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BiblioSpec specifications


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


  • BlibBuild
  • BlibFilter
  • BlibSearch
  • BlibToMS2
  • LibToSqlite3


No version available


  • person_outline Michael MacCoss

Additional information

The BiblioSpec source code is available as part of the ProteoWizard project on SourceForge (

Publications for BiblioSpec

BiblioSpec citations


On the Reproducibility of Label Free Quantitative Cross Linking/Mass Spectrometry

J Am Soc Mass Spectrom
PMCID: 5814520
PMID: 29256016
DOI: 10.1007/s13361-017-1837-2
call_split See protocol

[…] 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, oxidatio […]


Centriolar Satellites Control GABARAP Ubiquitination and GABARAP Mediated Autophagy

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

[…] e discovery rate on protein, peptide and site level.The PRM data was analyzed using Skyline 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 […]


Data Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer

PMCID: 5462478
PMID: 28615921
DOI: 10.1177/1177271917710948
call_split See protocol

[…] 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. […]


The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity

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

[…] 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. This […]


YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry based Proteomics Research

PMCID: 4411476
PMID: 25712262
DOI: 10.1016/j.gpb.2014.11.002

[…] M/MRM) candidates for future assays. We also have implemented the ability to export either individual samples or a project (series of samples) from Mascot search files to BiblioSpec format utilizing Blibbuild. The resulting spectral libraries can be utilized in searching MS/MS spectra or for Skyline. […]


Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005

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

[…] tering 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 into Skyl […]

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

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