes of human serum for untargeted and targeted proteomics-based antibody repertoire studies. J Food Drug Anal 27:475-482

Chapman EA, Lyon M, Simpson D, Mason D, Beynon RJ, Moots RJ, Wright HL (2019) Caught in a Trap? Proteomic Analysis of Neutrophil Extracellular Traps in Rheumatoid Arthritis and Systemic Lupus Erythematosus. Front Immunol 10:423

Chapman TP, Corridoni D, Shiraishi S, Pandey S, Aulicino A, Wigfield S, do Carmo Costa M, Thezenas ML, Paulson H, Fischer R, Kessler BM, Simmons A (2019) Ataxin-3 Links NOD2 and TLR2 Mediated Innate Immune Sensing and Metabolism in Myeloid Cells. Front Immunol 10:1495

Charkoftaki G, Thompson DC, Golla JP, Garcia-Milian R, Lam TT, Engel J, Vasiliou V (2019) Integrated multi-omics approach reveals a role of ALDH1A1 in lipid metabolism in human colon cancer cells. Chem Biol Interact 304:88-96

Chen F, Ma R, Chen XL (2019) Advances of Metabolomics in Fungal Pathogen-Plant Interactions. Metabolites 9

Chen X, Liu H, Sun W, Guo Z, Lang J (2019) Elevated urine histone 4 levels in women with ovarian endometriosis revealed by discovery and parallel reaction monitoring proteomics. J Proteomics 204:103398

Cheng HW, Hsiao CT, Chen YQ, Huang CM, Chan SI, Chiou A, Kuo JC (2019) Centrosome guides spatial activation of Rac to control cell polarization and directed cell migration. Life Sci Alliance 2 (in press)

Cho SY, Protzman RA, Kim YO, Vaidya B, Oh MJ, Kwon J, Kim D (2019) Elucidation of mechanism for host response to VHSV infection at varying temperatures in vitro and in vivo through proteomic analysis. Fish Shellfish Immunol 88:244-253

Coleman O, Suda S, Meiller J, Henry M, Riedl M, Barron N, Clynes M, Meleady P (2019) Increased growth rate and productivity following stable depletion of miR-7 in a mAb producing CHO cell line causes an increase in proteins associated with the Akt pathway and ribosome biogenesis. J Proteomics 195:23-32

Coliva G, Duarte S, Perez-Sala D, Fedorova M (2019) Impact of inhibition of the autophagy-lysosomal pathway on biomolecules carbonylation and proteome regulation in rat cardiac cells. Redox Biol:101123

Corridoni D, Shiraishi S, Chapman T, Steevels T, Muraro D, Thezenas ML, Prota G, Chen JL, Gileadi U, Ternette N, Cerundolo V, Simmons A (2019) NOD2 and TLR2 Signal via TBK1 and PI31 to Direct Cross-Presentation and CD8 T Cell Responses. Front Immunol 10:958

Couto N, Al-Majdoub ZM, Achour B, Wright PC, Rostami-Hodjegan A, Barber J (2019) Quantification of Proteins Involved in Drug Metabolism and Disposition in the Human Liver Using Label-Free Global Proteomics. Mol Pharm 16:632-647

Cury NF, RCC ES, Fayad M, Fontes W, Ricart CAO, Castro MS, Silveira C, Valle de Sousa M, Pereira LAR (2019) Proteome Dataset of Qualea grandiflora Mart. (Vochysiaceae) by LC-MS/MS Label-Free Identification in Response to Aluminum. Proteomics 19:e1900148

De Clerck L, Taelman J, Popovic M, Willems S, Van der Jeught M, Heindryckx B, De Sutter P, Marks H, Deforce D, Dhaenens M (2019) Untargeted histone profiling during naive conversion uncovers conserved modification markers between mouse and human. Sci Rep 9:17240

