BatMass: A Java software platform for LC-MS data visualization in proteomics and metabolomics

Journal of Proteome Research

Volumn 15, Issue 8, 2016, Pages 2500-2509

  Avtonomov, Dmitry M ^a   Raskind, Alexander ^b   Nesvizhskii, Alexey I ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF MICHIGAN   (United States)

Author keywords

data visualization; Java; LC MS; mass spectrometry

Indexed keywords

ALGORITHM; ARTICLE; BATMASS SOFTWARE; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; DATA PROCESSING; DOWNSTREAM PROCESSING; LIQUID CHROMATOGRAPHY; LIQUID CHROMATOGRAPHY MASS SPECTROMETRY; MASS SPECTROMETRY; METABOLOMICS; PEPTIDE LIBRARY; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEOMICS; QUALITY CONTROL; COMPUTER GRAPHICS; PROCEDURES; SOFTWARE;

CHROMATOGRAPHY, LIQUID; COMPUTER GRAPHICS; MASS SPECTROMETRY; METABOLOMICS; PROTEOMICS; QUALITY CONTROL; SOFTWARE;

EID: 84981295494     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.6b00021     Document Type: Article

References (36)

1. Bereman, M. S. Tools for monitoring system suitability in LC MS/MS centric proteomic experiments Proteomics 2015, 15, 891-902 10.1002/pmic.201400373
2. America, A. H.; Cordewener, J. H. Comparative LC-MS: a landscape of peaks and valleys Proteomics 2008, 8, 731-749 10.1002/pmic.200700694
3. Wang, X.; Chambers, M. C.; Vega-Montoto, L. J.; Bunk, D. M.; Stein, S. E.; Tabb, D. L. QC Metrics from CPTAC Raw LC-MS/MS Data Interpreted through Multivariate Statistics Anal. Chem. 2014, 86, 2497-2509 10.1021/ac4034455
4. 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. Proteomics 2010, 9, 225-241 10.1074/mcp.M900223-MCP200
5. Tabb, D. L. Quality assessment for clinical proteomics Clin. Biochem. 2013, 46, 411-420 10.1016/j.clinbiochem.2012.12.003
6. Ma, Z. Q.; Polzin, K. O.; Dasari, S.; Chambers, M. C.; Schilling, B.; Gibson, B. W.; Tran, B. Q.; Vega-Montoto, L.; Liebler, D. C.; Tabb, D. L. QuaMeter: multivendor performance metrics for LC-MS/MS proteomics instrumentation Anal. Chem. 2012, 84, 5845-5850 10.1021/ac300629p
7. Taylor, R. M.; Dance, J.; Taylor, R. J.; Prince, J. T. Metriculator: quality assessment for mass spectrometry-based proteomics Bioinformatics 2013, 29, 2948-2949 10.1093/bioinformatics/btt510
8. Walzer, M.; Pernas, L. E.; Nasso, S.; Bittremieux, W.; Nahnsen, S.; Kelchtermans, P.; Pichler, P.; van den Toorn, H. W.; Staes, A.; Vandenbussche, J.; Mazanek, M.; Taus, T.; Scheltema, R. A.; Kelstrup, C. D.; Gatto, L.; van Breukelen, B.; Aiche, S.; Valkenborg, D.; Laukens, K.; Lilley, K. S.; Olsen, J. V.; Heck, A. J.; Mechtler, K.; Aebersold, R.; Gevaert, K.; Vizcaino, J. A.; Hermjakob, H.; Kohlbacher, O.; Martens, L. qcML: an exchange format for quality control metrics from mass spectrometry experiments Mol. Cell. Proteomics 2014, 13, 1905-1913 10.1074/mcp.M113.035907
9. Simader, A. M.; Kluger, B.; Neumann, N. K. N.; Bueschl, C.; Lemmens, M.; Lirk, G.; Krska, R.; Schuhmacher, R. QCScreen: a software tool for data quality control in LC-HRMS based metabolomics BMC Bioinf. 2015, 16, 1-9 10.1186/s12859-015-0783-x
