Software:XCMS Online

From HandWiki
Short description: Bioinformatics software
XCMS nonlinear alignment of liquid chromatography mass spectrometry data sets
XCMS Online
Initial release25 April 2012; 12 years ago (2012-04-25)
Stable release
3.7.1
PlatformWeb
TypeBioinformatics / Mass spectrometry software
LicenseFreemium / commercial software
Websitexcmsonline.scripps.edu

XCMS Online is a cloud version of the original eXtensible Computational Mass Spectrometry (XCMS)[1][2] technology (a bioinformatics software designed for statistical analysis of mass spectrometry data), created by the Siuzdak Lab at Scripps Research. XCMS introduced the concept of nonlinear retention time alignment that allowed for the statistical assessment of the detected peaks across LCMS and GCMS datasets.[1] XCMS Online[3] was designed to facilitate XCMS analyses through a cloud portal and as a more straightforward[4] (non command driven) way to analyze, visualize and share untargeted metabolomic data.[3] Further to this, the combination of XCMS and METLIN[5][6][7] allows for the identification of known molecules using METLIN's tandem mass spectrometry data, and enables the identification of unknown (uncharacterized molecules) via similarity searching of tandem mass spectrometry data.[8][7][9] XCMS Online has also become a systems biology tool for integrating different omic data sets.[10] As of January 2021,[11] the XCMSOnline - METLIN platform has over 44,000 registered users. XCMS - METLIN was recognized in 2023 as the year's top analytical innovation.[9]

XCMS Online works by comparing groups of raw or preprocessed metabolomic data to discover metabolites using methods such as nonlinear retention time alignment and feature detection & matching. Once analysis is complete the data can be viewed several different ways including via bubble plots, heat maps, chromatograms, and box plots. In addition, XCMS Online is integrated with METLIN, a large metabolite database.[1][12] The following file formats are supported for direct upload to the site.[13]

File Type Vendor
mzXML Open Format
mzData Open Format
.cdf NetCDF (AIA/ANDI)
.d folders Agilent, Bruker
.wiff SCIEX
.RAW folders Waters
.RAW files Thermo

History

In 2005, the Siuzdak Lab created an open-source tool named XCMS[1] in the programming language R. Noticing the need for a more accessible, graphical data processing tool they created the cloud-based XCMS Online in 2012.[3][14] The ability for users to stream data directly from instruments while being acquired was added in 2014.[15] Also in that year a commercial version named XCMS Plus (owned by Mass Consortium Corporation) was released and, in 2015, SCIEX became a reseller.[16] In 2017 it was shown that XCMS Online could be used in a systems biology workflow.[17] One year later, in the absence of a publicly available alternative, a version of XCMS Online was released with the ability to perform multiple reaction monitoring (MRM).[18]

