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peptidew:start [2018/11/01 10:15] (current)
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 +~~NOTOC~~
 +====== NIST Libraries of Peptide Tandem Mass Spectra ======
 +
 +DOI: [[http://​dx.doi.org/​10.18434/​T4ZK5S|10.18434/​T4ZK5S]]
 +===== What they are=====
 +NIST peptide libraries are comprehensive,​ annotated mass spectral reference collections from various organisms and proteins useful for the rapid matching and identification of acquired MS/MS spectra. Spectra were produced by tandem mass spectrometers using liquid chromatographic separations followed by electrospray ionization. ​ Unlike the NIST small molecule electron ionization library which contains one spectrum per molecular structure, there are several different modes of fragmentation (ion trap and ‘beam-type’ collision cells are currently the most commonly used fragmentation devices) that result in spectra with different, energy dependent, patterns. ​ These result in multiple spectral libraries, distinguished by ionization mode, each of which may contain several spectra per peptide. ​ Different libraries have also been assembled for iTRAQ-4 derivatized peptides and for phosphorylated peptides. Separating libraries by animal species reduces search time, although investigators may elect to include several species in their searches. \\ 
 + ​\\ ​
 +Currently, there are >**4.3 million** spectra in the libraries, representing **1.26 million** different entities (derivative-peptide sequence-fragmentation mode). ​ Several of the largest libraries resulted from data collected by laboratories collaborating in the National Cancer Institutes Clinical Proteomic Tumor Analysis Consortium (CPTAC)[see [[http://​proteomics.cancer.gov/​]]]. ​ CPTAC laboratories conducted more than 6,000 2D-LC/MS/MS runs of human tumor and human-mouse xenograft samples producing >91 million MS/MS spectra. To reduce the variability introduced by disparate data analysis platforms, NIST created a Common Data Analysis Platform (CDAP). ​ In addition to the results reported and publicly accessible at [[https://​cptac-data-portal.georgetown.edu/​cptacPublic/​]],​ NIST assembled libraries of well-identified and annotated spectra for human and mouse, underivatized,​ iTRAQ, and phospho-iTRAQ peptides. ​  
 +
 +
 +===== Why they are useful =====
 +
 +  * A reference spectrum library provides a sensitive, reliable, fast, and comprehensive resource for peptide identification,​ taking advantage of previously encountered,​ identified, and annotated data.
 +  * A peptide mass spectrum library can be used for:
 +    * Direct peptide identification
 +    * Validating peptides identified by sequence search programs ​
 +    * Organizing and identifying recurring, unidentified spectra.
 +    * Sensitive, high reliability detection of internal standards, biomarkers, and target proteins
 +    * Subtracting a component from a mixture spectrum
 +
 +===== How to use libraries =====
 +
 +The libraries are provided in two formats - NIST MS Search binary format and ASCII text format ( MSP file).
 +You can use MSP files with many software programs. The NIST MS Search binary libraries are directly usable with the NIST MS Search and PepSearch programs. ​
 +
 +
 +==== Available Windows Software for Peptide Mass Spectral Libraries =====
 +
 +  - [[peptidew:​mspepsearch|MS PepSearch ]] - a fast library search algorithm for batch identification of peptides with a graphical user interface. ​ Accepts user mgf input files and outputs text lists of matches.
 +  - [[peptidew:​nistmssearch|NIST MS Search ]] - a full spectral library search and viewing utility with graphical user interface. Accepts multiple format input files (including mgf); output is msp text.
 +  - [[peptidew:​msqcpipeline|NIST MSQC Pipeline]] - a fully integrated software pipeline for identification and quantitation of peptides <color red>​(**Note:​**Support is discontinued)</​color>​.
 +  - [[chemdata:​libraryconversion|Lib2NIST]]:​ A utility for converting NIST MSP file formats to a peptide library
 +  - [[ftp://​chemdata.nist.gov/​download/​peptide_library/​software/​current_releases/​ReAdw4Mascot2/​ReAdw4Mascot_20130604a.zip|ReAdW4Mascot2]]:​ Thermo RAW data converter (direct download). ​
 +  - Other compatible software (external links)
 +    - [[http://​tools.proteomecenter.org/​wiki/​index.php?​title=Software:​SpectraST|SpectraST]]:​ a fast library search algorithm integrated into the TPP (developed at [[http://​www.systemsbiology.org/​|ISB]] and [[http://​www.ust.hk/​|HKUST]]).
 +    - [[https://​brendanx-uw1.gs.washington.edu/​labkey/​project/​home/​software/​Skyline/​begin.view|Skyline]]:​ a software package for design and analysis of SRM experiments (developed at [[http://​www.washington.edu|UW]]). ​
 +
 +==== Peptide Mass Spectral Libraries =====
 +
 +You can download different libraries here: [[peptidew:​cdownload|NIST Libraries of Peptide Tandem Mass Spectra]]
 +
 +
  
peptidew/start.txt · Last modified: 2018/11/01 10:15 (external edit)