De Meyer F, Eeckhaut V, Ducatelle R, Dhaenens M, Daled S, Dedeurwaerder A, De Gussem M, Haesebrouck F, Deforce D, Van Immerseel F (2019) Host intestinal biomarker identification in a gut leakage model in broilers. Vet Res 50:46

de Oliveira Gorgulho Silva C, de Castro Moreira Dos Santos Junior A, Santana RH, Kruger RH, Fontes W, de Sousa MV, Ricart CAO, Filho EXF (2019) Mild hydrothermal pretreatment of sugarcane bagasse enhances the production of holocellulases by Aspergillus niger. J Ind Microbiol Biotechnol 46:1517-1529

de Pablos LM, Ferreira TR, Dowle AA, Forrester S, Parry E, Newling K, Walrad PB (2019) The mRNA-bound Proteome of Leishmania mexicana: Novel Genetic Insight into an Ancient Parasite. Mol Cell Proteomics 18:1271-1284

Derricott H, Luu L, Fong WY, Hartley CS, Johnston LJ, Armstrong SD, Randle N, Duckworth CA, Campbell BJ, Wastling JM, Coombes JL (2019) Developing a 3D intestinal epithelium model for livestock species. Cell Tissue Res 375:409-424

Dhaenens L, Lierman S, De Clerck L, Govaert E, Deforce D, Tilleman K, De Sutter P (2019) Endometrial stromal cell proteome mapping in repeated implantation failure and recurrent pregnancy loss cases and fertile women. Reprod Biomed Online 38:442-454

Dietrich J, Roth M, Konig S, Geerling G, Mertsch S, Schrader S (2019) Analysis of lacrimal gland derived mesenchymal stem cell secretome and its impact on epithelial cell survival. Stem Cell Res 38:101477

Dorgau B, Felemban M, Hilgen G, Kiening M, Zerti D, Hunt NC, Doherty M, Whitfield P, Hallam D, White K, Ding Y, Krasnogor N, Al-Aama J, Asfour HZ, Sernagor E, Lako M (2019) Decellularised extracellular matrix-derived peptides from neural retina and retinal pigment epithelium enhance the expression of synaptic markers and light responsiveness of human pluripotent stem cell derived retinal organoids. Biomaterials 199:63-75

Dowling P, Zweyer M, Raucamp M, Henry M, Meleady P, Swandulla D, Ohlendieck K (2019) Proteomic and cell biological profiling of the renal phenotype of the mdx-4cv mouse model of Duchenne muscular dystrophy. Eur J Cell Biol:151059

Duijvesz D, Rodriguez-Blanco G, Hoogland AM, Verhoef EI, Dekker LJ, Roobol MJ, van Leenders G, Luider TM, Jenster G (2019) Differential tissue expression of extracellular vesicle-derived proteins in prostate cancer. Prostate 79:1032-1042

Duval C, Macabiou C, Garcia C, Lesuisse E, Camadro JM, Auchere F (2019) The adaptive response to iron involves changes in energetic strategies in the pathogen Candida albicans. Microbiologyopen:e970

Egloff P, Zimmermann I, Arnold FM, Hutter CAJ, Morger D, Opitz L, Poveda L, Keserue HA, Panse C, Roschitzki B, Seeger MA (2019) Engineered peptide barcodes for in-depth analyses of binding protein libraries. Nat Methods 16:421-428

Einer C, Leitzinger C, Lichtmannegger J, Eberhagen C, Rieder T, Borchard S, Wimmer R, Denk G, Popper B, Neff F, Polishchuk EV, Polishchuk RS, Hauck SM, von Toerne C, Muller JC, Karst U, Baral BS, DiSpirito AA, Kremer AE, Semrau J, Weiss KH, Hohenester S, Zischka H (2019) A High-Calorie Diet Aggravates Mitochondrial Dysfunction and Triggers Severe Liver Damage in Wilson Disease Rats. Cell Mol Gastroenterol Hepatol 7:571-596

El-Khateeb E, Vasilogianni AM, Alrubia S, Al-Majdoub ZM, Couto N, Howard M, Barber J, Rostami-Hodjegan A, Achour B (2019) Quantitative mass spectrometry-based proteomics in the era of model-informed drug development: Applications in translational pharmacology and recommendations for best practice. Pharmacol Ther 203:107397

