Design and application of a data-independent precursor and product ion repository

Journal of the American Society for Mass Spectrometry

Volumn 23, Issue 10, 2012, Pages 1808-1820

  Thalassinos, Konstantinos ^a,i   Vissers, Johannes P C ^b   Tenzer, Stefan ^c   Levin, Yishai ^d,j   Thompson, J Will ^e   Daniel, David ^e   Mann, Darrin ^e   DeLong, Mark R ^e   Moseley, M Arthur ^e   America, Antoine H ^f   Ottens, Andrew K ^g   Cavey, Greg S ^h   Efstathiou, Georgios ^a   Scrivens, James H ^a   Langridge, James I ^b   Geromanos, Scott J ^b  

^a UNIVERSITY OF WARWICK   (United Kingdom)

^b WATERS CORPORATION   (United States)

^c UNIVERSITY MEDICAL CENTER MAINZ   (Germany)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e DUKE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f WAGENINGEN UNIVERSITY   (Netherlands)

^g VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^h Southwest Michigan Innovation Center   (United States)

ⁱ UNIVERSITY COLLEGE LONDON   (United Kingdom)

^j WEIZMANN INSTITUTE OF SCIENCE   (Israel)

more..

Author keywords

Data independent analysis; Fragment ion identification repository; Label free; LC MS; Protein and peptide identification; Quantification and validation; Targeted and non targeted proteomics

Indexed keywords

DATA-INDEPENDENT ANALYSIS; FRAGMENT IONS; LABEL FREE; LC-MS; PEPTIDE IDENTIFICATION; PROTEOMICS; QUANTIFICATION AND VALIDATION;

AMINO ACIDS; EXPERIMENTS; IONIZATION; MACHINERY; MAMMALS; MOLECULAR BIOLOGY; PEPTIDES; PRODUCT DESIGN;

IONS;

AMINO ACID; PEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; FRAGMENTATION REACTION; IONIZATION; LIQUID CHROMATOGRAPHY; MAMMAL; MASS SPECTROMETRY; MOLECULAR MECHANICS; MOUSE; NONHUMAN; PEPTIDE ANALYSIS; PROTEIN ANALYSIS; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RAT; VALIDATION STUDY;

CHROMATOGRAPHY, LIQUID; DATABASE MANAGEMENT SYSTEMS; DATABASES, PROTEIN; IONS; MASS SPECTROMETRY; PEPTIDES; PROTEINS; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

MAMMALIA;

EID: 84868261208     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0416-9     Document Type: Article

References (70)

