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BiblioSpec specifications

Information


Unique identifier OMICS_19845
Name BiblioSpec
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A library file and an MS2 file containing query spectra.
Operating system Unix/Linux, Windows
Programming languages C++
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

Subtools


  • BlibBuild
  • BlibFilter
  • BlibSearch
  • BlibToMS2
  • LibToSqlite3

Versioning


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Maintainer


  • person_outline Michael MacCoss <>

Additional information


The BiblioSpec source code is available as part of the ProteoWizard project on SourceForge (https://sourceforge.net/projects/proteowizard/?source=navbar)

Publications for BiblioSpec

BiblioSpec in publications

 (14)
PMCID: 5814520
PMID: 29256016
DOI: 10.1007/s13361-017-1837-2

[…] in chen et al. 2016 and maiolica et al. 2007 [, ] (figure d and e). skyline uses the .ssl file and the assigned mzml files (created from raw files using msconvert []) to create a spectral library by bibliospec. peptide settings were as follows: enzyme: trypsin kr/p, max missed cleavages: 9, minimal length of peptide: 6, maximal length: 60, modifications: carbamidomethylation on cysteine, […]

PMCID: 5526835
PMID: 28712572
DOI: 10.1016/j.cub.2017.06.021

[…] rate on protein, peptide and site level., the prm data was analyzed using skyline 3.6.0.10162 software []. the spectral library was built in skyline using the maxquant msms.txt file and the bibliospec algorithm. the background proteome was generated using uniprotkb homo sapiens database. precursor and product ion extracted chromatograms (xics) were generated using the following settings […]

PMCID: 5462478
PMID: 28615921
DOI: 10.1177/1177271917710948

[…] cysteine as a static modification. the protein false discovery rate, which was determined by a target-decoy search strategy, was set to 1%. the spectral library was generated from dda data using the bibliospec algorithm and skyline open-source software. in the build library tab in skyline, the cut-off score was set to 0.99., all dia data were imported and processed directly in skyline without […]

PMCID: 4540001
PMID: 26306205
DOI: 10.1038/sdata.2015.41

[…] details can be found in the raw data files (.raw or.mzml)., software used in the generation of this project is largely third party software as described in the data records section, i.e., msgf+ and bibliospec. the only remaining software was to link protein identifications to kegg functional assignments. this was done via custom parsing of the files and cross-referencing the kegg database. […]

PMCID: 4398503
PMID: 25678338
DOI: 10.1002/mbo3.229

[…] and ms1 ion intensity chromatogram processing in skyline were described recently in detail by schilling et al. (). briefly, comprehensive spectral libraries were generated in skyline using the bibliospec algorithm (frewen and maccoss ) from database searches of the raw data files prior to ms1 filtering. subsequently, raw files acquired in data-dependent mode were directly imported […]


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BiblioSpec institution(s)
University of Washington, Seattle, WA, USA

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