The Progenesis LC-MS package has enabled our service lab customers to be taught in a very short time how to extract reliable results with they are happy.
Progenesis LC-MS software references
2011
Beck F, Lewandrowski U, Wiltfang M, Feldmann I, Geiger J, Sickmann A, Zahedi RP. The good, the bad, the ugly: validating the mass spectrometric analysis of modified peptides. Proteomics. Mar;(6):1099-109.
Blanchet L, Smolinska A, Attali A, Stoop MP, Ampt KAM, van Aken H, Suidgeest E, Tuinstra T, Wijmenga SS, Luider T, Buydens LMC. Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis. BMC Bioinformatics 2011, 12:254.
Dekker LJ, Zeneyedpour L, Brouwer E, van Duijn MM, Sillevis Smitt PA, Luider TM. 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. The neuroproteomics of schizophrenia. Biol Psychiatry 69:163-172.
Gil G-C, Brennana J, Throckmortona DJ, Brandaa SS, Chirica GS. Automated analysis of mouse serum peptidome using restricted access media and nanoliquid chromatography-tandem mass spectrometry. Journal of Chromatography B, published online.
Hansson J, Panchaud A, Favre L, Bosco N, Mansourian R, Benyacoub J, Blum S, Jensen ON, Kussmann M. Time-resolved Quantitative Proteome Analysis of In Vivo Intestinal Development. Mol Cell Proteomics. Mar;10(3).
Herzo RI,Lam TT, Sherwin RS. Acute Insulin-Induced Hypoglycemia Induces a Rapid Increase in Hypothalamic Synaptic Plasticity. Diabetes, Jul 2011; 60: A133 - A195.
Ijsselstijn L, Dekker LJ, Stingl C, van der Weiden MM, Hofman A, Kros JM, Koudstaal PJ, Sillevis Smitt PA, Ikram MA, Breteler MM, Luider TM. Serum Levels of Pregnancy Zone Protein are Elevated in Presymptomatic Alzheimer's Disease. J Proteome Res. 2011 Sep 28. Epub ahead of print.
Le Bihan T, Martin SF, Chirnside ES, van Ooijen G, Barrios-Llerena M, O'Neill JS, Shliaha PV, Kerr LE, Millar AJ. Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J Proteomics, May 24 (Epub ahead of print).
Matros A, Kaspar S, Witzel K, Mock HP. Recent progress in liquid chromatography-based separation and label-free quantitative plant proteomics. Phytochemistry (in press).
Mutsaers CA, Wishart TM, Lamont DJ, Riessland M, Schreml J, Comley LH, Murray LM, Parson SH, Lochmüller H, Wirth B, Talbot K, Gillingwater TH. Reversible molecular pathology of skeletal muscle in spinal muscular atrophy. Hum Mol Genet. 15;20(22):4334-44.
Neilson K, Ali N, Muralidharan S, Mirzaei M, Mariani M, Assadourian G, Le e A, van Sluyter S, Haynes P. Less label, more free: Approaches in label-free quantitative mass spectrometry. Proteomics, Feb;11(4):535-53.
Olsson N, Wingren C, Mattsson M, James P, O'Connell D, Nilsson F, Cahill DJ, Borrebaeck CAK. Proteomic analysis and discovery using affinity proteomics and mass spectrometry. Molecular and Cellular Proteomics, 10 (10).
Prapainop K, Wentworth P, Jr. A shotgun proteomic study of the protein corona associated with cholesterol and atheronal-B surface-modified quantum dots. Eur J Pharm Biopharm, Apr;77(3):353-9.
Reiland S, Finazzic G, Endlera A, Willigg A, Baerenfallera K, Grossmanna J, Gerritsa B, Rutishausera D, Gruissema W, Rochaixg JD, Baginskya S. Comparative phosphoproteome profiling reveals a function of the STN8 kinase in fine-tuning of cyclic electron flow (CEF). PNAS July 18, 2011.
Sandin M, Krogh M, Hansson K, Levander F. Generic workflow for quality assessment of quantitative label-free LC-MS analysis. Proteomics, Mar;11(6):1114-24.
Titulaer MK, de Costa D, Stingl C, Dekker LJ, Sillevis Smitt PA, Luider TM. Label-free peptide profiling of Orbitrap™ full mass spectra. BMC Res Notes. 2011 Jan 27;4:21.