Engstrom P, Burke TP, Mitchell G, Ingabire N, Mark KG, Golovkine G, Iavarone AT, Rape M, Cox JS, Welch MD (2019) Evasion of autophagy mediated by Rickettsia surface protein OmpB is critical for virulence. Nat Microbiol 4:2538-2551

Eshraghi M, Gombar R, De Repentigny Y, Vacratsis PO, Kothary R (2019) Pathologic Alterations in the Proteome of Synaptosomes from a Mouse Model of Spinal Muscular Atrophy. J Proteome Res 18:3042-3051

Esteves P, Dard L, Brillac A, Hubert C, Sarlak S, Rousseau B, Dumon E, Izotte J, Bonneu M, Lacombe D, Dupuy JW, Amoedo N, Rossignol R (2019) Nuclear control of lung cancer cells migration, invasion and bioenergetics by eukaryotic translation initiation factor 3F. Oncogene (in press)

Fernandez J, Machado AK, Lyonnais S, Chamontin C, Gartner K, Leger T, Henriquet C, Garcia C, Portilho DM, Pugniere M, Chaloin L, Muriaux D, Yamauchi Y, Blaise M, Nisole S, Arhel NJ (2019) Transportin-1 binds to the HIV-1 capsid via a nuclear localization signal and triggers uncoating. Nat Microbiol 4:1840-1850

Fernandez-Boo S, Gervais O, Prado-Alvarez M, Chollet B, Claverol S, Lecadet C, Dubreuil C, Arzul I (2019) Is pallial mucus involved in Ostrea edulis defenses against the parasite Bonamia ostreae? J Invertebr Pathol 169:107259

Fernandez-Tussy P, Fernandez-Ramos D, Lopitz-Otsoa F, Simon J, Barbier-Torres L, Gomez-Santos B, Nunez-Garcia M, et al. (2019) miR-873-5p targets mitochondrial GNMT-Complex II interface contributing to non-alcoholic fatty liver disease. Mol Metab 29:40-54

Fingas F, Volke D, Hassert R, Fornefett J, Funk S, Baums CG, Hoffmann R (2019) Sensitive and immunogen-specific serological detection of Rodentibacter pneumotropicus infections in mice. BMC Microbiol 19:43

Fisher P, Spencer H, Thomas-Oates J, Wood AJ, Ungar D (2019) Modeling Glycan Processing Reveals Golgi-Enzyme Homeostasis upon Trafficking Defects and Cellular Differentiation. Cell Rep 27:1231-1243 e1236

Ford MM, Smythers AL, McConnell EW, Lowery SC, Kolling DRJ, Hicks LM (2019) Inhibition of TOR in Chlamydomonas reinhardtii Leads to Rapid Cysteine Oxidation Reflecting Sustained Physiological Changes. Cells 8

Frischknecht L, Britschgi C, Galliker P, Christinat Y, Vichalkovski A, Gstaiger M, Kovacs WJ, Krek W (2019) BRAF inhibition sensitizes melanoma cells to alpha-amanitin via decreased RNA polymerase II assembly. Sci Rep 9:7779

Gannesen AV, Zdorovenko EL, Botchkova EA, Hardouin J, Massier S, Kopitsyn DS, Gorbachevskii MV, Kadykova AA, Shashkov AS, Zhurina MV, Netrusov AI, Knirel YA, Plakunov VK, Feuilloley MGJ (2019) Composition of the Biofilm Matrix of Cutibacterium acnes Acneic Strain RT5. Front Microbiol 10:1284

Gartner K, Klahn S, Watanabe S, Mikkat S, Scholz I, Hess WR, Hagemann M (2019) Cytosine N4-Methylation via M.Ssp6803II Is Involved in the Regulation of Transcription, Fine- Tuning of DNA Replication and DNA Repair in the Cyanobacterium Synechocystis sp. PCC 6803. Front Microbiol 10:1233

Gentric G, Kieffer Y, Mieulet V, Goundiam O, Bonneau C, Nemati F, Hurbain I, Raposo G, Popova T, Stern MH, Lallemand-Breitenbach V, Muller S, Caneque T, Rodriguez R, Vincent-Salomon A, de The H, Rossignol R, Mechta-Grigoriou F (2019) PML-Regulated Mitochondrial Metabolism Enhances Chemosensitivity in Human Ovarian Cancers. Cell Metab 29:156-173 e110

