The computational mass spectrometry group, headed by Professors Vineet Bafna and Pavel Pevzner, focuses on developing algorithms to process mass spectrometry data.
In our lab we have developed a number of tools for computational proteomics. Each one has it's own
purpose and setting. These tools are free for download, or are also integrated into a
web server.
News
Phosphate Localization ScoreApril 4, 2008
Phosphate Localization Score is an algorithm which determines the confidence of the placement
of a phosphate on a given residue. This method is similar to the AScore, and is described in
Albuquerque et al., Mol Cell Proteomics 2008. The program is integrated with the Inspect package,
download available
here. A tutorial for using the
program is in the Inspect documentation,
here.
MS-DictionaryNovember 30, 2007
MS-Dictionary is a software to generate all plausible de novo interpretations of a tandem mass spectrum(spectral dictionary) and matches them against a protein database quickly. It enables proteogenomic searches in six-frame translation of genomic sequences that may be prohibitively time-consuming for existing database search approaches.
MS-GeneratingFunctionNovember 28, 2007
MS-GF is a software for computing the generating function of a tandem mass spectrum.The generating functions and their derivatives represent new features of tandem mass spectra that improve peptide identifications. Further, they enable one to rigorously compute error rates of peptide identifications and get better sensitivity-specificity trade-off of existing MS/MS search tools.
MS-ClusteringNovember 26, 2007
MS-Clustering is a new program aimed at improving the analysis large MS/MS datasets by removing many of their redundant or low quality spectra. MS-Clustering is capable of reducing the number of spectra submitted for analysis from a large 10+ million dataset by 90% while increasing the number peptide/protein identifications by up to 10%.
Spectral NetworksOctober 24, 2007
Spectral networks are a novel approach to the identification of MS/MS spectra
that detects and combines spectra from overlapping peptides or
modified variants of the same peptide. This approach allows for the
blind indentification of unexpected post-translational modifications and
highly modified peptides. The spectral networks software package is now
available in open-source and Windows-binary versions.
PepNovoOctober 4, 2007
A new version of PepNovo is released. It contains optional quality filtering and models for several MS instrument types.
Web serverJuly 25, 2007
The
web server
hosting all of our software is up and running. Users may sign up
for an account and search spectra. The server posts jobs to a large compute grid.
Phosphorylation searchJuly 10, 2007
Inspect has been trained to score phosphorylated MS/MS spectra. The new scoring function
has been trained on LTQ machines, and works great.
Proteogenomics Consortium
HHMI suppports the Bioinformatics [Under]graduate Research Consortium in Comparative Proteogenomics at UCSD. Proteogenomics is a new research area that utilizes the whole genome MS/MS datasets to better characterize the genomic and proteomic annotations on a global scale. The consortium provides an opportunity to the undergraduate and fresh graduate students to get hands-on research experience with real and unsolved bioinformatics problems in this upcoming field.
More information.
