VEMS version after 1-08-2006 will be posted on the new CIC bioGUNE web-page
VEMS Virtual Expert Mass Spectrometrist is a program for integrated proteome analysis. VEMS offers processing of raw data, MSMS database searches with many variable modifications, correlation of spectra for finding more hits, validation functions, data mining functions, quantitative time studies both with and without stable isotope labelling, clustering of quantitative results and export of data in Proteios XML standard format. The functions are included in one user friendly executable file. The VEMS application also works as an interface to other programs such as blast, Lutefisk and a sequence analysis tool.
If you use VEMS in your research please reference the articles below
References
1. VEMS 3.0: Algorithms and Computational Tools for Tandem Mass Spectrometry Based Identification of Post-translational Modifications in Proteins J. Proteome Res. 2005, 4, 2338 - 2347 PMID: 16335983
2. Database-independent, database-dependent, and extended interpretation of peptide mass spectra in VEMS V2.0. Proteomics. 2004, 4, 2583-93. PMID: 15352233
3. Interpreting peptide mass spectra by VEMS. Bioinformatics. 2003, 19, 792-3. PMID: 12692000
Comments? then contact
Dr. Rune Matthiesen
Rune Matthiesen is starting as principle investigator at CIC bioGUNE, Bilbao, Spain from the 1st of January 2006. The VEMS project will continue as a collaboration between Ole N. Jensen, Protein Research Group, Department of Biochemistry & Molecular Biology, University of Southern Denmark and CIC bioGUNE.
Download VEMS v3_207
A bug in the peak penalty score in the viewer have been removed 12-12-2005 (Word document) (pdf document)
How to search (Word document) (pdf document)
Screen shots
Main Annotation Validation Quantitative validation LC-MS plot Scan view Fragment ion calibration Fragment ion calibration
Figure made in VEMS
External tools interfaced from VEMS
Retention time prediction Sequence handling by SATv1.0
Documents
Installation
Usages
User Manual in Word 2002 format
PostGreSQL database system
Related sites:
Data storage
1. Proteios VEMS v3.0 program can export data in the Proteios exchange format.
2. PRIDE for data storage. mzData, mzIdent
Data analysis
1. Systems biology a complete proteome package. Uses mzXML as data format
2. X!Tandem search engine and database storage
3. lutefisk de novo sequencing tool
Bioinformatics sites
Last updated 20-12-2005