10. Perez-Riverol, Y.; Xu, Q. W.; Wang, R.; Uszkoreit, J.; Griss, J.; Sanchez, A.; Reisinger, F.; Csordas, A.; Ternent, T.; del-Toro, N.; Dianes, J. A.; Eisenacher, M.; Hermjakob, H.; Vizcaino, J. A. PRIDE Inspector Toolsuite: moving towards a universal visualization tool for proteomics data standard formats and quality assessment of ProteomeXchange datasets Mol. Cell. Proteomics 2016, 15, 305-317 10.1074/mcp.O115.050229
11. Gillet, L. C.; Navarro, P.; Tate, S.; Rost, H.; Selevsek, N.; Reiter, L.; Bonner, R.; Aebersold, R. 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, DOI: 10.1074/mcp.O111.016717.
12. 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. 2005, 77, 2187-2200 10.1021/ac048455k
13. Prakash, A.; Peterman, S.; Ahmad, S.; Sarracino, D.; Frewen, B.; Vogelsang, M.; Byram, G.; Krastins, B.; Vadali, G.; Lopez, M. Hybrid data acquisition and processing strategies with increased throughput and selectivity: pSMART analysis for global qualitative and quantitative analysis J. Proteome Res. 2014, 13, 5415-5430 10.1021/pr5003017
14. Sajic, T.; Liu, Y.; Aebersold, R. Using data-independent, high-resolution mass spectrometry in protein biomarker research: perspectives and clinical applications Proteomics: Clin. Appl. 2015, 9, 307-321 10.1002/prca.201400117
15. 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 10.1002/mas.21400
16. Sturm, M.; Kohlbacher, O. TOPPView: an open-source viewer for mass spectrometry data J. Proteome Res. 2009, 8, 3760-3763 10.1021/pr900171m
17. Pluskal, T.; Castillo, S.; Villar-Briones, A.; Oresic, M. MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data BMC Bioinf. 2010, 11, 395 10.1186/1471-2105-11-395
18. Tanaka, S.; Fujita, Y.; Parry, H. E.; Yoshizawa, A. C.; Morimoto, K.; Murase, M.; Yamada, Y.; Yao, J.; Utsunomiya, S. I.; Kajihara, S.; Fukuda, M.; Ikawa, M.; Tabata, T.; Takahashi, K.; Aoshima, K.; Nihei, Y.; Nishioka, T.; Oda, Y.; Tanaka, K. Mass++: A Visualization and Analysis Tool for Mass Spectrometry J. Proteome Res. 2014, 13, 3846-3853 10.1021/pr500155z
19. Griss, J.; Reisinger, F.; Hermjakob, H.; Vizcaino, J. A. jmzReader: A Java parser library to process and visualize multiple text and XML-based mass spectrometry data formats Proteomics 2012, 12, 795-798 10.1002/pmic.201100578
20. Kessner, D.; Chambers, M.; Burke, R.; Agus, D.; Mallick, P. ProteoWizard: open source software for rapid proteomics tools development Bioinformatics 2008, 24, 2534-2536 10.1093/bioinformatics/btn323
21. Holman, J. D.; Tabb, D. L.; Mallick, P. Employing ProteoWizard to Convert Raw Mass Spectrometry Data Curr. Protoc. Bioinformatics 2014, 46, 13 24 11-19 10.1002/0471250953.bi1324s46
22. Teleman, J.; Dowsey, A. W.; Gonzalez-Galarza, F. F.; Perkins, S.; Pratt, B.; Rost, H. L.; Malmstrom, L.; Malmstrom, J.; Jones, A. R.; Deutsch, E. W.; Levander, F. Numerical compression schemes for proteomics mass spectrometry data Mol. Cell. Proteomics 2014, 13, 1537-1542 10.1074/mcp.O114.037879
