Database searching and accounting of multiplexed precursor and product ion spectra from the data independent analysis of simple and complex peptide mixtures

Proteomics

Volumn 9, Issue 6, 2009, Pages 1696-1719

  Li, Guo Zhong ^a   Vissers, Johannes P C ^a   Silva, Jeffrey C ^a,b   Golick, Dan ^a   Gorenstein, Marc V ^a   Geromanos, Scott J ^a  

^a WATERS CORPORATION   (United States)

^b CELL SIGNALING TECHNOLOGY   (United States)

Author keywords

Data independent LC MS; Database searching; Multiplexed LC MS; Parallel LC MS; Shotgun sequencing

Indexed keywords

ALCOHOL DEHYDROGENASE; ENOLASE; GLYCOGEN PHOSPHORYLASE; PEPTIDE; SERUM ALBUMIN;

ALGORITHM; ARTICLE; DATA ANALYSIS; DATA BASE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; PEPTIDE ANALYSIS; PHYSICAL CHEMISTRY; PHYSICOCHEMICAL MODEL; PRECURSOR; PRIORITY JOURNAL; PROTEIN ANALYSIS; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; AMINO ACID SEQUENCE; COMPLEX MIXTURES; DATABASES, PROTEIN; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; PEPTIDES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEINS; PROTEOME; ROC CURVE; TIME FACTORS;

EID: 63049138916     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800564     Document Type: Article

References (75)

