Vanderbilt University Medical Center

Supporting Tool Suite for Production Proteomics

Supporting Tool Suite for Production Proteomics

This site describes a suite of tools developed at Vanderbilt University to support production proteomics. The flowchart below illustrates the pipeline to manage the large amount of data produced by proteomics experiments.

The File Name Generator (FNG) is an instrument file naming utility to quickly generate filenames in a standard consistent fashion as opposed to manually entering each filename into the instrument control software. The Backup Utility Service (BUS) tool offers automated backup of raw data to file servers. The ScanSifter tool reads these proprietary format files and converts them to open format files, which are submitted to a queuing system and identified by database search engines such as SEQUEST1 and MyriMatch2. The identification results can be retrieved using the File Collector tool, enabling batch copying search results to local computer or network drives. Each tool can be used separately to fulfill its function. As shown in a demo, combining these tools offers an integrated solution for production proteomics.



Source code and executable versions of these tools are available under Apache 2.0 License at



This work was supported by the National Cancer Institute through the Clinical Proteomic Technology Assessment for Cancer (CPTAC) program [U24CA126470 to D.C.L. and R01CA126218 to D.L.T.].



Supporting Tool Suite for Production Proteomics. Ma Z.-Q., Tabb D.L., Burden J., Chambers M.C., Cox M.B, Cantrell M.J, Ham A.-J.L, Litton M.D., Oreto M.R., Schultz W.C., Sobecki S.M., Tsui T.Y., Wernke G.R. and Liebler D.C. (2011) Bioinformatics, submitted



1. Eng,J.K. et al. (1994) An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. Journal of the American Society for Mass Spectrometry, 5, 976-989.

2. Tabb,D.L. et al. (2007) MyriMatch: highly accurate tandem mass spectral peptide identification by multivariate hypergeometric analysis. Journal of Proteome Research, 6, 654-661