23. Marx, H.; Lemeer, S.; Schliep, J. E.; Matheron, L.; Mohammed, S.; Cox, J.; Mann, M.; Heck, A. J.; Kuster, B. A large synthetic peptide and phosphopeptide reference library for mass spectrometry-based proteomics Nat. Biotechnol. 2013, 31, 557-564 10.1038/nbt.2585
24. Tsugawa, H.; Cajka, T.; Kind, T.; Ma, Y.; Higgins, B.; Ikeda, K.; Kanazawa, M.; VanderGheynst, J.; Fiehn, O.; Arita, M. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis Nat. Methods 2015, 12, 523-526 10.1038/nmeth.3393
25. Tsou, C. C.; Avtonomov, D.; Larsen, B.; Tucholska, M.; Choi, H.; Gingras, A. C.; Nesvizhskii, A. I. DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics Nat. Methods 2015, 12, 258-264 10.1038/nmeth.3255
26. Johnson, C. H.; Ivanisevic, J.; Benton, H. P.; Siuzdak, G. Bioinformatics: The Next Frontier of Metabolomics Anal. Chem. 2015, 87, 147-156 10.1021/ac5040693
27. Cho, K.; Mahieu, N. G.; Johnson, S. L.; Patti, G. J. After the feature presentation: technologies bridging untargeted metabolomics and biology Curr. Opin. Biotechnol. 2014, 28, 143-148 10.1016/j.copbio.2014.04.006
28. Smith, C. A.; Want, E. J.; O'Maille, G.; Abagyan, R.; Siuzdak, G. XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification Anal. Chem. 2006, 78, 779-787 10.1021/ac051437y
29. Uppal, K.; Soltow, Q. A.; Strobel, F. H.; Pittard, W. S.; Gernert, K. M.; Yu, T.; Jones, D. P. xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data BMC Bioinf. 2013, 14, 1-12 10.1186/1471-2105-14-15
30. Libiseller, G.; Dvorzak, M.; Kleb, U.; Gander, E.; Eisenberg, T.; Madeo, F.; Neumann, S.; Trausinger, G.; Sinner, F.; Pieber, T.; Magnes, C. IPO: a tool for automated optimization of XCMS parameters BMC Bioinf. 2015, 16, 1-10 10.1186/s12859-015-0562-8
31. Hoekman, B.; Breitling, R.; Suits, F.; Bischoff, R.; Horvatovich, P. msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies Mol. Cell. Proteomics 2012, 11, M111.015974 10.1074/mcp.M111.015974
32. Karnovsky, A.; Weymouth, T.; Hull, T.; Tarcea, V. G.; Scardoni, G.; Laudanna, C.; Sartor, M. A.; Stringer, K. A.; Jagadish, H. V.; Burant, C.; Athey, B.; Omenn, G. S. Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data Bioinformatics 2012, 28, 373-380 10.1093/bioinformatics/btr661
33. Ebhardt, H. A.; Root, A.; Sander, C.; Aebersold, R. Applications of targeted proteomics in systems biology and translational medicine Proteomics 2015, 15, 3193-3208 10.1002/pmic.201500004
34. MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J. Skyline: an open source document editor for creating and analyzing targeted proteomics experiments Bioinformatics 2010, 26, 966-968 10.1093/bioinformatics/btq054
35. Sandin, M.; Teleman, J.; Malmström, J.; Levander, F. Data processing methods and quality control strategies for label-free LC-MS protein quantification Biochim. Biophys. Acta, Proteins Proteomics 2014, 1844, 29-41 10.1016/j.bbapap.2013.03.026
36. Barsnes, H.; Vaudel, M.; Colaert, N.; Helsens, K.; Sickmann, A.; Berven, F. S.; Martens, L. Compomics-utilities: an open-source Java library for computational proteomics. BMC Bioinf. 2011, 12, 70 10.1186/1471-2105-12-70