1. Henzel, W. J., Billeci, T. M., Stults, J. T., Wong, S. C. et al., Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 1993, 90, 5011-5015.
2. James, P., Quadroni, M., Carafoli, E., Gonnet, G., Protein identification by mass profile fingerprinting. Biochem. Biophys. Res. Commun. 1993, 195, 58-64.
3. Mann, M., Hojrup, P., Roepstorff, P., Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol. Mass Spectrom. 1993, 22, 338-345.
4. Pappin, D. J. C., Hojrup, P., Bleasby, A. J., Rapid identification of proteins by peptide-mass fingerprinting. Curr. Biol. 1993, 3, 327-332.
5. Yates, J. R. III, Speicher, S., Griffin, P. R., Hunkapiller, T., Peptide mass maps: A highly informative approach to protein identification. Anal. Biochem. 1993, 214, 397-408.
6. Strupat, K., Karas, M., Hillenkamp, F., Eckerskorn, C., Lottspeich, F., Matrix-assisted laser desorption ionization mass spectrometry of proteins electroblotted after polyacrylamide Gel Electrophoresis. Anal. Chem. 1994, 66, 464-470.
7. Mortz, E., O'Connor, P. B., Roepstorff, P., Kelleher, N. L. et al., Sequence tag identification of intact proteins by matching tandem mass spectral data against sequence data bases. Proc. Natl. Acad. Sci. USA 1996, 93, 8264-8267.
8. Mann, M., Wilm, M., Error-tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 1994, 66, 4390-4399.
9. Shevchenko, A., Jensen, O. N., Podtelejnikov, A. V., Sagliocco, F. et al., Linking genome and proteome by mass spectrometry: Large-scale identification of yeast proteins from two dimensional gels. Proc. Natl. Acad. Sci. USA 1996, 93, 14440-14445.
10. 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, 242-247.
11. Delahunty, C., Yates, J. R., III, Protein identification using 2D-LC-MS/MS. Mass Spectrom. Proteomics 2005, 35, 209-314.
12. Biemann, K., Papayannopoulos, I. A., Amino acid sequencing of proteins. Acc. Chem. Res. 1994, 27, 370-378.
13. Aebersold, R., Goodlett, D. R., Mass spectrometry in proteomics. Chem. Rev. 2001, 101, 269-295.
14. Aebersold, R., Mann, M., Mass spectrometry-based proteomics. Nature 2003, 422, 198-207.
15. Mikesh, L. M., Ueberheide, B., Chi, A., Coon, J. J. et al., The utility of ETD mass spectrometry in proteomic analysis. Biochim. Biophys. Acta 2006, 1764, 1811-1822.
16. Bakhtiar, R., Guan, Z., Electron capture dissociation mass spectrometry in characterization of peptides and proteins. Biotechnol. Lett. 2006, 28, 1047-1059.
17. Geromanos, S. J., Vissers, J. P. C., Silva, J. C., Dorschel, C. A. et al., The detection, correlation and comparison of peptide precursor and products ions from data independent LC-MS with data dependant LC-MS/MS. Proteomics, 2009, 9, 1683-1695.
18. Eng, J. K., McCormack, A. L., Yates, J. R., III, 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.
19. Craig, R., Cortens, J. P., Beavis, R. C., Open source system for analyzing, validating and storing protein identification data. J. Proteome Res. 2004, 3, 1234-1242.
20. Perkins, D. N., Pappin, D. J., Creasy, D. M., Cottrell, J. S., Probability-based protein identification by searching sequence database using mass spectrometry data. Electrophoresis 1999, 20, 3551-3567.
21. Skilling, J., Denny, R., Richardson, K., Young, P. et al., Prob-Seq - A fragmentation model for interpretation of electrospray tandem mass spectrometry data. Comp. Funct. Genom. 2004, 5, 61-68.
22. MacCoss, M. J., Wu, C. C., Yates, J. R., III, Probability-based validation of protein identifications using a modified SEQUESTalgorithm. Anal. Chem. 2002, 74, 5593-5599.
23. Wu, C. C., Yates, J. R., III, The application of mass spectrometry to membrane proteomics. Nat. Biotechnol. 2003, 21, 262-267.
24. Beynon, R. J., Bond, J. S., Proteolytic Enzymes: A Practical Approach, 2nd Edn., Oxford University Press, Oxford, UK 2001, pp. 149-183.
25. Olsen, J. V, Ong, S.-E, Mann, M., Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3, 608-614.
26. Elias, J. E., Gygi, S. P., Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 2007, 4, 207-214.
27. Tang, W. H., Shilov, I. V., Seymour, S. L., Nonlinear fitting method for determining local false discovery rates from decoy database searches. J. Proteome Res. 2008, 7, 3661-3667.
