msCompare: A framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies

Molecular and Cellular Proteomics

Volumn 11, Issue 6, 2012, Pages

  Hoekman, Berend ^a,d   Breitling, Rainer ^a,b,d   Suits, Frank ^c   Bischoff, Rainer ^a,d   Horvatovich, Peter ^a,d  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c IBM T J WATSON RESEARCH CENTER   (United States)

^d NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; PEPTIDE FRAGMENT;

ALGORITHM; ARTICLE; BIOINFORMATICS; CEREBROSPINAL FLUID; COMPUTER PROGRAM; CONCEPTUAL FRAMEWORK; DATA PROCESSING; HUMAN; INFORMATION PROCESSING; INTERNET; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NETHERLANDS; ONLINE ANALYTICAL PROCESSING; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SCORING SYSTEM; URINE; WORKFLOW; ADULT; AGED; ANIMAL; CHEMISTRY; COMPARATIVE STUDY; FEMALE; MALE; MIDDLE AGED; ONLINE SYSTEM; PEPTIDE MAPPING; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; STANDARD; STATISTICAL ANALYSIS; SWINE;

ADULT; AGED; ALGORITHMS; ANIMALS; BIOLOGICAL MARKERS; CHROMATOGRAPHY, LIQUID; CHROMATOGRAPHY, REVERSE-PHASE; DATA INTERPRETATION, STATISTICAL; FEMALE; HUMANS; MALE; MASS SPECTROMETRY; MIDDLE AGED; ONLINE SYSTEMS; PEPTIDE FRAGMENTS; PEPTIDE MAPPING; PROTEOMICS; REFERENCE STANDARDS; SOFTWARE; SWINE;

EID: 84862316959     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.M111.015974     Document Type: Article

References (59)

