MS1-based label-free proteomics using a quadrupole orbitrap mass spectrometer

Journal of Proteome Research

Volumn 14, Issue 4, 2015, Pages 1979-1986

  Shalit, Tali ^a   Elinger, Dalia ^a   Savidor, Alon ^a   Gabashvili, Alexandra ^a   Levin, Yishai ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

informatics tools; label free proteomics; quantification

Indexed keywords

PROTEOME;

ACCURACY; ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; FEMALE; HUMAN; HUMAN CELL; MASS SPECTROMETER; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; QUADRUPOLE MASS SPECTROMETRY; QUALITY CONTROL; QUANTITATIVE ANALYSIS; BENCHMARKING; BIOLOGY; DEVICES; GENE EXPRESSION REGULATION; HELA CELL LINE; MASS SPECTROMETRY; PHYSIOLOGY; PROCEDURES;

ESCHERICHIA COLI;

BENCHMARKING; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; HELA CELLS; HUMANS; MASS SPECTROMETRY; PROTEOMICS;

EID: 84926444106     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr501045t     Document Type: Article

References (32)

1. Altelaar, A. F. Next-generation proteomics: Towards an integrative view of proteome dynamics Nat. Rev. Genet. 2013, 14, 35-48
2. Bantscheff, M. Quantitative mass spectrometry in proteomics: A critical review Anal. Bioanal. Chem. 2007, 389, 1017-1031
3. Cox, J. Is proteomics the new genomics? Cell 2007, 130, 395-398
4. Ong, S. E. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 2002, 1, 376-386
5. Ross, P. L. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents Mol. Cell. Proteomics 2004, 3, 1154-1169
6. Thompson, A. Tandem mass tags: A novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS Anal. Chem. 2003, 75, 1895-1904
7. Liu, H. A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal. Chem. 2004, 76, 4193-4201
8. Collins, B. C. Quantifying protein interaction dynamics by SWATH mass spectrometry: Application to the 14-3-3 system Nat. Methods 2013, 10, 1246-1253
9. Egertson, J. D. Multiplexed MS/MS for improved data-independent acquisition Nat. Methods 2013, 10, 744-746
10. Levin, Y. Label-free LC-MS/MS quantitative proteomics for large-scale biomarker discovery in complex samples J. Sep. Sci. 2007, 30, 2198-2203
11. Cox, J. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ Molecular & cellular proteomics: MCP 2014, 13, 2513-2526
12. Wang, G. Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes J. Proteome Res. 2006, 5, 1214-1223
13. Asara, J. M. A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen Proteomics 2008, 8, 994-999
14. Levin, Y. Quantification of proteins using data-independent analysis (MSE) in simple andcomplex samples: a systematic evaluation Proteomics 2011, 11, 3273-3287
15. Silva, J. C. Absolute quantification of proteins by LCMSE: A virtue of parallel MS Acquisition Mol. Cell. Proteomics 2006, 5, 144-156
16. Nagaraj, N. Deep proteome and transcriptome mapping of a human cancer cell line Mol. Syst. Biol. 2011, 7, 548
17. Lu, P. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat. Biotechnol. 2007, 25, 117-124
18. Rosenberger, G. aLFQ: An R-package for estimating absolute protein quantities from label-free LC-MS/MS proteomics data Bioinformatics 2014, 30, 2511-2513
19. Silva, J. C. Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition Mol. Cell. Proteomics 2006, 5, 144-156
20. Vizcaino, J. A. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nat. Biotechnol. 2014, 32, 223-226
21. Cox, J. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26, 1367-1372
22. Ow, S. Y. iTRAQ underestimation in simple and complex mixtures: "The good, the bad and the ugly" J. Proteome Res. 2009, 8, 5347-5355
23. Huang, T. Protein inference: A review Briefings Bioinf. 2012, 13, 586-614
24. Li, Y. F. Computational approaches to protein inference in shotgun proteomics BMC Bioinformatics 2012, 13 (Suppl 16) S4
25. Song, C. Improvement of the quantification accuracy and throughput for phosphoproteome analysis by a pseudo triplex stable isotope dimethyl labeling approach Anal. Chem. 2011, 83, 7755-7762
26. Ding, C. A fast workflow for identification and quantification of proteomes Mol. Cell. Proteomics 2013, 12, 2370-2380
27. Cox, J. Andromeda: A peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011, 10, 1794-1805
28. Cox, J. Quantitative, high-resolution proteomics for data-driven systems biology Annu. Rev. Biochem. 2011, 80, 273-299
29. Schilling, B. Platform-independent and label-free quantitation of proteomic data using MS1 extracted ion chromatograms in skyline: application to protein acetylation and phosphorylation Mol. Cell. Proteomics 2012, 11, 202-214
30. Qavi, A. J. Label-free technologies for quantitative multiparameter biological analysis Anal. Bioanal. Chem. 2009, 394, 121-135
31. Mosley, A. L. A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus J. Proteomics 2009, 72, 110-120
32. Schiess, R. Analysis of cell surface proteome changes via label-free, quantitative mass spectrometry Mol. Cell. Proteomics 2009, 8, 624-638