28. Fenyo, D., Ossipova, E., Eriksson, J., On the peptide fragment mass information required to identify peptides. HUPO 7th Annual World Congress, Amsterdam 2008, poster PTUE-147.
29. Keller, A., Purvine, S., Nesvizhskii, A. I., Stolyar, S. et al., Experimental protein mixture for validating tandem mass spectral analysis. OMICS 2002, 6, 207-212.
30. Sadygov, R. G., Eng, J., Durr, E., Saraf, A. et al., Code development to improve the efficiency of automated MS/MS spectra interpretation. J. Proteome Res. 2002, 1, 211-215.
31. Moore, R. E., Young, M. K., Lee, T. D., Method for screening peptide fragment ion mass spectra prior to database searching. J. Am. Soc. Mass Spectrom. 2000, 11, 422-426.
32. Tabb, D. L., MacCoss, M. J., Wu, C. C., Anderson, S. D., Yates, J. R., III, Similarity among tandem mass spectra from proteomic experiments: Detection, significance, and utility. Anal. Chem. 2003, 75, 2470-2477.
33. Beer, I., Barnea, E., Ziv, T., Admon, A., Improving large-scale proteomics by clustering of mass spectrometry data. Proteomics 2004, 4, 950-960.
34. Colinge, J., Masselot, A., Giron, M., Dessingy, T., Magnin, J., OLAV: Towards high-throughput tandem mass spectrometry data identification. Proteomics 2003, 3, 1454-1463.
35. Liebler, D. C., Hansen, B. T., Davey, S. W., Tiscareno, L., Mason, D. E., Peptide sequence motif analysis of tandem MS data with the SALSA algorithm. Anal. Chem. 2002, 74, 203-210.
36. Kristensen, D. B., Brond, J. C., Nielsen, P. A., Andersen, J. R. et al., Experimental peptide identification repository EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol. Cell. Proteomics 2004, 3, 1023-1038.
37. Krokhin, O. V., Craig, R., Spicer, V., Ens, W. et al., An improved model for prediction of retention time of tryptic peptides in ion pair reversed-phase HPLC: Its applications to protein peptide mapping by off-Line HPLC-MALDI MS. Mol. Cell. Proteomics 2004, 3, 908-919.
38. Elias, J. E., Haas, W., Faherty, B. K., Gygi, S. P., Comparative evaluation of mass spectrometry platforms used in large-scale proteomics investigations. Nat. Methods 2005, 2, 667-675.
39. Resing, K. A., Meyer-Arendt, K., Mendoza, A. M., Aveline-Wolf, L. D. et al., Improving reproducibility and sensitivity in identifying human proteins by shotgun proteomics. Anal. Chem. 2004, 76, 3556-3568.
40. Miyamoto., M., Yoshida, Y., Taguchi, I., Nagasaka, Y. et al., In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J. Proteome Res. 2007, 6, 3680-3690.
41. Faca, V., Coram, M., Phanstiel, D., Glukhova, V. et al., Quantitative analysis of acrylamide labeled serum proteins by LCMS/ MS. J. Proteome Res. 2006, 5, 2009-2018.
42. E; A virtue of parallel MS acquisition. Mol. Cell. Proteomics 2006, 5, 144-156.
43. Ishihama, Y., Oda, Y., Tabata, T., Sato, T. et al., Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol. Cell. Proteomics 2005, 4, 1265-1271.
44. Bateman, R. H., Carruthers, R., Hoyes, J. B., Jones, C. et al., A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight mass spectrometer for studying protein phosphorylation. J. Am. Soc. Mass Spectrom. 2002, 13, 792-803.
45. Silva, J. C., Denny, R., Dorschel, C. A., Gorenstein, M. et al., Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 2005, 77, 2187-2200.
46. Nielsen, M. L., Bennett, K. L., Larsen, B., Moniatte, M., Mann, M., Peptide end sequencing by orthogonal MALDI tandem mass spectrometry. J. Proteome Res. 2002, 1, 63-71.
47. Jensen, O. N., Podtelejnikov, A. V., Mann, M., Identification of the components of simple protein mixtures by high-accuracy peptide mass mapping and database searching. Anal. Chem. 1997, 69, 4741-4750.
48. Petritis, K., Kangas, L. J., Yan, B., Strittmatter, E. F. et al., Improved peptide elution time prediction for reversed-phase liquid chromatography-MS by incorporating peptide sequence information. Anal. Chem. 2006, 78, 5026-5039.
49. Mant, C. T., Burke, T. W. L., Black, J. A., Hodges, R. S., Effect of peptide chain length on peptide retention behaviour in reversed-phase chromatography. J. Chromatogr. A 1988, 458, 193-205.
50. Kaliszan, R., Baczek, T., Cimochowska, A., Juszczyk, P. et al., Prediction of high-performance liquid chromatography retention of peptides with the use of quantitative structure-retention relationships. Proteomics 2005, 5, 409-415.