1. Chen, G., and Pramanik, B. N. (2009) Application of LC/MS to proteomics studies: Current status and future prospects. Drug Discov. Today 14, 465-471
2. Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., 3rd, Bairoch, A., and Bergeron, J. J. (2010) Mass spectrometry in high-throughput proteomics: Ready for the big time. Nat. Methods 7, 681-685
3. Domon, B., and Aebersold, R. (2010) Options and considerations when selecting a quantitative proteomics strategy. Nat. Biotechnol. 28, 710-721
4. Allwood, J. W., and Goodacre, R. (2010) An introduction to liquid chromatography-mass spectrometry instrumentation applied in plant metabolomic analyses. Phytochem. Anal. 21, 33-47
5. Griffiths, W. J., and Wang, Y. (2009) Mass spectrometry: From proteomics to metabolomics and lipidomics. Chem. Soc. Rev. 38, 1882-1896
6. Choudhary, C., and Mann, M. (2010) Decoding signalling networks by mass spectrometry-based proteomics. Nat. Rev. Mol. Cell Biol. 11, 427-439
7. Wepf, A., Glatter, T., Schmidt, A., Aebersold, R., and Gstaiger, M. (2009) Quantitative interaction proteomics using mass spectrometry. Nat. Methods 6, 203-205
8. Yang, W., Cai, Q., Lui, V. W., Everley, P. A., Kim, J., Bhola, N., Quesnelle, K. M., Zetter, B. R., Steen, H., Freeman, M. R., and Grandis, J. R. (2010) Quantitative proteomics analysis reveals molecular networks regulated by epidermal growth factor receptor level in head and neck cancer. J. Proteome Res. 9, 3073-3082
9. America, A. H., and Cordewener, J. H. (2008) Comparative LC-MS: A landscape of peaks and valleys. Proteomics 8, 731-749
10. Katajamaa, M., and Oresic, M. (2007) Data processing for mass spectrometry-based metabolomics. J. Chromatogr. A 1158, 318-328
11. Mueller, L. N., Brusniak, M. Y., Mani, D. R., and Aebersold, R. (2008) An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data. J. Proteome Res. 7, 51-61
12. Shinoda, K., Tomita, M., and Ishihama, Y. (2010) emPAI Calc: For the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics 26, 576-577
13. Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., and Mann, M. (2005) 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 4, 1265-1272
14. Lundgren, D. H., Hwang, S. I., Wu, L., and Han, D. K. (2010) Role of spectral counting in quantitative proteomics. Expert Rev. Proteomics 7, 39-53
15. Schulze, W. X., and Usadel, B. (2010) Quantitation in mass-spectrometry-based proteomics. Annu. Rev. Plant Biol. 61, 491-516
16. Grossmann, J., Roschitzki, B., Panse, C., Fortes, C., Barkow-Oesterreicher, S., Rutishauser, D., and Schlapbach, R. (2010) Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods. J. Proteomics 73, 1740-1746
17. Bantscheff, M., Schirle, M., Sweetman, G., Rick, J., and Kuster, B. (2007) Quantitative mass spectrometry in proteomics: A critical review. Anal. Bioanal. Chem. 389, 1017-1031
18. Brun, V., Masselon, C., Garin, J., and Dupuis, A. (2009) Isotope dilution strategies for absolute quantitative proteomics. J. Proteomics 72, 740-749
19. Silva, J. C., Gorenstein, M. V., Li, G. Z., Vissers, J. P., and Geromanos, S. J. (2006) Absolute quantification of proteins by LCMSE: A virtue of parallel MS acquisition. Mol. Cell. Proteomics 5, 144-156
20. Christin, C., Hoefsloot, H. C., Smilde, A. K., Suits, F., Bischoff, R., and Horvatovich, P. L. (2010) Time alignment algorithms based on selected mass traces for complex LC-MS data. J. Proteome Res. 9, 1483-1495
21. Christin, C., Smilde, A. K., Hoefsloot, H. C., Suits, F., Bischoff, R., and Horvatovich, P. L. (2008) Optimized time alignment algorithm for LC-MS data: Correlation optimized warping using component detection algorithm-selected mass chromatograms. Anal. Chem. 80, 7012-7021
22. Clifford, D., Stone, G., Montoliu, I., Rezzi, S., Martin, F. P., Guy, P., Bruce, S., and Kochhar, S. (2009) Alignment using variable penalty dynamic time warping. Anal. Chem. 81, 1000-1007
23. Lange, E., Gröpl, C., Schulz-Trieglaff, O., Leinenbach, A., Huber, C., and Reinert, K. (2007) A geometric approach for the alignment of liquid chromatography-mass spectrometry data. Bioinformatics 23, 273-281
24. Lommen, A. (2009) MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal. Chem. 81, 3079-3086
25. Prakash, A., Mallick, P., Whiteaker, J., Zhang, H., Paulovich, A., Flory, M., Lee, H., Aebersold, R., and Schwikowski, B. (2006) Signal maps for mass spectrometry-based comparative proteomics. Mol. Cell. Proteomics 5, 423-432
26. Sadygov, R. G., Maroto, F. M., and Hühmer, A. F. (2006) ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces. Anal. Chem. 78, 8207-8217
27. Suits, F., Lepre, J., Du, P., Bischoff, R., and Horvatovich, P. (2008) Two-dimensional method for time aligning liquid chromatography-mass spectrometry data. Anal. Chem. 80, 3095-3104
28. Scheltema, R. A., Kamleh, A., Wildridge, D., Ebikeme, C., Watson, D. G., Barrett, M. P., Jansen, R. C., and Breitling, R. (2008) Increasing the mass accuracy of high-resolution LC-MS data using background ions: A case study on the LTQ-Orbitrap. Proteomics 8, 4647-4656
29. Jaitly, N., Mayampurath, A., Littlefield, K., Adkins, J. N., Anderson, G. A., and Smith, R. D. (2009) Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 10, 87
30. Strohalm, M., Kavan, D., Novák, P., Volný, M., and Havlícek, V. (2010) mMass 3: A cross-platform software environment for precise analysis of mass spectrometric data. Anal. Chem. 82, 4648-4651
31. Bowen, B. P., and Northen, T. R. (2010) Dealing with the unknown: Metabolomics and metabolite atlases. J. Am. Soc. Mass. Spectrom. 21, 1471-1476
32. Neumann, S., and Bocker, S. (2010) Computational mass spectrometry for metabolomics: Identification of metabolites and small molecules. Anal. Bioanal Chem. 398, 2779-2788
