Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics

Journal of Proteome Research

Volumn 9, Issue 4, 2010, Pages 1902-1912

  Fang, Yuan ^a   Robinson, Dale P ^a   Foster, Leonard J ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

ANIMAL TISSUE; ARTICLE; CELL FRACTIONATION; HONEYBEE; ION EXCHANGE CHROMATOGRAPHY; ISOELECTRIC FOCUSING; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS;

ANIMALS; BEES; CHROMATOGRAPHY, GEL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HEAD; ISOELECTRIC FOCUSING; LINEAR MODELS; PEPTIDES; PROTEINS; PROTEOME; PROTEOMICS;

EID: 77950669475     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr901063t     Document Type: Article

References (33)

1. C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology Science 1998, 282 (5396) 2012 - 8
2. Anderson, N. L.; Anderson, N. G.; Pearson, T. W.; Borchers, C. H.; Paulovich, A. G.; Patterson, S. D.; Gillette, M.; Aebersold, R.; Carr, S. A. A human proteome detection and quantitation project Mol. Cell. Proteomics 2009, 8 (5) 883 - 6
3. Cox, J.; Mann, M. Is proteomics the new genomics Cell 2007, 130 (3) 395 - 8
4. Aebersold, R.; Mann, M. Mass spectrometry-based proteomics Nature 2003, 422 (6928) 198 - 207 (Pubitemid 36362757)
5. Lasonder, E.; Ishihama, Y.; Andersen, J. S.; Vermunt, A. M.; Pain, A.; Sauerwein, R. W.; Eling, W. M.; Hall, N.; Waters, A. P.; Stunnenberg, H. G.; Mann, M. Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry Nature 2002, 419 (6906) 537 - 42
6. Washburn, M. P.; Wolters, D.; Yates, J. R., III. Large-scale analysis of the yeast proteome by multidimensional protein identification technology Nat. Biotechnol. 2001, 19 (3) 242 - 7 (Pubitemid 32220565)
7. Peng, J.; Elias, J. E.; Thoreen, C. C.; Licklider, L. J.; Gygi, S. P. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome J. Proteome Res. 2003, 2 (1) 43 - 50 (Pubitemid 36207189)
8. Ishihama, Y.; Rappsilber, J.; Mann, M. Modular stop and go extraction tips with stacked disks for parallel and multidimensional Peptide fractionation in proteomics J. Proteome Res. 2006, 5 (4) 988 - 94
9. Thorsell, A.; Portelius, E.; Blennow, K.; Westman-Brinkmalm, A. Evaluation of sample fractionation using micro-scale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment Rapid Commun. Mass Spectrom. 2007, 21 (5) 771 - 8 (Pubitemid 46340321)
10. Li, Y.; Yu, J.; Wang, Y.; Griffin, N. M.; Long, F.; Shore, S.; Oh, P.; Schnitzer, J. E. Enhancing identifications of lipid-embedded proteins by mass spectrometry for improved mapping of endothelial plasma membranes in vivo Mol. Cell. Proteomics 2009
11. Hubner, N. C.; Ren, S.; Mann, M. Peptide separation with immobilized pI strips is an attractive alternative to in-gel protein digestion for proteome analysis Proteomics 2008, 8 (23-24) 4862 - 72
12. Fraterman, S.; Zeiger, U.; Khurana, T. S.; Rubinstein, N. A.; Wilm, M. Combination of peptide OFFGEL fractionation and label-free quantitation facilitated proteomics profiling of extraocular muscle Proteomics 2007, 7 (18) 3404 - 16 (Pubitemid 47517955)
13. Waller, L. N.; Shores, K.; Knapp, D. R. Shotgun proteomic analysis of cerebrospinal fluid using off-gel electrophoresis as the first-dimension separation J. Proteome Res. 2008, 7 (10) 4577 - 84
14. Slebos, R. J.; Brock, J. W.; Winters, N. F.; Stuart, S. R.; Martinez, M. A.; Li, M.; Chambers, M. C.; Zimmerman, L. J.; Ham, A. J.; Tabb, D. L.; Liebler, D. C. Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry J. Proteome Res. 2008, 7 (12) 5286 - 94
15. Heller, M.; Michel, P. E.; Morier, P.; Crettaz, D.; Wenz, C.; Tissot, J. D.; Reymond, F.; Rossier, J. S. Two-stage Off-Gel isoelectric focusing: protein followed by peptide fractionation and application to proteome analysis of human plasma Electrophoresis 2005, 26 (6) 1174 - 88 (Pubitemid 40514809)