51. Meek, J. L., Prediction of peptide retention times in high-pressure liquid chromatography on the basis of amino acid composition. Proc. Natl. Acad. Sci. USA 1980, 77, 1632-1636.
52. Palmblad, M., Ramström, M., Markides, K. E., Håkansson, P., Bergquist, J., Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry. Anal. Chem. 2002, 74, 5826-5830.
53. Biemann, K., Martin, S. A., Mass spectrometric determination of the amino acid sequence of peptides and proteins. Mass Spectrom. Rev. 1987, 6, 1-76.
54. McCormack, A. L., Somogyi, A., Dongre, A. R., Wysocki, V. H., Fragmentation of protonated peptides: Surface-induced dissociation in conjunction with a quantum mechanical approach. Anal. Chem. 1993, 65, 2859-2872.
55. Wysocki, V. H., Tsaprailis, G., Smith, L. L., Breci, L. A., Mobile and localized protons: A framework for understanding peptide dissociation. J. Mass Spectrom. 2000, 35, 1399-1406.
56. Zhang, Z., Prediction of low-energy collision-induced dissociation spectra of peptides. Anal. Chem. 2004, 76, 3908-3922.
57. Elias, J. E., Gibbons, F. D., King, O. D., Roth, F. P., Gygi, S. P., Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nat. Biotechnol. 2004, 22, 214-219.
58. Zhang, Z., Prediction of low-energy collision-induced dissociation spectra of peptides with three or more charges. Anal. Chem. 2005, 77, 6364-6373.
59. Rappsilber, J., Ryder, U., Lamond, A. I., Mann, M., Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002, 12, 1231-1245.
60. Liu, H., Sadygov, R. G., Yates, J. R., III, A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 2004, 76, 4193-4201.
61. Colinge, J., Chiappe, D., Lagache, S., Moniatte, M., Bougueleret, L., Differential proteomics via probabilistic peptide identification scores. Anal. Chem. 2005, 77, 596-606.
62. Old, W. M., Meyer-Arendt, K., Aveline-Wolf, L., Pierce, K. G. et al., Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol. Cell. Proteomics 2005, 4, 1487-1502.
63. Li, X.-J., Yi, E. C., Kemp, C. J., Zhang, H., Aebersold, R., A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 2005, 4, 1328-1340.
64. Kristensen, D. B., Brønd, J. C., Nielsen, P. A., Andersen, J. R. et al., Experimental peptide identification repository (EPIR): An integrated peptide-centric platform for validation and mining of tandem mass spectrometry data. Mol. Cell. Proteomics 2004, 3, 1023-1038.
65. Craig, R., Beavis, R. C., TANDEM: Matching proteins with tandem mass spectra. Bioinformatics 2004, 20, 1466-1467.
66. 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. Anal. Chem. 2007, 79, 5620-5632.
67. 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.
68. Kapp, E. A., Schütz, F., Reid, G. E., Eddes, J. S. et al., Mining a tandem mass spectrometry database to determine the trends and global factors influencing peptide fragmentation. Anal. Chem. 2003, 75, 6251-6264.
69. Barton, S. J., Richardson, S., Perkins, D. N., Bellahn, I. et al., Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS. Anal. Chem. 2007, 79, 5601-5607.
70. Gilar, M., Jaworski, A., Olivova, P., Gebler, J. C., Peptide retention prediction applied to proteomic data analysis. Rapid Commun. Mass Spectrom. 2007, 21, 813-2821.
71. Papayannopoulos, I. A., The interpretation of collision-induced dissociation tandem mass spectra of peptides. Mass Spectrom. Rev. 1995, 14, 49-73.
72. Li, G.-Z., Golick, D., Gorenstein, M. V., Vissers, J. P. C. et al., A novel "ion accounting" algorithm for protein database searches. HUPO 5th Annual World Congress, Long Beach, CA 2006, Abstract 658.
73. Vissers, J. P. C., Langridge, J. I., Aerts, J. M. F. G., Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell. Proteomics 2007, 6, 755-766.
74. Vissers, J. P. C., Pons, S., Hulin, A., Tissier, R. et al., The use of proteome similarity for the qualitative and quantitative profiling of reperfused myocardium. J. Chromatogr. B (in press), doi: 10.1016/j.jchromb.2008.10.024).
75. Hollak, C. E. M., van Weely, S., van Oers, M. H. J., Aerts, J. M. F. G., Marked elevation of plasma chitotriosidase activity: A novel hallmark of Gaucher disease. J. Clin. Invest. 1994, 93, 1288-1292.