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MS2Analyzer specifications


Unique identifier OMICS_23161
Name MS2Analyzer
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Medium
Version 2.1
Maintained Yes


No version available



  • person_outline Oliver Fiehn
  • person_outline Yan Ma

Additional information

Publication for MS2Analyzer

MS2Analyzer citations


From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] ms/ms spectra and their comparison to database matches. additionally, it was shown to be able to predict with 91.8% accuracy over 80% of the manually annotated metabolites in test samples []. ms2analyzer [] is a java software for identifying neutral losses, precursor ions, product ions, and m/z differences from ms2 spectra based on a list of predefined transitions. these features […]


Urinary antihypertensive drug metabolite screening using molecular networking coupled to high resolution mass spectrometry fragmentation

PMCID: 4932139
PMID: 27471437
DOI: 10.1007/s11306-016-1064-z

[…] high-resolution mass spectrometry (hr-ms) data combined with data-dependent analysis (dda) fragmenting the most abundant ions (i.e., the topn ions) entering the mass spectrometer. more recently, the ms2analyzer tool was developed to screen for specific product ions (mass fragments), neutral losses (difference between precursor ion and a product ion), and mass differences (difference between two […]


Lipidomic Analysis of Chlamydomonas reinhardtii under Nitrogen and Sulfur Deprivation

PLoS One
PMCID: 4574153
PMID: 26375463
DOI: 10.1371/journal.pone.0137948

[…] homoserine ether lipids and tag triacylglycerols. individual lipid species were annotated by matching mass precursors and ms/ms fragmentations to the in-house lipidblast mass spectral database and ms2analyzer. multivariate statistics showed a clear impact on overall lipidomic phenotypes on both the temporal and the nutrition stress level. homoserine-lipids were found up-regulated at late […]

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MS2Analyzer institution(s)
UC Davis Genome Center−Metabolomics, University of California, Davis, CA, USA; SPKLOMHNM and Central Laboratory, Zhong Yuan Academy of Biological Medicine, Liaocheng University, Liaocheng People’s Hospital, Liaocheng, Shandong, China; Biomedical Engineering School, Carlos III University, Madrid, Spain
MS2Analyzer funding source(s)
Supported by NSF Grant MCB 1139644, NSF Grant MCB 1153491, and Grant U24 DK097154.

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