Whole cell, label free protein quantitation with data independent acquisition: Quantitation at the MS2 level

Proteomics

Volumn 15, Issue 1, 2015, Pages 16-24

  Mcqueen, Peter ^a   Spicer, Vic ^b   Schellenberg, John ^b   Krokhin, Oleg ^a,b   Sparling, Richard ^b   Levin, David ^b   Wilkins, John A ^a,b,c  

^a UNIVERSITY OF MANITOBA   (Canada)

^b UNIVERSITY OF MANITOBA   (Canada)

^c HEALTH SCIENCES CENTRE   (Canada)

Author keywords

Bottom up proteomics; Data dependent acquisition; Data independent acquisition; Label free quantitation; Relative protein quantitation; SWATH; Technology

Indexed keywords

BACTERIAL PROTEIN; MS2 PROTEIN; PEPTIDE FRAGMENT; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; CLOSTRIDIUM; CLOSTRIDIUM STERCORARIUM; CONTROLLED STUDY; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NONHUMAN; PREDICTION AND FORECASTING; PROTEIN ANALYSIS; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; WHOLE CELL; CHEMISTRY; PROCEDURES; PROTEOMICS; TANDEM MASS SPECTROMETRY;

BACTERIA (MICROORGANISMS); CLOSTRIDIUM STERCORARIUM;

BACTERIAL PROTEINS; CHROMATOGRAPHY, LIQUID; CLOSTRIDIUM; PEPTIDE FRAGMENTS; PROTEOMICS; TANDEM MASS SPECTROMETRY;

EID: 84920592722     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400188     Document Type: Article

References (40)

