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MRMer specifications


Unique identifier OMICS_03327
Name MRMer
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format mzXML
Operating system Unix/Linux
Programming languages Java
License Apache License version 2.0
Computer skills Medium
Stability No
Maintained No


No version available

Additional information

Institute for Systems Biology, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; University of Washington Medicine at South Lake Union, Seattle, WA, USA

Publication for MRMer

MRMer citations


Advances in Proteomic Technologies and Its Contribution to the Field of Cancer

PMCID: 4590950
PMID: 26556407
DOI: 10.1155/2014/238045

[…] eotypic peptides and chromatographic retention time would be extremely useful for the generation of maximal product ion signal and the proteomics community in MRM-MS assay development. Skyline [] and MRMer [] are two open source software for developing MRM-MS-based assays by the proteomics community. Skyline (downloadable from […]


The role of quantitative mass spectrometry in the discovery of pancreatic cancer biomarkers for translational science

J Transl Med
PMCID: 3998064
PMID: 24708694
DOI: 10.1186/1479-5876-12-87

[…] picking of peptide, precursor and transition in silico from proteins and fragment peptides []. Other platform-specific tools include TIQAM, MRMPilot, SRM Workflow Software, Verify, and Optimizer []. MRMer is another open source software tool, for the analysis of data generated by highly complex MRM-MS experiments. It provides a rapid visual inspection of over 1000 precursor-product pairs [].The h […]


Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

Biochim Biophys Acta
PMCID: 3898926
PMID: 23467006
DOI: 10.1016/j.bbapap.2013.02.032

[…] or lists of peptides, precursors and product ion transitions either into a dialog, or directly into the document. Additionally, transition lists and results, for private and published experiments on MRMer (see next section) are easily recreated in Skyline. […]


Targeted Quantitation of Proteins by Mass Spectrometry

PMCID: 3674507
PMID: 23517332
DOI: 10.1021/bi400110b

[…] for selecting target peptides exist, characteristic peptide fragmentations empirically found to provide a high signal intensity have been described. Several software tools, such as MRMaid, SRMAtlas, MRMer, and MaRiMba, for facilitating transition selection have been described. Because MRM assays are largely conducted with triple quadrupole instruments (see below), optimization has been directed t […]


Automated Selected Reaction Monitoring Software for Accurate Label Free Protein Quantification

J Proteome Res
PMCID: 3426189
PMID: 22658081
DOI: 10.1021/pr300256x

[…] ng custom scores for quality control but in return have the drawbacks of relying on decoy measurements and requiring a large assay database respectively. Most current SRM software (Skyline, Pinpoint, MRMer) focus on assisting in construction of SRM assays, presenting the data, and assisting manual quantification. Skyline does perform detection and quantification, but without any clear measure of q […]


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MRMer institution(s)
Supported, in whole or in part, by National Institutes of Health Grants R21-CA126216 and P50 GM076547 and Grant (U01 CA111273-04S1) by NCI, National Institutes of Health, the Allen Family Foundation, the Department of Defense Grant W81XWH-06- 1-0100, and in part by the University of Washington’s Proteomics Resource as well as the Canary Foundation.

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