33. Li, M., Zhou, Z., Nie, H., Bai, Y., and Liu, H. (2010) Recent advances of chromatography and mass spectrometry in lipidomics. Anal. Bioanal. Chem. 399, 243-249
34. Menschaert, G., Vandekerckhove, T. T., Baggerman, G., Schoofs, L., Luyten, W., and Van Criekinge, W. (2010) Peptidomics coming of age: A review of contributions from a bioinformatics angle. J. Proteome Res. 9, 2051-2061
35. Duncan, M. W., Aebersold, R., and Caprioli, R. M. (2010) The pros and cons of peptide-centric proteomics. Nat. Biotechnol. 28, 659-664
36. Katajamaa, M., Miettinen, J., and Oresic, M. (2006) MZmine: Toolbox for processing and visualization of mass spectrometry based molecular profile data. Bioinformatics 22, 634-636
37. Kohlbacher, O., Reinert, K., Gröpl, C., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., and Sturm, M. (2007) TOPP: The OpenMS proteomics pipeline. Bioinformatics 23, e191-197
38. Mueller, L. N., Rinner, O., Schmidt, A., Letarte, S., Bodenmiller, B., Brusniak, M. Y., Vitek, O., Aebersold, R., and Müller, M. (2007) SuperHirn: A novel tool for high resolution LC-MS-based peptide/protein profiling. Proteomics 7, 3470-3480
39. Leptos, K. C., Sarracino, D. A., Jaffe, J. D., Krastins, B., and Church, G. M. (2006) MapQuant: Open-source software for large-scale protein quantification. Proteomics 6, 1770-1782
40. Yu, T., Park, Y., Johnson, J. M., and Jones, D. P. (2009) apLCMS: Adaptive processing of high-resolution LC/MS data. Bioinformatics 25, 1930-1936
41. Li, X. J., Yi, E. C., Kemp, C. J., Zhang, H., and Aebersold, R. (2005) A software suite for the generation and comparison of peptide arrays from sets of data collected by liquid chromatography-mass spectrometry. Mol. Cell. Proteomics 4, 1328-1340
42. Zhang, J., Gonzalez, E., Hestilow, T., Haskins, W., and Huang, Y. (2009) Review of peak detection algorithms in liquid-chromatography-mass spectrometry. Curr. Genomics 10, 388-401
43. Lange, E., Tautenhahn, R., Neumann, S., and Gröpl, C. (2008) Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements. BMC Bioinformatics 9, 375
44. Zhang, R., Barton, A., Brittenden, J., Huang, J., and Crowther, D. (2010) Evaluation of computational platforms for LC-MS based label-free quantitative proteomics: A global view. J. Proteomics Bioinformatics 3, 260-265
45. Brusniak, M. Y., Bodenmiller, B., Campbell, D., Cooke, K., Eddes, J., Garbutt, A., Lau, H., Letarte, S., Mueller, L. N., Sharma, V., Vitek, O., Zhang, N., Aebersold, R., and Watts, J. D. (2008) Corra: Computational framework and tools for LC-MS discovery and targeted mass spectrometry-based proteomics. BMC Bioinformatics 9, 542
46. Hwang, D., Zhang, N., Lee, H., Yi, E., Zhang, H., Lee, I. Y., Hood, L., and Aebersold, R. (2008) MS-BID: A Java package for label-free LC-MS-based comparative proteomic analysis. Bioinformatics 24, 2641-2642
47. Orchard, S., Jones, A., Albar, J. P., Cho, S. Y., Kwon, K. H., Lee, C., and Hermjakob, H. (2010) Tackling quantitation: A report on the annual Spring Workshop of the HUPO-PSI 28-30 March 2010, Seoul, South Korea. Proteomics 10, 3062-3066
48. Radulovic, D., Jelveh, S., Ryu, S., Hamilton, T. G., Foss, E., Mao, Y., and Emili, A. (2004) Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry. Mol. Cell. Proteomics 3, 984-997
49. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A., and Taylor, J. (2010) Galaxy: A web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol. Chapter 19, Unit 19.10, 11-21
50. Giardine, B., Riemer, C., Hardison, R. C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J., Miller, W., Kent, W. J., and Nekrutenko, A. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Res. 15, 1451-1455
51. Sturm, M., Bertsch, A., Gröpl, C., Hildebrandt, A., Hussong, R., Lange, E., Pfeifer, N., Schulz-Trieglaff, O., Zerck, A., Reinert, K., and Kohlbacher, O. (2008) OpenMS: An open-source software framework for mass spectrometry. BMC Bioinformatics 9, 163
52. Reinert, K., and Kohlbacher, O. (2010) OpenMS and TOPP: Open source software for LC-MS data analysis. Methods Mol. Biol. 604, 201-211
53. Sturm, M., and Kohlbacher, O. (2009) TOPPView: An open-source viewer for mass spectrometry data. J. Proteome Res. 8, 3760-3763
54. Pluskal, T., Castillo, S., Villar-Briones, A., and Oresic, M. (2010) MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. BMC Bioinformatics 11, 395
55. Katajamaa, M., and Oresic, M. (2005) Processing methods for differential analysis of LC/MS profile data. BMC Bioinformatics 6, 179
56. Pedrioli, P. G., Eng, J. K., Hubley, R., Vogelzang, M., Deutsch, E. W., Raught, B., Pratt, B., Nilsson, E., Angeletti, R. H., Apweiler, R., Cheung, K., Costello, C. E., Hermjakob, H., Huang, S., Julian, R. K., Kapp, E., McComb, M. E., Oliver, S. G., Omenn, G., Paton, N. W., Simpson, R., Smith, R., Taylor, C. F., Zhu, W., and Aebersold, R. (2004) A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 22, 1459-1466
57. Orchard, S., Montechi-Palazzi, L., Deutsch, E. W., Binz, P. A., Jones, A. R., Paton, N., Pizarro, A., Creasy, D. M., Wojcik, J., and Hermjakob, H. (2007) Five years of progress in the Standardization of Proteomics Data 4th Annual Spring Workshop of the HUPO-Proteomics Standards Initiative April 23-25, 2007 Ecole Nationale Superieure (ENS), Lyon, France. Proteomics 7, 3436-3440
58. Deutsch, E. (2008) mzML: A single, unifying data format for mass spectrometer output. Proteomics 8, 2776-2777
59. Horvatovich, P., Govorukhina, N. I., Reijmers, T. H., van der Zee, A. G., Suits, F., and Bischoff, R. (2007) Chip-LC-MS for label-free profiling of human serum. Electrophoresis 28, 4493-4505