1. Aebersold, R., Goodlett, D. R., Mass spectrometry in proteomics. Chem. Rev. 2001, 101, 269-295.
2. Craig, R., Cortens, J. C., Fenyo, D., Beavis, R. C., Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 2006, 5, 1843-1849.
3. Nesvizhskii, A. I., Protein identification by tandem mass spectrometry and sequence database searching. Methods Mol. Biol. 2007, 367, 87-119.
4. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., Kuster, B., Quantitative mass spectrometry in proteomics: a critical review. Anal. Bioanal. Chem. 2007, 389, 1017-1031.
5. Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F. et al., Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 1999, 17, 994-999.
6. Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K. et al., High sensitivity detection of plasma proteins by multiple reaction monitoring of N-glycosites. Mol. Cell Proteomics 2007, 6, 1809-1817.
7. Wiese, S., Reidegeld, K. A., Meyer, H. E., Warscheid, B., Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007, 7, 340-350.
8. Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol. 2008, 4, 222-236.
9. Evans, C., Noirel, J., Ow, S. Y., Salim, M. et al., An insight into iTRAQ: where do we stand now? Anal. Bioanal. Chem. 2012, 404, 1011-1027.
10. Wong, J. W., Cagney, G., An overview of label-free quantitation methods in proteomics by mass spectrometry. Methods Mol. Biol. 2010, 604, 273-283.
11. Schilling, B., Rardin, M. J., MacLean, B. X., Zawadzka, A. M. et al., 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.
12. Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J. et al., Deep proteome and transcriptome mapping of a human cancer cell line. Mol. Syst. Biol. 2011, 7, 548-556.
13. Griffin, N. M., Yu, J., Long, F., Oh, P. et al., Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis. Nat. Biotechnol. 2010, 28, 83-89.
14. Lundgren, D. H., Hwang, S. I., Wu, L., Han, D. K., Role of spectral counting in quantitative proteomics. Expert Rev. Proteomics 2010, 7, 39-53.
15. Stahl, D. C., Swiderek, K. M., Davis, M. T., Lee, T. D., Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures. J. Am. Soc. Mass Spectrom 1996, 7, 532-540.
16. Krey, J. F., Wilmarth, P. A., Shin, J. B., Klimek, J. et al., Accurate label-free protein quantitation with high- and low-resolution mass spectrometers. J. Proteome Res. 2014, 13, 1034-1044.
17. Spinelli, K. J., Klimek, J. E., Wilmarth, P. A., Shin, J. B. et al., Distinct energy metabolism of auditory and vestibular sensory epithelia revealed by quantitative mass spectrometry using MS2 intensity. Proc. Natl. Acad Sci USA 2012, 109, E268-E277.
18. Shin, J. B., Streijger, F., Beynon, A., Peters, T. et al., Hair bundles are specialized for ATP delivery via creatine kinase. Neuron 2007, 53, 371-386.
19. Liu, H., Sadygov, R. G., Yates, J. R., 3rd, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
20. Holcapek, M., Jirasko, R., Lisa, M., Recent developments in liquid chromatography-mass spectrometry and related techniques. J. Chromatogr. A 2012, 1259, 3-15.
21. Andrews, G. L., Simons, B. L., Young, J. B., Hawkridge, A. M., Muddiman, D. C., Performance characteristics of a new hybrid quadrupole time-of-flight tandem mass spectrometer (TripleTOF 5600). Anal. Chem. 2011, 83, 5442-5446.
22. Panchaud, A., Scherl, A., Shaffer, S. A., von Haller, P. D. et al., Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Anal. Chem. 2009, 81, 6481-6488.
23. Silva, J. C., Denny, R., Dorschel, C., Gorenstein, M. V. et al., Simultaneous qualitative and quantitative analysis of the Escherichia coli proteome: a sweet tale. Mol. Cell. Proteomics 2006, 5, 589-607.
24. Gillet, L. C., Navarro, P., Tate, S., Rost, H. et al., Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 2012, 11, O111 016717.
25. Moran, D., Cross, T., Brown, L. M., Colligan, R. M., Dunbar, D., Data-independent acquisition (MSE) with ion mobility provides a systematic method for analysis of a bacteriophage structural proteome. J. Virol. Methods 2014, 195, 9-17.
26. Helm, S., Dobritzsch, D., Rodiger, A., Agne, B., Baginsky, S., Protein identification and quantification by data-independent acquisition and multi-parallel collision-induced dissociation mass spectrometry (MS(E)) in the chloroplast stroma proteome. J. Proteomics 2014, 98, 79-89.
27. Liu, Y., Huttenhain, R., Surinova, S., Gillet, L. C. et al., Quantitative measurements of N-linked glycoproteins in human plasma by SWATH-MS. Proteomics 2012, 13, 1247-1256.
28. Madden, R. H., Isolation and characterization of Clostridium stercorarium sp. nov., cellulolytic thermophile. Int. J. Syst. Bacteriol. 1983, 33, 837-840.
29. Sparling, R., Islam, R., Cicek, N., Carere, C. et al., Formate synthesis by Clostridium thermocellum during anaerobic fermentation. Can. J. Microbiol. 2006, 52, 681-688.
30. Wisniewski, J. R., Zougman, A., Nagaraj, N., Mann, M., Universal sample preparation method for proteome analysis. Nat. Methods 2009, 6, 359-362.
31. Smith, P. K., Krohn, R. I., Hermanson, G. T., Mallia, A. K. et al., Measurement of protein using bicinchoninic acid. Anal. Biochem. 1985, 150, 76-85.
32. Krokhin, O. V., Spicer, V., Peptide retention standards and hydrophobicity indexes in reversed-phase high-performance liquid chromatography of peptides. Anal. Chem. 2009, 81, 9522-9530.
33. Craig, R., Cortens, J. P., Beavis, R. C., The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom. 2005, 19, 1844-1850.
34. Fenyo, D., Beavis, R. C., A method for assessing the statistical significance of mass spectrometry-based protein identifications using general scoring schemes. Anal. Chem. 2003, 75, 768-774.
35. Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., 3rd et al., Mass spectrometry in high-throughput proteomics: ready for the big time. Nat. Methods 2010, 7, 681-685.
36. Bateman, N. W., Goulding, S. P., Shulman, N. J., Gadok, A. K. et al., Maximizing peptide identification events in proteomic workflows using data-dependent acquisition (DDA). Mol. Cell. Proteomics 2014, 13, 329-338.
37. Unwin, R. D., Evans, C. A., Whetton, A. D., Relative quantification in proteomics: new approaches for biochemistry. Trends Biochem. Sci. 2006, 31, 473-484.
38. Aggarwal, K., Choe, L. H., Lee, K. H., Shotgun proteomics using the iTRAQ isobaric tags. Brief Funct. Genomic Proteomic 2006, 5, 112-120.
39. Corthals, G. L., Wasinger, V. C., Hochstrasser, D. F., Sanchez, J. C., The dynamic range of protein expression: a challenge for proteomic research. Electrophoresis 2000, 21, 1104-1115.
40. Dwivedi, R. C., Spicer, V., Harder, M., Antonovici, M. et al., Practical implementation of 2D HPLC scheme with accurate peptide retention prediction in both dimensions for high-throughput bottom-up proteomics. Anal. Chem. 2008, 80, 7036-7042.