1. Ptolemy, A.S., Rifai, N.: What is a biomarker? Research investments and lack of clinical integration necessitate a review of biomarker terminology and validation schema. Scand. J. Clin. Lab. Invest. Suppl 242, 6-14 (2010)
2. Ransohoff, D.F.: How to improve reliability and efficiency of research about molecular markers: roles of phases, guidelines, and study design. J. Clin. Epidemiol. 60(12), 1205-1219 (2007)
3. White, F.M.: The potential cost of high-throughput proteomics. Sci. Signal. 4(160), pe8 (2011)
4. Kaur, P., O'Connor, P.B.: Algorithms for automatic interpretation of high resolution mass spectra. J. Am. Soc. Mass Spectrom. 17(3), 459-468 (2006)
5. 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. 79(15), 5620-32 (2007)
6. Sun, Y., Zhang, J., Braga-Neto, U., Dougherty, E.R.: BPDA - a Bayesian peptide detection algorithm for mass spectrometry. BMC Bioinformatics 11, 490 (2010)
7. Hoopmann, M.R., Merrihew, G.E., von Haller, P.D., MacCoss, M.J.: Post analysis data acquisition for the iterative MS/MS sampling of proteomics mixtures. J. Proteome Res. 8(4), 1870-1875 (2009)
8. 2 enrichment method for label-free quantitative phosphoproteomics. Methods 54(4), 370-378 (2011)
9. Geromanos, S.J., Vissers, J.P., Silva, J.C., Dorschel, C.A., Li, G.Z., Gorenstein, M.V., Bateman, R.H., Langridge, J.I.: The detection, correlation, and comparison of peptide precursor and product ions from data-independent LC-MS with data dependant LC-MS/MS. Proteomics 9(6), 1683-1695 (2009)
10. 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. 10(4), 1785-1793 (2011)
11. Houel, S., Abernathy, R., Renganathan, K., Meyer-Arendt, K., Ahn, N., Old, W.M.: Quantifying the impact of chimera MS/MS spectra on peptide identification in large scale proteomics tudies. J. Proteome Res 9(8), 4152-4160 (2010)
12. Vissers, J.P., Pons, S., Hulin, A., Tissier, R., Berdeaux, A., Connolly, J.B., Langridge, J.I., Geromanos, S.J., Ghaleh, B.: The use of proteome similarity for the qualitative and quantitative profiling of reperfused myocardium. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 877 (13), 1317-1326 (2009)
13. Frahm, J.L., Howard, B.E., Heber, S., Muddiman, D.C.: Accessible proteomics space and its implications for peak capacity for zero-, one-, and two-dimensional separations coupled with FT-ICR and TOF mass spectrometry. J. Mass Spectrom. 41(3), 281-288 (2006)
14. Rodrìguez-Suárez, E., Hughes, C., Gethings, L., Giles, K., Wildgoose, J., Stapels, M., Fadgen, K.E., Geromanos, S.J., Vissers, J.P., Elortza, F., Langridge, J.I.: An ion mobility assisted data-independent LC-MS strategy for the analysis of complex biological samples. Current. Anal. Chem. Special Issue: Ion Mobility Spectrometry: Using Size and Shape to Understand Real-World Systems at the Molecular Level, HT-SBJ-CAC-0005
15. Geromanos, S.J., Hughes, C., Golick, D., Ciavarini, S., Gorenstein, M.V., Richardson, K., Hoyes, J.B., Vissers, J.P., Langridge, J.I.: Simulating and validating proteomics data and search results. Proteomics 11(6), 1189-1211 (2011)
16. Blackburn, K., Mbeunkui, F., Mitra, S.K., Mentzel, T., Goshe, M.B.: Improving protein and proteome coverage through data-independent multiplexed peptide fragmentation. J. Proteome Res. 9(7), 3621-3637 (2010)
17. Wang, J., Pérez-Santiago, J., Katz, J.E., Mallick, P., Bandeira, N.: Peptide identification from mixture tandem mass spectra. Mol. Cell. Proteom. 9(7), 1476-1485 (2010)
18. Bern, M., Finney, G., Hoopmann, M.R., Merrihew, G., Toth, M.J., MacCoss, M.J.: Deconvolution of mixture spectra from ion-trap data-independent- acquisition tandem mass spectrometry. Anal. Chem. 82(3), 833-841 (2010)
19. Bell, A.W., Deutsch, E.W., Au, C.E., Kearney, R.E., Beavis, R., Sechi, S., Nilsson, T., Bergeron, J.J.: A HUPO test sample study reveals common problems in mass spectrometry-based proteomics. Nat. Methods 6(6), 423-430 (2009)
20. Elias, J.E., Gygi, S.P.: Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat. Methods 4(3), 207-214 (2007)
