PeptideAtlas
PeptideAtlas Home
 Seattle Proteome
 Center
  
PeptideAtlas:
  Overview
  Contacts
  Data Contributors
  Publications
  Software
  Database Schema
  Feedback
  FAQ


Atlas Data:
  Data Repository
  HPPP Data Central
  PeptideAtlas Builds
  Search Database
  

  Contribute Data
  Genome Browser
Setup

Spectral Libs:
  Libraries + Info
  SpectraST Search


Glossary/Terms:
  Atlas nomenclature
  SGD nomenclature

  

Spectrum Library Central at PeptideAtlas

Welcome to the Spectrum Library Central, hosted at PeptideAtlas. We provide a list and links to Spectrum Libraries built specifically for spectrum library searching of tandem mass-spec data.

Spectral Library Search Projects

Spectral library searching, unlike sequence database searches, involve finding the best match of an acquired MS/MS spectrum to a library of pre-searched spectra for which the sequences have been determined. This approach can be hundreds of times faster than traditional searching, with comparable or better accuracy.

SpectraST Developed at ISB by H.Lam. Included as part of the Trans-Proteomic Pipeline (TPP) distribution. A stand-alone Windows version can now be downloaded from the ISB download section below. An online query form is also available. For more information, please consult the SpectraST information page
NIST MS Search The National Institute of Standards and Technology (NIST) distributes an updated version of their NIST MS Search Program for Windows, which includes the ability to perform Peptide searches via spectrum matching. The NIST Peptide Library Search Engine is also available from the NIST download section below.
X! Hunter Developed by the The Global Proteome Machine Organization. Online query forms for submitting a file or a single spectrum are available.
BlibSearch Part of the BiblioSpec suite, developed at the MacCoss Lab at the University of Washington.
Bonanza A spectral comparison algorithm developed by the Andrews Lab at the University of Michigan. (No website or data yet).

Download Spectrum Libraries

Links to download reference spectra and related documentation from vaious sources.

   ISB

Libraries built from PeptideAtlas data by H. Lam, specifically for use with SpectraST.

File Size Date md5 checksum* Download
ISB_Hs_plasma_20070706_PUBLIC.zip 218MB 2007-07-20 
d81cf3d9e5e1966541ed801d61b42de7
Consensus spectral libraries constructed from the 40 public datasets in Human Plasma PeptideAtlas (Human)
ISB_Dm_phospho_20070326.zip 129MB 2007-03-26 
5d8da0e78c74c469260d2b7280ed0919
Quality-filtered consensus spectral libraries of Drosophila melanogaster peptides enriched for phosphorylation by 3 different methods. (Bodenmiller et al. (2007) Mol. Systems Biol. 3, 139)
SpectraST_2008_07_01.zip 27MB 2008-07-01 
545600349c50613c03c3c5a65974ffec
Stand-alone Windows native version of SpectraST (also available as part of the TPP distribution)


   NIST

These libraries are built by S. Stein at NIST. The Institute for Systems Biology asks that anyone wishing to download any of the NIST Libraries of Peptide Fragmentation Spectra read the following paragraph and acknowledge before downloading:

"I recognize that this data collection, the NIST Library of Peptide Fragmentation Spectra, is copyrighted by the Department of Commerce, U.S. Government and shall not be redistributed in any manner without a valid Distribution Agreement. To receive such an agreement, contact the Standard Reference Data Program, National Institute of Standards and Technology, at data*at*nist.gov or 301-975-2008."   

File Size Date md5 checksum* Download
yeast.msp.zip 110MB 2006-12-13 
2f2334b878bcab6be635de0eb84f013e
NIST Library of Peptide Ion Fragmentation Spectra (Saccharomyces Cerevisae)
yeast_consensus.splib 152MB 2006-12-13 
795549516f75e849e0e5212bc66bab36
Same as above, but converted to the special SpectraST format
human.msp.zip 137MB 2006-12-13 
d7c7baba10ef6ab2592665689e3dc4ef
NIST Library of Peptide Ion Fragmentation Spectra (Human)
human_consensus.splib 193MB 2006-12-13 
a2b8dc52513348ed3850d9d8a20d2b25
Same as above, but converted to the special SpectraST format
NIST_PepLib_6_06.doc 240kB 2006-12-13 
65db452fe09d5713498493fb75bae6e1
Documentation for NIST Libraries (doc)
NIST_PepLib_6_06.pdf 114kB 2006-12-13 
1319192a585c138a57ba6179d9f8a40b
Documentation for NIST Libraries (pdf)
Read_Me_First.txt 4kB 2006-12-13 
0020d9ae92dbdc0d19cc13a529548e0a
Read this file first! For more info on the files that follow.
NIST_Pep_Setup.zip 467MB 2006-12-13 
7849225ab794b73373b639966644e4ee
NIST MS Search and complete NIST Library of Peptide Ion Fragmentation Spectra setup
NIST_Pep_Demo_Setup.zip 22MB 2006-12-13 
75ecd2186b8d050445be8652bc8147aa
Demo (abbreviated) version of the above
NIST_PEPLIB_TXT.ZIP 306MB 2006-12-13 
9efff01550fbb9dc32a1efa80326cb85
Text version of the NIST Library of Peptide Ion Fragmentation Spectra with protein sequences
NIST_PEP_SRCH_ENGINE.ZIP 3MB 2006-12-13 
8ee0c07e118d134ec38f062f0ee971dc
NIST MS/MS Peptide Libraries DLL version 2.1.1. Sample code and documentation for using the DLL


   GPM

The Global Proteome Database builds consensus Annotated Spectral Libraries (ASL) for several organisms (human, yeast, mouse, dog, cow, etc), for use with the X!Hunter application, and are available for download via ftp. Please note that these libraries are not suitable to be used with SpectraST.



   BiblioSpec

Libraries can be built using the BlibBuild program that is part of the software distribution. Pre-built reference libraries should be available for download from this link.

* To make sure that you have a complete and uncorrupted download, please verify that the md5 checksum of each downloaded file matches the posted value on this website. (On most Unix-type systems, you can use the md5sum utility: md5sum filename).
© 2005, Institute for Systems Biology, All Rights Reserved