MS2 Spectrum Processor specifications

Information


Unique identifier OMICS_21792
Name MS2 Spectrum Processor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2.1
Stability Stable
Requirements
Proteome Discoverer
Maintained Yes

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MS2 Spectrum Processor in publications

 (7)
PMCID: 5785504
PMID: 29371649
DOI: 10.1038/s41598-018-20041-9

[…] to 28. the underfill ratio was defined as 0.1%, raw data files were converted into the mascot generic file format using proteome discoverer version 1.4 (thermo electron, bremen, germany) with the ms2 spectrum processor for de-isotoping the ms/ms spectra. the concatenated target-decoy uniprot human database (sequence 90411, total residues 358, 86,945, downloaded on april 1, 2015) was used […]

PMCID: 5795388
PMID: 29222160
DOI: 10.1074/mcp.RA117.000470

[…] into three mgf files, respectively containing the cid-ms2, etd-ms2, and cid-ms3 data. during mgf conversion, the cid- and etd-ms2 spectra were additionally deconvoluted to charge state 1 using the ms2 spectrum processor add-on node in proteome discoverer v1.4. the mgf files were used as input to identify cross-linked peptides with standalone xlinkx v2.0 (), which was operated using […]

PMCID: 5647383
PMID: 29044157
DOI: 10.1038/s41598-017-13663-y

[…] injection time was set to 100 ms., raw data files were converted to *.mgf files using proteome discoverer 1.4 software (thermo fisher scientific) with deconvolution option provided by add-on node ms2-spectrum processor (imp, vienna). xlinkx v2.0 algorithm was used for cross-link identification. the following settings were used: ms ion mass tolerance: 10 ppm; ms2 ion mass tolerance: 20 ppm; […]

PMCID: 5640616
PMID: 29030565
DOI: 10.1038/s41598-017-13197-3

[…] to 28. the underfill ratio was defined as 0.1%. raw data files were converted into the mascot generic file format using proteome discoverer version 1.4 (thermo electron, bremen, germany) with the ms2 spectrum processor for de-isotoping the ms/ms spectra. the concatenated target-decoy uniprot human database (total sequences 92867, total residues 36953354, downloaded on 25 july 2016) was used […]

PMCID: 5493756
PMID: 28656966
DOI: 10.1038/ncomms15865

[…] the underfill ratio was defined as 0.1%., briefly, raw data files were converted to the mascot generic file format using proteome discoverer version 1.4 (thermo electron, bremen, germany) with the ms2 spectrum processor for deisotoping the ms/ms spectra. the concatenated target-decoy uniprot human database (sequence 88,473, downloaded on 29 november 2013) was used for ms/ms spectra searches. […]


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