References

  1. ↑ 1.0 1.1 1.2 1.3 Smith, Colin A.; Want, Elizabeth J.; O'Maille, Grace; Abagyan, Ruben; Siuzdak, Gary (February 2006). "XCMS: Processing Mass Spectrometry Data for Metabolite Profiling Using Nonlinear Peak Alignment, Matching, and Identification". Analytical Chemistry 78 (3): 779–787. doi:10.1021/ac051437y. PMID 16448051. 
  2. ↑ Domingo-Almenara, Xavier; Siuzdak, Gary (2020), Li, Shuzhao, ed., "Metabolomics Data Processing Using XCMS" (in en), Computational Methods and Data Analysis for Metabolomics, Methods in Molecular Biology (New York, NY: Springer US): pp. 11–24, doi:10.1007/978-1-0716-0239-3_2, ISBN 978-1-0716-0239-3, https://doi.org/10.1007/978-1-0716-0239-3_2, retrieved 2023-07-19 
  3. ↑ 3.0 3.1 3.2 Tautenhahn, Ralf; Patti, Gary J.; Rinehart, Duane; Siuzdak, Gary (5 June 2012). "XCMS Online: A Web-Based Platform to Process Untargeted Metabolomic Data". Analytical Chemistry 84 (11): 5035–5039. doi:10.1021/ac300698c. PMID 22533540. 
  4. ↑ Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H.; Kurczy, Michael E.; Benton, H. Paul; Rinehart, Duane; Nguyen, Thomas; Ray, Jayashree et al. (2014-07-15). "Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses". Analytical Chemistry 86 (14): 6931–6939. doi:10.1021/ac500734c. ISSN 0003-2700. PMID 24934772. 
  5. ↑ Smith, Colin A.; Maille, Grace O'; Want, Elizabeth J.; Qin, Chuan; Trauger, Sunia A.; Brandon, Theodore R.; Custodio, Darlene E.; Abagyan, Ruben et al. (December 2005). "METLIN: A Metabolite Mass Spectral Database" (in en-US). Therapeutic Drug Monitoring 27 (6): 747–751. doi:10.1097/01.ftd.0000179845.53213.39. ISSN 0163-4356. PMID 16404815. https://journals.lww.com/drug-monitoring/Abstract/2005/12000/METLIN__A_Metabolite_Mass_Spectral_Database.16.aspx. 
  6. ↑ Tautenhahn, Ralf; Cho, Kevin; Uritboonthai, Winnie; Zhu, Zhengjiang; Patti, Gary J.; Siuzdak, Gary (September 2012). "An accelerated workflow for untargeted metabolomics using the METLIN database" (in en). Nature Biotechnology 30 (9): 826–828. doi:10.1038/nbt.2348. ISSN 1546-1696. PMID 22965049. 
  7. ↑ 7.0 7.1 Guijas, Carlos; Montenegro-Burke, J. Rafael; Domingo-Almenara, Xavier; Palermo, Amelia; Warth, Benedikt; Hermann, Gerrit; Koellensperger, Gunda; Huan, Tao et al. (2018-03-06). "METLIN: A Technology Platform for Identifying Knowns and Unknowns". Analytical Chemistry 90 (5): 3156–3164. doi:10.1021/acs.analchem.7b04424. ISSN 0003-2700. PMID 29381867. 
  8. ↑ Benton, H. P.; Wong, D. M.; Trauger, S. A.; Siuzdak, G. (2008-08-01). "XCMS2: Processing Tandem Mass Spectrometry Data for Metabolite Identification and Structural Characterization". Analytical Chemistry 80 (16): 6382–6389. doi:10.1021/ac800795f. ISSN 0003-2700. PMID 18627180. 
  9. ↑ 9.0 9.1 "The Analytical Scientist Innovation Awards 2023" (in en). 2023-12-12. https://theanalyticalscientist.com/techniques-tools/the-analytical-scientist-innovation-awards-2023. 
  10. ↑ Huan, Tao; Forsberg, Erica M.; Rinehart, Duane; Johnson, Caroline H.; Ivanisevic, Julijana; Benton, H. Paul; Fang, Mingliang; Aisporna, Aries et al. (May 2017). "Systems biology guided by XCMS Online metabolomics" (in en). Nature Methods 14 (5): 461–462. doi:10.1038/nmeth.4260. ISSN 1548-7105. PMID 28448069. 
  11. ↑ Majumder, Erica L.-W.; Billings, Elizabeth M.; Benton, H. Paul; Martin, Richard L.; Palermo, Amelia; Guijas, Carlos; Rinschen, Markus M.; Domingo-Almenara, Xavier et al. (2021-01-22). "Cognitive analysis of metabolomics data for systems biology" (in en). Nature Protocols 16 (3): 1376–1418. doi:10.1038/s41596-020-00455-4. ISSN 1750-2799. PMID 33483720. PMC 10357461. https://www.nature.com/articles/s41596-020-00455-4. 
  12. ↑ Gowda, Harsha; Ivanisevic, Julijana; Johnson, Caroline H.; Kurczy, Michael E.; Benton, H. Paul; Rinehart, Duane; Nguyen, Thomas; Ray, Jayashree et al. (25 June 2014). "Interactive XCMS Online: Simplifying Advanced Metabolomic Data Processing and Subsequent Statistical Analyses". Analytical Chemistry 86 (14): 6931–6939. doi:10.1021/ac500734c. PMID 24934772. 
  13. ↑ "XCMS Online - Documentation". https://xcmsonline.scripps.edu/docs/fileformats.html. 
  14. ↑ Perkel, Jeffrey M.. "Name That Metabolite!" (in en). The Scientist. https://www.the-scientist.com/lab-tools/name-that-metabolite-39110. 
  15. ↑ Rinehart, Duane; Johnson, Caroline H.; Nguyen, Thomas; Ivanisevic, Julijana; Benton, H. Paul; Lloyd, Jessica; Arkin, Adam P.; Deutschbauer, Adam M. et al. (June 2014). "Metabolomic data streaming for biology-dependent data acquisition" (in en). Nature Biotechnology 32 (6): 524–527. doi:10.1038/nbt.2927. ISSN 1546-1696. PMID 24911492. 
  16. ↑ Evans, Jon. "SCIEX becomes exclusive reseller for XCMS plus - News - spectroscopyNOW.com". Spectroscopy Now. https://www.spectroscopynow.com/details/news/14c7587423f/SCIEX-becomes-exclusive-reseller-for-XCMSplus.html?tzcheck=1. 
  17. ↑ Huan, Tao; Forsberg, Erica M; Rinehart, Duane; Johnson, Caroline H; Ivanisevic, Julijana; Benton, H Paul; Fang, Mingliang; Aisporna, Aries et al. (1 May 2017). "Systems biology guided by XCMS Online metabolomics". Nature Methods 14 (5): 461–462. doi:10.1038/nmeth.4260. PMID 28448069. 
  18. ↑ Domingo-Almenara, Xavier; Montenegro-Burke, J. Rafael; Ivanisevic, Julijana; Thomas, Aurelien; Sidibé, Jonathan; Teav, Tony; Guijas, Carlos; Aisporna, Aries E. et al. (27 August 2018). "XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules". Nature Methods 15 (9): 681–684. doi:10.1038/s41592-018-0110-3. PMID 30150755. 

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