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 16 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.

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 libraries from this page: NIST Peptide MS/MS libraries.

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 compatible 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.

• 1. Download the MSPepSearch appropriate for your Windows operation system. If you are in doubt, select 32-bit version.

• 2. Extract the MSPepSearch zip archive in a working directory on your hard drive (e.g., C:\projects\MSPepSearch).

• 3. Download one or more peptide libraries in NIST MS format from here and extract them to a directory of your choice.

• 4. Additional “how to” information about MSPepSearch with GUI is available: MSPepSearch GUI.

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.