Processing strategies and software solutions for data-independent acquisition in mass spectrometry

Proteomics

Volumn 15, Issue 5-6, 2015, Pages 964-980

  Bilbao, Aivett ^a,b   Varesio, Emmanuel ^b   Luban, Jeremy ^c   Strambio De Castillia, Caterina ^c   Hopfgartner, Gérard ^b   Müller, Markus ^a,b   Lisacek, Frédérique ^a,b  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b UNIVERSITY OF GENEVA   (Switzerland)

^c UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

Author keywords

Bottom up proteomics; Data processing and analysis; Data independent acquisition; Label free quantification; Mass spectrometry LC MS MS

Indexed keywords

ALGORITHM; COMPUTER LANGUAGE; COMPUTER PROGRAM; DATA INDEPENDENT ACQUISITION; DATA PROCESSING; MASS SPECTROMETRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; REVIEW; WORKFLOW; LIQUID CHROMATOGRAPHY; PROCEDURES; PROTEOMICS; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY;

CHROMATOGRAPHY, LIQUID; MASS SPECTROMETRY; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 84924712451     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201400323     Document Type: Review

References (54)

1. Nesvizhskii, A. I., A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics. J. Proteomics 2010, 73, 2092-2123.
2. Blackburn, K., Mbeunkui, F., Mitra, S. K., Mentzel, T. et al., Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation. J. Proteome Res. 2010, 9, 3621-3637.
3. Wenner, B. R., Lynn, B. C., Factors that affect ion trap data-dependent MS/MS in proteomics. J. Am. Soc. Mass Spectrom. 2004, 15, 150-157.
4. Kuster, B., Schirle, M., Mallick, P., Aebersold, R., Scoring proteomes with proteotypic peptide probes. Nat. Rev. Mol. Cell Biol. 2005, 6, 577-583.
5. Michalski, A., Cox, J., Mann, M., More than 100, 000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data-dependent LC- MS/MS. J. Proteome Res. 2011, 10, 1785-1793.
6. Purvine, S., Eppel, J. T., Yi, E. C., Goodlett, D. R. Shotgun collision-induced dissociation of peptides using a time of flight mass analyzer. Proteomics 2003, 3, 847-850.
7. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Analyt. Chem. 2005, 77, 2187-2200.
8. 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.
9. Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. et al., Absolute quantification of proteins by LCMSE a virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
10. Geiger, T., Cox, J., Mann, M., Proteomics on an Orbitrap benchtop mass spectrometer using all-ion fragmentation. Mol. Cell. Proteomics 2010, 9, 2252-2261.
11. Venable, J. D., Dong, M.-Q., Wohlschlegel, J., Dillin, A. et al., Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra. Nat. Methods 2004, 1, 39-45.
12. Panchaud, A., Scherl, A., Shaffer, S. A., Haller, P. D. von et al., Precursor acquisition independent from ion count: how to dive deeper into the proteomics ocean. Analyt. Chem. 2009, 81, 6481-6488.
13. Panchaud, A., Jung, S., Shaffer, S. A., Aitchison, J. D. et al., Faster, quantitative, and accurate precursor acquisition independent from ion count. Analyt. Chem. 2011, 83, 2250-2257.
14. Carvalho, P. C., Han, X., Xu, T., Cociorva, D. et al., XDIA: improving on the label-free data-independent analysis. Bioinformatics 2010, 26, 847-848.
15. Weisbrod, C. R., Eng, J. K., Hoopmann, M. R., Baker . et al., Accurate peptide fragment mass analysis: multiplexed peptide identification and quantification. J. Proteome Res. 2012, 11, 1621-1632.
16. Gillet, L. C., Navarro, P., Tate, S., Röst, 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, 111-16717.
17. Egertson, J. D., Kuehn, A., Merrihew, G. E., Bateman, N. W. et al., Multiplexed MS/MS for improved data-independent acquisition. Nat. Methods 2013, 10, 744-746.
18. Chapman, J. D., Goodlett, D. R., Masselon, C. D., Multiplexed and data-independent tandem mass spectrometry for global proteome profiling. Mass Spectrom. Rev. 2014, 33, 452-470.
19. Shliaha, P. V., Bond, N. J., Gatto, L., Lilley, K. S., Effects of traveling wave ion mobility separation on data-independent acquisition in proteomics studies. J. Proteome Res. 2013, 12, 2323-2339.
20. Distler, U., Kuharev, J., Navarro, P., Levin, Y. et al., Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics. Nat. Methods 2014, 11, 167-170.
21. Chambers, M. C., Maclean, B., Burke, R., Amodei, D. et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920.
22. Eng, J. K., McCormack, A. L., Yates, J. R., An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5, 976-989.
23. Houel, S., Abernathy, R., Renganathan, K., Meyer-Arendt, K. et al., Quantifying the impact of chimera MS/MS spectra on peptide identification in large-scale proteomics studies. J. Proteome Res. 2010, 9, 4152-4160.
24. Alves, G., Ogurtsov, A. Y., Kwok, S., Wu, W. W. et al., Detection of co-eluted peptides using database search methods. Biol. Direct 2008, 3, 1-16.
25. Hoopmann, M. R., Finney, G. L., MacCoss, M. J., High-speed data reduction, feature detection, and MS/MS spectrum quality assessment of shotgun proteomics data sets using high-resolution mass spectrometry. Analyt. Chem. 2007, 79, 5620-5632.