Ghousein A, Mosca N, Cartier F, Charpentier J, Dupuy JW, Raymond AA, Bioulac-Sage P, Grosset CF (2019) miR-4510 blocks hepatocellular carcinoma development through RAF1 targeting and RAS/RAF/MEK/ERK signalling inactivation. Liver Int 40:240-251

Gilbert HTJ, Mallikarjun V, Dobre O, Jackson MR, Pedley R, Gilmore AP, Richardson SM, Swift J (2019) Nuclear decoupling is part of a rapid protein-level cellular response to high-intensity mechanical loading. Nat Commun 10:4149

Gilgunn S, El-Sabbahy H, Albrecht S, Gaikwad M, Corrigan K, Deakin L, Jellum G, Bones J (2019) Identification and tracking of problematic host cell proteins removed by a synthetic, highly functionalized nonwoven media in downstream bioprocessing of monoclonal antibodies. J Chromatogr A 1595:28-38

Gonzalez-Morales A, Zabaleta A, Garcia-Moure M, Alonso MM, Fernandez-Irigoyen J, Santamaria E (2019) Oncolytic adenovirus Delta-24-RGD induces a widespread glioma proteotype remodeling during autophagy. J Proteomics 194:168-178

Graham LC, Naldrett MJ, Kohama SG, Smith C, Lamont DJ, McColl BW, Gillingwater TH, Skehel P, Urbanski HF, Wishart TM (2019) Regional Molecular Mapping of Primate Synapses during Normal Healthy Aging. Cell Rep 27:1018-1026 e1014

Guo XH, Cheng XL, Liu WX, Li MH, Wei F, Ma SC (2019) Identification of velvet antler and its mixed varieties by UPLC-QTOF-MS combined with principal component analysis. J Pharm Biomed Anal 165:18-23

Gutsch A, Sergeant K, Keunen E, Prinsen E, Guerriero G, Renaut J, Hausman JF, Cuypers A (2019) Does long-term cadmium exposure influence the composition of pectic polysaccharides in the cell wall of Medicago sativa stems? BMC Plant Biol 19:271

Hadjidemetriou M, Al-Ahmady Z, Buggio M, Swift J, Kostarelos K (2019) A novel scavenging tool for cancer biomarker discovery based on the blood-circulating nanoparticle protein corona. Biomaterials 188:118-129

Ham AS, Chojnowska K, Tintignac LA, Lin S, Schmidt A, Ham DJ, Sinnreich M, Ruegg MA (2019) mTORC1 signalling is not essential for the maintenance of muscle mass and function in adult sedentary mice. J Cachexia Sarcopenia Muscle (in press)

Hayashi N, Doi H, Kurata Y, Kagawa H, Atobe Y, Funakoshi K, Tada M, Katsumoto A, Tanaka K, Kunii M, Nakamura H, Takahashi K, Takeuchi H, Koyano S, Kimura Y, Hirano H, Tanaka F (2019) Proteomic analysis of exosome-enriched fractions derived from cerebrospinal fluid of amyotrophic lateral sclerosis patients. Neurosci Res (in press)

Haythorne E, Rohm M, van de Bunt M, Brereton MF, Tarasov AI, Blacker TS, Sachse G, Silva Dos Santos M, Terron Exposito R, Davis S, Baba O, Fischer R, Duchen MR, Rorsman P, MacRae JI, Ashcroft FM (2019) Diabetes causes marked inhibition of mitochondrial metabolism in pancreatic beta-cells. Nat Commun 10:2474

Hiroshima Y, Kasajima R, Kimura Y, Komura D, Ishikawa S, Ichikawa Y, Bouvet M, Yamamoto N, Oshima T, Morinaga S, Singh SR, Hoffman RM, Endo I, Miyagi Y (2019) Novel targets identified by integrated cancer-stromal interactome analysis of pancreatic adenocarcinoma. Cancer Lett 469:217-227