21. Käll, L., Canterbury, J.D., Weston, J., Noble, W.S., MacCoss, M.J.: Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4(11), 923-925 (2007)
22. Reiter, L., Claassen, M., Schrimpf, S.P., Jovanovic, M., Schmidt, A., Buhmann, J.M., Hengartner, M.O., Aebersold, R.: Protein identification false discovery rates for very large proteomics data sets generated by tandem mass spectrometry. Mol. Cell. Proteom. 8(11), 2405-2417 (2009)
23. Cargile, B.J., Bundy, J.L., Stephenson Jr., J.L.: Potential for false positive identifications from large databases through tandem mass spectrometry. J. Proteome Res. 3(5), 1082-1085 (2004)
24. Zhu, P., Bowden, P., Tucholska, M., Zhang, D., Marshall, J.G.: Peptide-to-protein distribution versus a competition for significance to estimate error rate in blood protein identification. Anal. Biochem. 411(2), 241-253 (2011)
25. Bowden, P., Beavis, R., Marshall, J.: Tandem mass spectrometry of human tryptic blood peptides calculated by a statistical algorithm and captured by a relational database with exploration by a general statistical analysis system. J Proteom. 73(1), 103-111 (2009)
26. Craig, R., Cortens, J.P., Beavis, R.C.: The use of proteotypic peptide libraries for protein identification. Rapid Commun. Mass Spectrom. 19 (13), 1844-1850 (2005)
27. Domokos, L., Hennberg, D., Weimann, B.: Computer-aided identification of compounds by comparison of mass spectra. Anal. Chim. Acta 165, 61-74 (1985)
28. Stein, S.E., Scott, D.R.: Optimization and testing of mass spectral library search algorithms for compound identification. J. Am. Soc. Mass Spectrom. 5(9), 859-866 (1994)
29. Ausloos, P., Clifton, C.L., Lias, S.G., Mikaya, A.I., Stein, S.E., Tchekhovskoi, D.V., Sparkman, O.D., Zaikin, V., Zhu, D.: The critical evaluation of a comprehensive mass spectral library. J. Am. Soc. Mass Spectrom 10(4), 287-299 (1999)
30. Craig, R., Cortens, J.C., Fenyo, D., Beavis, R.C.: Using annotated peptide mass spectrum libraries for protein identification. J. Proteome Res. 5(8), 1843-1849 (2006)
31. Frewen, B.E., Merrihew, G.E., Wu, C.C., Noble, W.S., MacCoss, M.J.: Analysis of peptide MS/MS spectra from large-scale proteomics experiments using spectrum libraries. Anal. Chem. 78(16), 5678-5684 (2006)
32. Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., King, N., Stein, S.E., Aebersold, R.: Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics 7(5), 655-667 (2007)
33. Lam, H., Deutsch, E.W., Eddes, J.S., Eng, J.K., Stein, S.E., Aebersold, R.: Building consensus spectral libraries for peptide identification in proteomics. Nat. Methods 5(10), 873-875 (2008)
34. Yen, C.Y., Houel, S., Ahn, N.G., Old, W.M.: Spectrum-to-spectrum searching using a proteome-wide spectral library. Mol. Cell. Proteom. 10(7), M111.007666 (2011)
35. Frank, A.M., Monroe, M.E., Shah, A.R., Carver, J.J., Bandeira, N., Moore, R.J., Anderson, G.A., Smith, R.D., Pevzner, P.A.: Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra. Nat. Methods 8(7), 587-591 (2011)
36. Frank, A.M.: Predicting intensity ranks of peptide fragment ions. J. Proteome Res. 8(5), 2226-2240 (2009)
37. Frank, A.M., Bandeira, N., Shen, Z., Tanner, S., Briggs, S.P., Smith, R.D., Pevzner, P.A.: Clustering millions of tandem mass spectra. J. Proteome Res 7(1), 113-122 (2008)
38. Vizcaìno, J.A., Côté, R., Reisinger, F., Foster, J.M., Mueller, M., Rameseder, J., Hermjakob, H., Martens, L.: A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9(18), 4276-4283 (2009)
39. Smith, B.E., Hill, J.A., Gjukich, M.A., Andrews, P.C.: Tranche distributed repository and ProteomeCommons.org. Methods Mol. Biol 696, 123-145 (2011)
40. Deutsch, E.W., Lam, H., Aebersold, R.: PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5), 429-434 (2008)
41. Ji, L., Barrett, T., Ayanbule, O., Troup, D.B., Rudnev, D., Muertter, R.N., Tomashevsky, M., Soboleva, A., Slotta, D.J.: NCBI Peptidome: a new repository for mass spectrometry proteomics data. Nucleic Acids Res. 38, D731-D735 (2010)