26. Luethy, R., Kessner, D. E., Katz, J. E., MacLean, B. et al., Precursor-ion mass re-estimation improves peptide identification on hybrid instruments. J. Proteome Res. 2008, 7, 4031-4039.
27. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individualized ppb-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
28. Pak, H., Nikitin, F., Gluck, F., Lisacek, F. et al., Clustering and filtering tandem mass spectra acquired in data-independent mode. J. Am. Soc. Mass Spectrom. 2013, 24, 1862-1871.
29. Venable, J. D., Xu, T., Cociorva, D., Yates, J. R., Cross-correlation algorithm for calculation of peptide molecular weight from tandem mass spectra. Analyt. Chem. 2006, 78, 1921-1929.
30. Ledvina, A., Savitski, M., Zubarev, A., Good, D. et al., Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra. Analyt. Chem. 2011, 83, 7651-7656.
31. Kryuchkov, F., Verano-Braga, T., Hansen, T. A., Sprenger, R. R. et al., Deconvolution of mixture spectra and increased throughput of peptide identification by utilization of intensified complementary ions formed in tandem mass spectrometry. J. Proteome Res. 2013, 12, 3362-3371.
32. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
33. Kryuchkov, F., Verano-Braga, T., Kjeldsen, F., N-terminal sequence tagging using reliably determined b2 ions: a useful approach to deconvolute tandem mass spectra of co-fragmented peptides in proteomics. J. Proteomics 2014, 103, 254-260.
34. Masselon, C., Paša-Toli, L., Lee, S.-W., Li, L. et al., Identification of tryptic peptides from large databases using multiplexed tandem mass spectrometry: simulations and experimental results. Proteomics 2003, 3, 1279-1286.
35. Zhang, N., Li, X., Ye, M., Pan, S. et al., ProbIDtree: An automated software program capable of identifying multiple peptides from a single collision-induced dissociation spectrum collected by a tandem mass spectrometer. Proteomics 2005, 5, 4096-4106.
36. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A. et al., Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 2011, 10, 1794-1805.
37. Wang, J., Pérez-Santiago, J., Katz, J. E., Mallick, P. et al., Peptide identification from mixture tandem mass spectra. Mol. Cell. Proteomics 2010, 9, 1476-1485.
38. Wang, J., Bourne, P. E., Bandeira, N., Peptide identification by database search of mixture tandem mass spectra. Mol. Cell. Proteomics 2011, 10, M111.010017.
39. Li, G.-Z., Vissers, J. P., Silva, J. C., Golick, D. et al., Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures. Proteomics 2009, 9, 1696-1719.
40. Lange, V., Picotti, P., Domon, B., Aebersold, R., Selected reaction monitoring for quantitative proteomics: a tutorial. Mol. Syst. Biol 2008, 4, 222-236.
41. Lesur, A., Varesio, E., Domon, B., Hopfgartner, G., Peptides quantification by liquid chromatography with matrix-assisted laser desorption/ionization and selected reaction monitoring detection. J. Proteome Res. 2012, 11, 4972-4982.
42. Picotti, P., Aebersold, R., Selected reaction monitoring-based proteomics: workflows, potential, pitfalls and future directions. Nat. Methods 2012, 9, 555-566.
43. Liu, Y., Hüttenhain, R., Collins, B., Aebersold, R., Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Rev. Mol. Diagn. 2013, 13, 811-825.
44. Reiter, L., Rinner, O., Picotti, P., Hüttenhain, R. et al., mProphet: automated data processing and statistical validation for large-scale SRM experiments. Nat. Methods 2011, 8, 430-435.
45. Bernhardt, O. M., Selevsek, N., Gillet, L. C., Rinner, O. et al., Proceedings of the 60th ASMS Conference on Mass Spectrometry and Allied Topics. Vancouver, Canada, 2012, pp. 20-24.
46. Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L. et al., OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nat. Biotechnol. 2014, 32, 219-223.
47. Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A. et al., OpenMS-an open-source software framework for mass spectrometry. BMC Bioinformatics 2008, 9, 163.
48. MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M. et al., Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26, 966-968.
49. Cappadona, S., Baker, P. R., Cutillas, P. R., Heck, A. J. et al., Current challenges in software solutions for mass spectrometry-based quantitative proteomics. Amino Acids 2012, 43, 1087-1108.
50. Escher, C., Reiter, L., MacLean, B., Ossola, R. et al., Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics 2012, 12, 1111-1121.
51. Choi, M., Chang, C.-Y., Clough, T., Broudy, D. et al., MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014, 30, 2524-2526.
52. Bond, N. J., Shliaha, P. V., Lilley, K. S., Gatto, L., Improving qualitative and quantitative performance for MSe-based label-free proteomics. J. Proteome Res. 2013, 12, 2340-2353.
53. Aebersold, R., A stress test for mass spectrometry-based proteomics. Nat. Methods 2009, 6, 411.
54. Bern, M., Finney, G., Hoopmann, M. R., Merrihew, G. et al., Deconvolution of mixture spectra from ion-trap data-independent-acquisition tandem mass spectrometry. Analyt. Chem. 2009, 82, 833-841.