MultiAlign: A multiple LC-MS analysis tool for targeted omics analysis

BMC Bioinformatics

Volumn 14, Issue 1, 2013, Pages

  LaMarche, Brian L ^a   Crowell, Kevin L ^a   Jaitly, Navdeep ^a   Petyuk, Vladislav A ^a   Shah, Anuj R ^a   Polpitiya, Ashoka D ^a   Sandoval, John D ^a   Kiebel, Gary R ^a   Monroe, Matthew E ^a   Callister, Stephen J ^a   Metz, Thomas O ^a   Anderson, Gordon A ^a   Smith, Richard D ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

Author keywords

Alignment; Liquid chromatography; Mass spectrometry; Metabolomics; Proteomics; Spectral clustering

Indexed keywords

COMMUNITY STRUCTURES; HUMAN HEPATOCARCINOMA; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; MASS SPECTROMETRIC ANALYSIS; METABOLOMICS; MICROBIAL COMMUNITIES; PROTEOMICS; SPECTRAL CLUSTERING;

ALIGNMENT; LIQUID CHROMATOGRAPHY; MASS SPECTROMETERS; MASS SPECTROMETRY; PEPTIDES;

MOLECULAR BIOLOGY;

PEPTIDE; PROTEOME;

ALGORITHM; ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER PROGRAM; HUMAN; LIQUID CHROMATOGRAPHY; LIVER CELL CARCINOMA; LIVER TUMOR; MASS SPECTROMETRY; METABOLISM; METABOLOMICS; METHODOLOGY; PROTEOMICS; TANDEM MASS SPECTROMETRY;

ALGORITHMS; CARCINOMA, HEPATOCELLULAR; CHROMATOGRAPHY, LIQUID; CLUSTER ANALYSIS; HUMANS; LIVER NEOPLASMS; MASS SPECTROMETRY; METABOLOMICS; PEPTIDES; PROTEOME; PROTEOMICS; SOFTWARE; TANDEM MASS SPECTROMETRY;

EID: 84873700958     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-49     Document Type: Article

References (23)

1. Craig R, Beavis RC. TANDEM: matching proteins with tandem mass spectra. Bioinformatics 2004, 20(9):1466-1467. 10.1093/bioinformatics/bth092, 14976030.
2. Eng JK, McCormack AL, Yates JR. 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(11):976-989.
3. Perkins DN, Pappin DJC, Creasy DM, Cottrell JS. Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 1999, 20(18):1522-2683.
4. Zimmer JSD, Monroe ME, Qian W-J, Smith RD. Advances in Proteomics Data Analysis and Display Using an Accurate Mass and Time Tag Approach. Mass Spectrom Rev 2006, 25(3):450-482. 10.1002/mas.20071, 1829209, 16429408.
5. Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD. Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. BMC Bioinformatics 2009, 10(87). http://dx.doi.org/10.1186/1471-2105-10-87.
6. Horn DM, Zubarev RA, McLafferty FW. Automated Reduction and Interpretation of High Resolution Electrospray Mass Spectra of Large Molecules. J Am Soc Mass Spectrom 2000, 11(4):320-332. 10.1016/S1044-0305(99)00157-9, 10757168.
7. Park K, Yoon JY, Lee S, Paek E, Park H, Jung H-J, Lee S-W. Isotopic Peak Intensity Ratio Based Algorithm for Determination of Isotopic Clusters and Monoisotopic Masses of Polypeptides from High-Resolution Mass Spectrometric Data. Anal Chem 2008, 80(19):7294-7303. 10.1021/ac800913b, 18754627.
8. Monroe METN, Jaitly N, Shaw JL, Adkins JN, Smith RD. VIPER: an advanced software package to support high-throughput LC-MS peptide identification. Bioinformatics 2007, 23(15):2021-2023. 10.1093/bioinformatics/btm281, 17545182.
9. Cox J, Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 2008, 26:1367-1372. 10.1038/nbt.1511, 19029910.
10. May D, Fitzgibbon M, Liu Y, Holzman T, Eng J, Kemp CJ, Whiteaker J, Paulovich A, McIntosh M. A Platform for Accurate Mass and Time Analyses of Mass Spectrometry Data. J Proteome Res 2007, 6:2685-2694. 10.1021/pr070146y, 17559252.
11. Pluskal T, Castillo S, Villar-Briones A, Orešič M. MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry based molecular profile data. BMC Bioinformatics 2010, 11(395). http://dx.doi.org/10.1186/1471-2105-11-395.
12. Li X-J, Yi EC, Kemp CJ, 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. 10.1074/mcp.M500141-MCP200, 16048906.
13. Callister SJ, Wilkins MJ, Nicora CD, Williams KH, Banfield JF, Verberkmoes NC, Hettich RL, Guessan LE, Mouser PJ, Elifantz HL. Analysis of Biostimulated Microbial Communities from Two Field Experiments Reveals Temporal and Spatial Differences in Proteome Profiles. Environ Sci Technol 2010, 44:88978903.
14. Wilkins MJ NV, Williams KH, Callister SJ, Mouser P, Elifantz H, N'Guessan AL, Thomas BC, Nicora CD, Shah MB, Abraham P, Lipton MS, Lovely DR, Hettich RL, Long PE, Banfield JF. Proteogenomic monitoring of Geobacter physiology during stimulated uranium bioremediation. Appl Environ Microbiol 2009, 75(20):6591-6599. 10.1128/AEM.01064-09, 2765142, 19717633.
15. PEAKS Mass Spectrometry http://www.bioinfor.com/peaks-overview.
16. Frank A, Pevzner P. PepNovo: De Novo Peptide Sequencing via Probabilistic Network Modeling. Anal Chem 2005, 77:946-973.
17. Smith CA, Want EJ, 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, 16448051.
18. Jaitly N, Monroe ME, Petyuk VA, Clauss TRW, Adkins JN, Smith RD. Robust Algorithm for Alignment of Liquid Chromatography-Mass Spectrometry Analyses in an Accurate Mass and Time Tag Data Analysis Pipeline. Anal Chem 2006, 78(21):7397-7409. 10.1021/ac052197p, 17073405.
19. Stanley JR, Adkins JN, Slysz GW, Monroe ME, Purvine SO, Karpievitch YV, Anderson GA, Smith RD, Dabney AR. A Statistical Method for Assessing Peptide Identification Confidence in Accurate Mass and Time Tag Proteomics. Anal Chem 2011, 83(16):4.
20. Frank AM, Bandeira N, Shen Z, Tanner S, Briggs SP, Smith RD, Pevzner PA. Clustering millions of tandem mass spectra. J Proteome Res 2008, 7(01):113-122. 10.1021/pr070361e, 2533155, 18067247.
21. Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Tolić N, Anderson GA, Smith RD. PRISM: A data management system for high-throughput proteomics. Proteomics 2006, 6:1783-1790. 10.1002/pmic.200500500, 16470653.
22. Rasmussen A, Diamond D, McDermott J, Gao X, Metz T, Matzke M, Carter V, Belisle S, Korth M, Waters K. Systems virology identifies a mitochondrial fatty acid oxidation enzyme, dodecenoyl coenzyme A delta isomerase, required for hepatitis C virus replication and likely pathogenesis. J Virol 2011, 85(22):11646-11654. 10.1128/JVI.05605-11, 3209311, 21917952.
23. Fahy E, Subramaniam S, Brown HA, Glass CK AHM, Murphy RC, Raetz CRH, Russell DW, Seyama Y, Shaw W. A comprehensive classification system for lipids. J Lipid Res 2005, 46:839-862. 10.1194/jlr.E400004-JLR200, 15722563.