Trudgian DC, Ridlova G, Fischer R, Mackeen MM, Ternette N, Acuto O, Kessler BM, Thomas B. Comparative evaluation of label-free SINQ normalized spectral index quantitation in the central proteomics facilities pipeline. Proteomics.Jul;11(14):2790-7.
Visioli G, Marmiroli N. Proteomics of Plant Hyperaccumulators. Metal Toxicity in Plants: Perception, Signaling and Remediation 2012, 165-186.
Wiedl T, Arni S, Roschitzki B, Grossmann J, Collaud S, Soltermann A, S. Hillinger, Aebersold R, Weder W. Activity-based proteomics: Identification of ABHD11 and ESD activities as potential biomarkers for human lung adenocarcinoma. Journal of Proteomics, available online 9 May 2011.
2010
Abdul-Salam VB, Wharton J, Cupitt J, Berryman M, Edwards RJ, Wilkins MR,. 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. Qualitative and quantitative profiling of the bovine milk fat globule membrane proteome. J Proteomics Volume 73, Issue 6, 18 Pages 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. Sequencing and quantifying IgG fragments and antigen-binding regions by mass spectrometry. J Proteome Res 9:2937-2945.
Dicker L, Lin X, Ivanov AR,. 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, Image analysis tools and emerging algorithms for expression proteomics. Proteomics 2010 Dec;10(23):4226-57.
Hauck SM, Dietter J, Kramer RL, Hofmaier F, Zipplies JK, Amann B, Feuchtinger A, Deeg CA, Ueffing M. Deciphering membrane-associated molecular processes in target tissue of autoimmune uveitis by label-free quantitative mass spectrometry. Mol Cell Proteomics, Mol Cell Proteomics 9:2292-2305.
Levin Y, Bahn S,.Quantification of proteins by label-free LC-MS/MS. Methods Mol Biol 658:217-231.
Lalmahomed Z, Roest H, Woltman K, Verhoef C, Luider T, IJzermans J. Identification of urinary biomarkers for colorectal liver metastases. Annals of Oncology 21 Annals of Oncology 21 (Supplement 6): vi31-vi121, 2010 (June).
Magdeldin S, Li H, Yoshida Y, Satokata I, Maeda Y, Yokoyama M, Enany S, Zhang Y, Xu B, Fujinaka H, Yaoita E, Yamamoto T. 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. Comparative Proteomic Analysis of Early-Stage Soybean Seedlings Responses to Flooding by Using Gel and Gel-Free Techniques. J Proteome Res. Aug 6;9(8):3989-4002.
Petutschnig EK, Jones AME, Serazetdinova L, Lipka U, Lipka V. The Lysin Motif Receptor-like Kinase (LysM-RLK) CERK1 Is a Major Chitin-binding Protein in Arabidopsis thaliana and Subject to Chitin-induced Phosphorylation. The Journal of Biological Chemistry, vol. 285, no. 37, pp28902–2891.
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. 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. Chemical proteomic and bioinformatic strategies for the identification and quantification of vascular antigens in cancer. J Proteomics. 2010 Sep 10;73(10):1954-73.
Vanduijn MM, Dekker LJ, Zeneyedpour L, Sillevis Smitt PA, Luider TM. Immune responses are characterized by specific shared immunoglobulin peptides which can be detected by proteomic techniques. J Biol Chem 285:29247-29253.
Zhang R, Barton A, Bittenden J, Huang J, Crowther D,. Evaluation for Computational Platforms of LC-MS Based Label-Free Quantitative Proteomics: A Global View. Journal of Proteomics & Bioinformatics 3:260-265.
2009
Peltoniemi H et al (2009) G110 Automated N-Glycan Composition Analysis with LC-MS/MS. Clinical Proteomics, Volume 5, Supplement 1, Page 112.
Magdeldin S et al (2009) T117 Comprehensive Analysis of Wild and AQP 8 Knockout Mouse Colon by Nanoflow LC-MS/MS. Clinical Proteomics, Volume 5, Supplement 1, Page 236.
Goodbrand SA, Lamont D, Ferguson MA, Steele RJ (May 2009) W1897 Colorectal Cancer Biomarker Discovery Using Quantitative Proteomics. Gastroenterology, Volume 136, Issue 5, Supplement 1, Pages A-749.
Daknaa M, Heb Z, Yub WC, Mischaka H, Kolchc 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. Journal of Chromatography B, 877, 1250-1258.
