Mass Spectrometry Data center
This program was developed for proteomics and metabolomics applications, in which hundreds or thousands of unknown tandem mass spectra are generated. The program works by searching a peak list file against up to 4 MS/MS reference libraries. MSPepSearch may input centroided mass spectra in MGF and MSP formats. The output is a match list in tab-delimited text format which can easily be viewed in a spreadsheet application or parsed with scripts as part of a pipeline. To speed-up the searches and properly weight the scoring algorithm, many modifications to the program have been made.
MSPepSearch is intended for evaluation and use by researchers interested in identification of peptides (i.e., mainly those generated by digestion with trypsin) and metabolites by mass spectral library searching. You can download the NIST Peptide MS/MS libraries on this page.
The peptide software does not contain the NIST/EPA/NIH Mass Spectral Library for interpretation of EI mass spectra. However, MSPepSearch.exe console application is fully compaible with NIST EI and small molecules MS/MS libraries.
MSPepSearch is a simple Windows program that allows to select data files for processing, select parameters and run the search against spectral libraries.
The main window of the program can be divided into 4 parts:
When all input files are processed the program will automatically open the directory in which the output files are located. The output files are best viewed in a spread sheet program.
MSPepSearch program may be redistributed without restriction.
Peptide mass spectral libraries are freely available. However, the libraries may not be redistributed without permission. The National Institute of Standards and Technology (NIST) uses its best efforts to deliver high-quality reference data and software products. However, NIST makes no warranties to that effect; and NIST shall not be liable for any damage that may result from the use of the above mentioned products.
Certain commercial equipment, instruments, or materials are identified in this document. Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the products identified are necessarily the best available for the purpose.