Hladik D, Dalke C, von Toerne C, Hauck SM, Azimzadeh O, Philipp J, Ung MC, Schlattl H, Rossler U, Graw J, Atkinson MJ, Tapio S (2019) CREB Signaling Mediates Dose-Dependent Radiation Response in the Murine Hippocampus Two Years after Total Body Exposure. J Proteome Res (in press)

Hu C, Sun J, Du J, Wen D, Lu H, Zhang H, Xue Y, Zhang A, Yang C, Zeng L, Jiang J (2019) The Hippo-YAP Pathway Regulates the Proliferation of Alveolar Epithelial Progenitors after Acute Lung Injury. Cell Biol Int (in press)

Imrie L, Le Bihan T, O'Toole A, Hickner PV, Dunn WA, Weise B, Rund SSC (2019) Genome annotation improvements from cross-phyla proteogenomics and time-of-day differences in malaria mosquito proteins using untargeted quantitative proteomics. PLoS One 14:e0220225

Irshad Z, Xue M, Ashour A, Larkin JR, Thornalley PJ, Rabbani N (2019) Activation of the unfolded protein response in high glucose treated endothelial cells is mediated by methylglyoxal. Sci Rep 9:7889

Jaleel A, Aneesh Kumar A, Ajith Kumar GS, Surendran A, Kartha CC (2019) Label-free quantitative proteomics analysis reveals distinct molecular characteristics in endocardial endothelium. Mol Cell Biochem 451:1-10

James KL, Kung JW, Crable BR, Mouttaki H, Sieber JR, Nguyen HH, Yang Y, Xie Y, Erde J, Wofford NQ, Karr EA, Loo JA, Ogorzalek Loo RR, Gunsalus RP, McInerney MJ (2019) Syntrophus aciditrophicus uses the same enzymes in a reversible manner to degrade and synthesize aromatic and alicyclic acids. Environ Microbiol 21:1833-1846

Jing J, Du Z, Ji S, Han K (2019) Urinary proteome analysis of acute hypercoagulable state in rat model induced by epsilon-aminocaproic acid. Biomed Pharmacother 110:275-284

Jourdan J, Walz A, Matile H, Schmidt A, Wu J, Wang X, Dong Y, Vennerstrom JL, Schmidt RS, Wittlin S, Maser P (2019) Stochastic Protein Alkylation by Antimalarial Peroxides. ACS Infect Dis 5:2067-2075

Jung MH, Chico V, Ciordia S, Mena MC, Jung SJ, Ortega-Villaizan MDM (2019) The Megalocytivirus RBIV Induces Apoptosis and MHC Class I Presentation in Rock Bream (Oplegnathus fasciatus) Red Blood Cells. Front Immunol 10:160

Kadri S, El Ayed M, Cosette P, Jouenne T, Elkhaoui S, Zekri S, Limam F, Aouani E, Mokni M (2019) Neuroprotective effect of grape seed extract on brain ischemia: a proteomic approach. Metab Brain Dis 34:889-907

Kay LJ, Sangal V, Black GW, Soundararajan M (2019) Proteomics and bioinformatics analyses identify novel cellular roles outside mitochondrial function for human miro GTPases. Mol Cell Biochem 451:21-35

Kelly PS, Dorival-Garcia N, Pare S, Carillo S, Ta C, Alarcon Miguez A, Coleman O, Harper E, Shannon M, Henry M, Connolly L, Clynes M, Meleady P, Bones J, Barron N (2019) Improvements in single-use bioreactor film material composition leads to robust and reliable Chinese hamster ovary cell performance. Biotechnol Prog:e2824

Kleinwort KJH, Hauck SM, Degroote RL, Scholz AM, Holzel C, Maertlbauer EP, Deeg C (2019) Peripheral blood bovine lymphocytes and MAP show distinctly different proteome changes and immune pathways in host-pathogen interaction. PeerJ 7:e8130

Koelschbach JS, Mouttaki H, Merl-Pham J, Arnold ME, Meckenstock RU (2019) Identification of naphthalene carboxylase subunits of the sulfate-reducing culture N47. Biodegradation 30:147-160

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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

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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

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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

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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

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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)

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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

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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

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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

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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

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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

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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


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

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