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MS2Assign specifications


Unique identifier OMICS_27495
Name MS2Assign
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The peptide amino acid sequence.
Operating system Unix/Linux, Windows
Programming languages C
Computer skills Advanced
Maintained Yes


No version available


  • person_outline Bradford Gibson

Publication for MS2Assign

MS2Assign citations


An efficient algorithmic approach for mass spectrometry based disulfide connectivity determination using multi ion analysis

BMC Bioinformatics
PMCID: 3044266
PMID: 21342541
DOI: 10.1186/1471-2105-12-S1-S12

[…] At the state-of-the-art MS2Assign [] and MassMatrix [] are two MS-based methods that can be applied to the problem of determining S-S bond connectivity. In our previous work [], the MS2DB system developed by us was found to […]


Probing Native Protein Structures by Chemical Cross linking, Mass Spectrometry, and Bioinformatics*

PMCID: 2938055
PMID: 20360032
DOI: 10.1074/mcp.R000001-MCP201

[…] , which are particularly relevant for cross-linked samples. Therefore, candidate cross-links identified by accurate mass data alone must be further confirmed at the MS/MS level using programs such as MS2Assign (). […]


Quaternary structure of Artemia haemoglobin II: analysis of T and C polymer alignment and interpolymer interface

BMC Struct Biol
PMCID: 1865544
PMID: 17439665
DOI: 10.1186/1472-6807-7-26

[…] o acids) were identified. Fragment ions of types b/y-CO2, y-CO and y+H2O were also identified (Figure ). Formations of all these ions are possible according to Schilling et al. (2003) []. The program MS2Assign [] considers b or y-ions losing NH3, H2O, CO or CO2, or gaining of H2O in sequence-independent, and ion-type-independent manners.The immonium y-ion is 2 Da lighter than the conventional, amm […]

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MS2Assign institution(s)
Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA; Buck Institute for Age Research, Novato, CA, USA; Sandia National Laboratory, Livermore, CA, USA
MS2Assign funding source(s)
Supported by the National Science Foundation (CHE-0118481), the Sandler Foundation, the Department of Energy, the Irwin Foundation by its financial support of mass spectrometry at the Buck Institute and the NCRR for partial support of instrumentation at UCSF (RR01614).

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