16. Foster, L. J.; de Hoog, C. L.; Mann, M. Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors Proc. Natl. Acad. Sci., U.S.A. 2003, 100 (10) 5813 - 8 (Pubitemid 36576890)
17. Chan, Q. W.; Howes, C. G.; Foster, L. J. Quantitative comparison of caste differences in honeybee hemolymph Mol. Cell. Proteomics 2006, 5 (12) 2252 - 2262
18. Boersema, P. J.; Aye, T. T.; van Veen, T. A.; Heck, A. J.; Mohammed, S. Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates Proteomics 2008, 8 (22) 4624 - 32
19. Mortensen, P.; Gouw, J. W.; Olsen, J. V.; Ong, S. E.; Rigbolt, K. T.; Bunkenborg, J.; Cox, J.; Foster, L.; Heck, A. J.; Blagoev, B.; Andersen, J. S.; Mann, M. MSQuant, an open source platform for mass spectrometry-based quantitative proteomics J. Proteome Res. 2010, 9 (1) 393 - 403
20. Elsik, C. G.; Mackey, A. J.; Reese, J. T.; Milshina, N. V.; Roos, D. S.; Weinstock, G. M. Creating a honey bee consensus gene set Genome Biol. 2007, 8 (1) R13
21. Yates, J.; Ruse, C. I.; Nakorchevsky, A. Proteomics by mass spectrometry: approaches, advances, and applications Annu. Rev. Biomed. Eng. 2009, 11, 49 - 79
22. Schirle, M.; Heurtier, M. A.; Kuster, B. Profiling core proteomes of human cell lines by one-dimensional PAGE and liquid chromatography-tandem mass spectrometry Mol. Cell. Proteomics 2003, 2 (12) 1297 - 305
23. Bendall, S. C.; Hughes, C.; Campbell, J. L.; Stewart, M. H.; Pittock, P.; Liu, S.; Bonneil, E.; Thibault, P.; Bhatia, M.; Lajoie, G. A. An enhanced mass spectrometry approach reveals human embryonic stem cell growth factors in culture Mol. Cell. Proteomics 2009, 8 (3) 421 - 32
24. Gilar, M.; Olivova, P.; Daly, A. E.; Gebler, J. C. Orthogonality of separation in two-dimensional liquid chromatography Anal. Chem. 2005, 77 (19) 6426 - 34 (Pubitemid 41436983)
25. Barnea, E.; Sorkin, R.; Ziv, T.; Beer, I.; Admon, A. Evaluation of prefractionation methods as a preparatory step for multidimensional based chromatography of serum proteins Proteomics 2005, 5 (13) 3367 - 75 (Pubitemid 41192042)
26. Elschenbroich, S.; Ignatchenko, V.; Sharma, P.; Schmitt-Ulms, G.; Gramolini, A. O.; Kislinger, T. Peptide separations by on-line MudPIT compared to isoelectric focusing in an off-gel format: application to a membrane-enriched fraction from C2C12 mouse skeletal muscle cells J. Proteome Res. 2009, 8 (10) 4860 - 9
27. de Godoy, L. M.; Olsen, J. V.; Cox, J.; Nielsen, M. L.; Hubner, N. C.; Frohlich, F.; Walther, T. C.; Mann, M. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast Nature 2008, 455 (7217) 1251 - 4
28. Lu, P.; Vogel, C.; Wang, R.; Yao, X.; Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat. Biotechnol. 2007, 25 (1) 117 - 24 (Pubitemid 46087910)
29. Foster, L. J. Large-scale subcellular localization of proteins by protein correlation profiling. In Comprehensive Analytical Chemistry; Barceló, D., Ed.; Elsevier: Amsterdam, 2009; pp 468 - 478.
30. Cabecinha, A.; Petrotchenko, E.; Borchers, C. H. Out-gel digest procedure for protein crosslinking applications J. Am. Soc. Mass Spectrom. 2009, 20 (5S1) S105
31. Adachi, J.; Kumar, C.; Zhang, Y.; Olsen, J. V.; Mann, M. The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins Genome Biol. 2006, 7 (9) R80 (Pubitemid 44614864)
32. Ong, S. E.; Blagoev, B.; Kratchmarova, I.; Kristensen, D. B.; Steen, H.; Pandey, A.; Mann, M. Stable Isotope Labeling by Amino Acids in Cell Culture, SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 2002, 1 (5) 376 - 86
33. Honeybee Genome Sequencing Consortium nsights into social insects from the genome of the honeybee Apis mellifera Nature 2006, 443 (7114) 931 - 49