Comprehensive analysis of LC/MS data using pseudocolor plots

Journal of the American Society for Mass Spectrometry

Volumn 24, Issue 2, 2013, Pages 230-237

  Crutchfield, Christopher A ^a   Olson, Matthew T ^b   Gourgari, Evgenia ^a   Nesterova, Maria ^a   Stratakis, Constantine A ^a   Yergey, Alfred L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b JOHNS HOPKINS HOSPITAL   (United States)

Author keywords

APCI; Characteristic fragmentation; Data visualization; Precursor ion scan; Quantification; Steroid analysis

Indexed keywords

APCI; CHARACTERISTIC FRAGMENTATION; PRECURSOR-ION SCAN; QUANTIFICATION; STEROID ANALYSIS;

DATA VISUALIZATION; MASS SPECTROMETRY;

STEROID HORMONES;

STEROID HORMONE;

ARTICLE; BODY FLUID; CHEMICAL STRUCTURE; CONTROLLED STUDY; CUSHING DISEASE; DATA ANALYSIS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HISTOGRAM; HUMAN; METABOLOMICS; PLOTS AND CURVES; PROCESS DEVELOPMENT; PRODUCT RECOVERY; PSEUDOCOLOR PLOT; QUALITATIVE ANALYSIS; QUALITY CONTROL; SIGNAL NOISE RATIO; TANDEM MASS SPECTROMETRY; URINALYSIS;

ANALYSIS OF VARIANCE; CASE-CONTROL STUDIES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; HORMONES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MASS SPECTROMETRY; METABOLOMICS; PITUITARY ACTH HYPERSECRETION; STEROIDS;

EID: 84877047554     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-012-0524-6     Document Type: Article

References (24)

1. Sturm, M.; Bertsch, A.; Gropl, C.; Hildebrandt, A.; Hussong, R.; Lange, E.; Pfeifer, N.; Schulz-Trieglaff, O.; Zerck, A.; Reinert, K.; Kohlbacher, O.: OpenMS - An open-source software framework for mass spectrometry. BMC Bioinforma. 9, 163 (2008)
2. Khan, Z.; Bloom, J.S.; Garcia, B.A.; Singh, M.; Kruglyak, L.: Protein quantification across hundreds of experimental conditions. Proc. Nat. Acad. Sci. 106, 15544-15548 (2009)
3. 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 Bioinforma. 11, 395 (2010)
4. Sugimoto, M.; Hirayama, A.; Ishikawa, T.; Robert, M.; Baran, R.; Uehara, K.; Kawai, K.; Soga, T.; Tomita, M.: Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis. Metabolomics 6, 27-41 (2010)
5. Grigsby, C.C.; Rizki, M.M.; Tamburino, L.A.; Pitsch, R.L.; Shiyanov, P.A.; Cool, D.R.: Metabolite Differentiation and Discovery Lab (MeDDL): A new tool for biomarker discovery and mass spectral visualization. Anal. Chem. 82, 4386-4395 (2010)
6. 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. 78, 779-787 (2006)
7. 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, 113-122 (2007)
8. Benton, H.P.; Wong, D.M.; Trauger, S.A.; Siuzdak, G.: XCMS2: Processing Tandem mass spectrometry data for metabolite identification and structural characterization. Anal. Chem. 80, 6382-6389 (2008)
9. Tautenhahn, R.; Bottcher, C.; Neumann, S.: Highly sensitive feature detection for high resolution LC/MS. BMC Bioinforma. 9, 504 (2008)
10. Hoffmann, N.; Stoye, J.: ChromA: Signal-based retention time alignment for chromatography-mass spectrometry data. Bioinformatics 25, 2080-2081 (2009)
11. Hiller, K.; Hangebrauk, J.; JaÃàger, C.; Spura, J.; Schreiber, K.; Schomburg, D.: MetaboliteDetector: Comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis. Anal. Chem. 81, 3429-3439 (2009)
12. Lommen, A.: MetAlign: Interface-driven, versatile metabolomics tool for hyphenated full-scan mass spectrometry data preprocessing. Anal. Chem. 81, 3079-3086 (2009)
13. Biswas, A.; Mynampati, K.C.; Umashankar, S.; Reuben, S.; Parab, G.; Rao, R.; Kannan, V.S.; Swarup, S.: MetDAT: A modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation. Bioinformatics 26, 2639-2640 (2010)
14. Cottret, L.; Wildridge, D.; Vinson, F.; Barrett, M.P.; Charles, H.; Sagot, M.-F.; Jourdan, F.: MetExplore: A web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res. 38, W132-W137 (2010)
15. Tautenhahn, R.; Patti, G.J.; Kalisiak, E.; Miyamoto, T.; Schmidt, M.; Lo, F.Y.; McBee, J.; Baliga, N.S.; Siuzdak, G.: metaXCMS: Second-order analysis of untargeted metabolomics data. Anal. Chem. 83, 696-700 (2010)
16. Melamud, E.; Vastag, L.; Rabinowitz, J.D.: Metabolomic analysis and visualization engine for LC-MS data. Anal. Chem. 82, 9818-9826 (2010)
17. Olson, M.; Epstein, J.; Sackett, D.; Yergey, A.: Production of reliable MALDI spectra with quality threshold clustering of replicates. J. Am. Soc. Mass Spectrom. 22, 969-975 (2011)
18. Sugimoto, M.; Kawakami, M.; Robert, M.; Soga, T.; Tomita, M.: Bioinformatics Tools for mass spectroscopy-based metabolomic data processing and analysis. Curr. Bioinforma. 7, 96-108 (2012)
19. R Development Core Team: R: A Language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria (2010)
20. Fischer, B.; Neumann, S.; Gatto, L.: mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data). 2011; Available from: http://www.bioconductor.org/packages/release/bioc/html/mzR.html. Accessed 19 December 2011
21. Wickham, H.: Reshaping data with the reshape package. J. Stat. Softw. 21, 1-20 (2007)
22. Brewer, C.A.: Basic mapping principles for visualizing cancer data using geographic information systems (GIS). Am. J. Prev. Med. 30, S25-S36 (2006)
23. Advanced Chemistry Development Inc.: ACD/ChemSketch Freeware. Toronto, ON, Canada (2010)
24. Xia, Y.-Q.; Jemal, M.: Phospholipids in liquid chromatography/mass spectrometry bioanalysis: Comparison of three tandem mass spectrometric techniques for monitoring plasma phospholipids, the effect of mobile phase composition on phospholipids elution and the association of phospholipids with matrix effects. Rapid Commun. Mass Spectrom. 23, 2125-2138 (2009)