BiblioSpec is a suite of software tools for creating and searching MS/MS peptide spectrum libraries. BiblioSpec is available free of charge for noncommercial use through an interactive web-site at http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/bibliospec.php The BiblioSpec package contains the following programs:

• BlibBuild creates a library of peptide MS/MS spectra from MS2 files.
• BlibFilter removes redundant spectra from a library.
• BlibSearch searches a spectrum library for matches to query spectra, reporting the results in an SQT file.

In addition to the primary programs, the following auxiliary programs are available:

• BlibStats writes summary statistics describing a library.
• BlibToMS2 writes a library in MS2 file format.
• BlibUpdate adds, deletes, or annotates spectra.
• BlibPpMS2 processes spectra (bins peaks, removes noise, normalizes intensity) as done in BlibSearch and prints the resulting spectra to a text file.

Several reference libraries are available for download. These libraries are updated regularly and are for use under the Linux operating system. You will find libraries for

• Escherichia coli
• Saccharomyces cerevisiae
• Caenorhabditis elegans

If you are looking for libraries to use under windows, they can be found here.

An overview of all file formats used is available. For a complete description of the MS2 and SQT file formats, see McDonald et al. (2004).

BiblioSpec Version 1.0 Copyright 2006 University of Washington. All rights reserved. Written by Barbara Frewen, Michael J. MacCoss, William Stafford Noble in the Department of Genome Sciences at the University of Washington.