MSFragger statistics

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Citations per year

Number of citations per year for the bioinformatics software tool MSFragger

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MSFragger specifications


Unique identifier OMICS_17459
Name MSFragger
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Alexey Nesvizhskii

Additional information

Publication for MSFragger

MSFragger citations


Phosphorylation of Ribosomal Protein RPS6 Integrates Light Signals and Circadian Clock Signals

Front Plant Sci
PMCID: 5780430
PMID: 29403507
DOI: 10.3389/fpls.2017.02210

[…] ant proteins (). A decoy database, consisting of the reversed sequences of the target database, was appended to discern the false-discovery rate (FDR). Assignment of MS/MS spectra was performed using MSFragger algorithm (). The MSFragger closed search was configured to derive fully tryptic peptides with the following parameters: parent mass tolerance of 20 ppm, a fragment mass tolerance of 20 ppm, […]


Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell lines

Genome Med
PMCID: 5514513
PMID: 28716134
DOI: 10.1186/s13073-017-0454-9

[…] mic variants, highlighting the potential for these methodologies to expand our capacity for variant protein detection. Other semi-supervised or “open search algorithms,” such as the recently released MSFragger [] and spectral network inference [], could also be used as additional strategies for the parallel identification of PTMs or proteoform variants. While beyond the scope of the current manusc […]

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MSFragger institution(s)
Department of Computational Medicine and Bioinformatics, University of Michigan, MI, USA; Department of Pathology, University of Michigan, MI, USA

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