42. Ma, D., Chan, M.K., Lockstone, H.E., Pietsch, S.R., Jones, D.N., Cilia, J., Hill, M.D., Robbins, M.J., Benzel, I.M., Umrania, Y., Guest, P.C., Levin, Y., Maycox, P.R., Bahn, S.: Antipsychotic treatment alters protein expression associated with presynaptic function and nervous system development in rat frontal cortex. J. Proteome Res. 8(7), 3284-3297 (2009)
43. Krämer-Albers, E.M., Bretz, N., Tenzer, S., Winterstein, C., Möbius, W., Berger, H., Nave, K.A., Schild, H., Trotter, J.: Oligodendrocytes secrete exosomes containing major myelin and stress-protective proteins: Trophic support for axons? Proteomics Clin. Appl. 1(11), 1446-1461 (2007)
44. Reidel, B., Thompson, J.W., Farsiu, S., Moseley, M.A., Skiba, N.P., Arshavsky, V.Y.: Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells. Mol. Cell. Proteom. 10 (3), M110.002469 (2011)
45. Fuller, B.F., Lewis, M.H., Ottens, A.K.: Systems biology reveals altered metabolism and mitochondrial proliferation in developing brain consequent to environmental tobacco smoke exposure. manuscript submitted (2012)
46. Silva, J.C., Gorenstein, M.V., Li, G.Z., Vissers, J.P., Geromanos, S.J.: Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol. Cell. Proteom. 5(1), 144-156 (2006)
47. Bradshaw, R.A., Burlingame, A.L., Carr, S., Aebersold, R.: Reporting protein identification data: the next generation of guidelines. Mol. Cell. Proteom. 5(5), 787-788 (2006)
48. Li, G.Z., Vissers, J.P., Silva, J.C., Golick, D., Gorenstein, M.V., Geromanos, S.J.: Database searching and accounting of multiplexed precursor and product ion spectra from the data-independent analysis of simple and complex peptide mixtures. Proteomics 9(6), 1696-1719 (2009)
49. Tarasova, I.A., Guryca, V., Pridatchenko, M.L., Gorshkov, A.V., Kieffer-Jaquinod, S., Evreinov, V.V., Masselon, C.D., Gorshkov, M.V.: Standardization of retention time data for AMT tag proteomics database generation. J. Chromatogr. B Analyt. Technol. Biomed Life Sci. 877(4), 433-440 (2009)
50. Krokhin, O.V., Craig, R., Spicer, V., Ens, W., Standing, K.G., Beavis, R.C., Wilkins, J.A.: An improved model for prediction of retention times of tryptic peptides in ion pair reversed-phase HPLC: its application to protein peptide mapping by off-line HPLC-MALDI MS. Mol. Cell. Proteom. 3(9), 908-919 (2004)
51. Valentine, S.J., Ewing, M.A., Dilger, J.M., Glover, M.S., Geromanos, S., Hughes, C., Clemmer, D.E.: Using ion mobility data to improve peptide identification: intrinsic amino acid size parameters. J. Proteome Res. 10(5), 2318-2329 (2011)
52. Côté, R.G., Jones, P., Martens, L., Kerrien, S., Reisinger, F., Lin, Q., Leinonen, R., Apweiler, R., Hermjakob, H.: The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. BMC Bioinformatics 8, 401 (2007)
53. Rudnick, P.A., Clauser, K.R., Kilpatrick, L.E., Tchekhovskoi, D.V., Neta, P., Blonder, N., Billheimer, D.D., Blackman, R.K., Bunk, D.M., Cardasis, H.L., Ham, A.J., Jaffe, J.D., Kinsinger, C.R., Mesri, M., Neubert, T.A., Schilling, B., Tabb, D.L., Tegeler, T.J., Vega-Montoto, L., Variyath, A.M., Wang, M., Wang, P., Whiteaker, J.R., Zimmerman, L.J., Carr, S.A., Fisher, S.J., Gibson, B.W., Paulovich, A.G., Regnier, F.E., Rodriguez, H., Spiegelman, C., Tempst, P., Liebler, D.C., Stein, S.E.: Performance metrics for liquid chromatography-tandem mass spectrometry systems in proteomics analyses. Mol. Cell. Proteom 9(2), 225-241 (2010)
54. Paulovich, A.G., Billheimer, D., Ham, A.J., Vega-Montoto, L., Rudnick, P.A., Tabb, D.L., Wang, P., Blackman, R.K., Bunk, D.M., Cardasis, H.L., Clauser, K.R., Kinsinger, C.R., Schilling, B., Tegeler, T.J., Variyath, A.M., Wang, M., Whiteaker, J.R., Zimmerman, L.J., Fenyo, D., Carr, S.A., Fisher, S.J., Gibson, B.W., Mesri, M., Neubert, T.A., Regnier, F.E., Rodriguez, H., Spiegelman, C., Stein, S.E., Tempst, P., Liebler, D.C.: Interlaboratory study characterizing a yeast performance standard for benchmarking LC-MS platform performance. Mol. Cell. Proteom. 9(2), 242-254 (2010)
