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peptidew:pepsoftware [2016/08/28 15:16]
 peptidew:pepsoftware [2022/02/02 16:20] (current)
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 +====== Software for Peptide Mass Spectral Libraries ======
 +
 +  - [[peptidew:mspepsearch|MS PepSearch program]] - a Windows fast library search algorithm for batch identification of peptides with a graphical user interface. An mgf or msp format user input file can be searched against multiple NIST libraries.  Output is a list of matches in tab-delimited text format which can easily be viewed in a spreadsheet application or parsed with scripts as part of a pipeline. 
 +  - [[peptidew:nistmssearch|NIST Peptide Library Browser (NIST MS Search) and BSA Library]] - a Windows full spectral library search and viewing utility with graphical user interface. Each of the NIST libraries can be added and viewed by downloading the file into the same folder as the NIST MS Search program, and then restarting the program.
 +  - [[chemdata:libraryconversion|Lib2NIST]]: A Windows converter of NIST MSP file format to a peptide library.
 +  - [[peptidew:ms_piano|MS_Piano]] - a software tool for annotating peaks in mass spectra of peptides and glycopeptides
 +  - [[peptidew:msqcpipeline|NIST MSQC Pipeline]] - a Windows fully integrated software pipeline for identification and quantitation of peptides <color red>(**Note:**Support is discontinued)</color>.
 +  - [[https://chemdata.nist.gov/download/peptide_library/libraries/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]]). 
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