55. Giles, K., Williams, J.P., Campuzano, I.: Enhancements in traveling wave ion mobility resolution. Rapid Commun. Mass Spectrom. 25(11), 1559-1566 (2011)
56. Thalassinos, K., Grabenauer, M., Slade, S.E., Hilton, G.R., Bowers, M.T., Scrivens, J.H.: Characterization of phosphorylated peptides using traveling wave-based and drift cell ion mobility mass spectrometry. Anal. Chem. 81(1), 248-254 (2009)
57. Barsnes, H., Eidhammer, I., Martens, L.: A global analysis of peptide fragmentation variability. Proteomics 11(6), 1181-1188 (2011)
58. Li, Y.F., Arnold, R.J., Tang, H., Radivojac, P.: The importance of peptide detectability for protein identification, quantification, and experiment design in MS/MS proteomics. J. Proteome Res. 9(12), 6288-6297 (2010)
59. Baker, E.S., Livesay, E.A., Orton, D.J., Moore, R.J., Danielson 3rd, W.F., Prior, D.C., Ibrahim, Y.M., LaMarche, B.L., Mayampurath, A.M., Schepmoes, A.A., Hopkins, D.F., Tang, K, Smith, RD, Belov, ME.: An LC-IMS-MS platform providing increased dynamic range for high-throughput proteomic studies. J. Proteome Res. 9(2), 997-1006 (2010)
60. Vissers, J.P., Langridge, J.I., Aerts, J.M.: Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol. Cell. Proteom. 6(5), 755-766 (2007)
61. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., Speleman, F.: Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, RESEARCH0034 (2002)
62. Martens, G.A., Jiang, L., Verhaeghen, K., Connolly, J.B., Geromanos, S.G., Stangé, G., Van Oudenhove, L., Devreese, B., Hellemans, K.H., Ling, Z., Van Schravendijk, C., Pipeleers, D.G., Vissers, J.P., Gorus, F.K.: Protein markers for insulin-producing beta cells with higher glucose sensitivity. PLoS One 5(12), e14214 (2010)
63. Röwer, C., Vissers, J.P., Koy, C., Kipping, M., Hecker, M., Reimer, T., Gerber, B., Thiesen, H.J., Glocker, M.O.: Towards a proteome signature for invasive ductal breast carcinoma derived from label-free nanoscale LC-MS protein expression profiling of tumors and glandular tissue. Anal. BioAnal. Chem. 395(8), 2443-2456 (2009)
64. Muñoz, I.G., Yébenes, H., Zhou, M., Mesa, P., Serna, M., Park, A.Y., Bragado-Nilsson, E., Beloso, A., de Cárcer, G., Malumbres, M., Robinson, C.V., Valpuesta, J.M, Montoya, G.: Crystal structure of the open conformation of the mammalian chaperonin CCT in complex with tubulin. Nat. Struct. Mol. Biol. 18(1), 14-19 (2011)
65. Arnott, D., Kishiyama, A., Luis, E.A., Ludlum, S.G., Marsters Jr., J.C., Stults, J.T.: Selective detection of membrane proteins without antibodies: a mass spectrometric version of the Western blot. Mol. Cell. Proteomics 1(2), 148-156 (2002)
66. Anderson, L., Hunter, C.L.: Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell. Proteom. 5(4), 573-588 (2006)
67. Lucas, J.E., Thompson, J.W., Dubois, L.G., McCarthy, J., Tillmann, H., Thompson, A., Shire, N., Hendrickson, R., Dieguez, F., Goldman, P., Schwarz, K., Patel, K., McHutchison, J., Moseley, M.A.: Metaprotein expression modeling for label-free quantitative proteomics. BMC Bioinformatics. 13(1):74 (2012)
68. Silva, J.C., Denny, R., Dorschel, C.A., Gorenstein, M., Kass, I.J., Li, G.Z., McKenna, T., Nold, M.J., Richardson, K., Young, P., Geromanos, S.: Quantitative proteomic analysis by accurate mass retention time pairs. Anal. Chem. 77(7), 2187-2200 (2005)
69. Castro-Perez, J.M., Kamphorst, J., Degroot, J., Lafeber, F., Goshawk, J., Yu, K., Shockcor, J.P., Vreeken, R.J., Hankemeier, T.: Comprehensive LC-MS(E) lipidomic analysis using a shotgun approach and its application to biomarker detection and identification in osteoarthritis patients. J. Proteome Res 10(7), 3303-3308 (2011)
70. Crockford, D.J., Maher, A.D., Ahmadi, K.R., Barrett, A., Plumb, R.S., Wilson, I.D., Nicholson, J.K.: 1H NMR and UPLC-MS(E) statistical heterospectroscopy: characterization of drug metabolites (xenometabolome) in epidemiological studies. Anal. Chem. 80(18), 6835-6844 (2008)