Software

A suite of software tools for creating and searching MS/MS peptide spectrum libraries. The software is particularly useful for those performing repeated proteomics profiling experiments on the same organism. After the identity of a peptide spectrum has been determined, this information can be used to speed and improve all future analyses.

Crux analyzes shotgun proteomics tandem mass spectra, associating peptides with observed spectra.

DTASelect and Contrast were designed to make interpretation and comparison of proteomic data faster and more effective. DTASelect organizes and filters SEQUEST identifications, reducing the time required to interpret the results for each sample. Contrast differentiates multiple samples and comprises a powerful meta-analytical tool.

Lorikeet is a JQuery plugin to view MS/MS spectra annotated with fragment ions. The viewer is interactive with zoom capabilities, selection of fragment types, switching annotations on and off etc. The plugin can, optionally, also render a MS1 spectrum below the MS/MS spectrum. Lorikeet uses the Flot plotting library.

A relational database and accompanying web application for unifying, storing, viewing, and comparing protein mass spectrometry results from a wide range of proteomics platforms.

A semi-supervised machine learning approach for improving the analysis of tandem mass spectrometry data of peptides. Percolator uses a machine learning technique call a support vector machine to dynamically discriminate between correct and decoy spectrum identifications obtained by database searching. By using our approach, we are able to identify approximately 50% more peptides from a given μLC-MS/MS dataset.

A method for performing protein identification & peptide sequencing by utilizing mass spectrometry fragmentation patterns to search protein and nucleotide databases has been developed by our lab. Our program, SEQUEST, converts the character-based representation of amino acid sequences in a protein database to fragmentation patterns which are compared against the MS/MS spectrum generated on the target peptide. The algorithm initially identifies amino acid sequences in the database that match the measured mass of the peptide, compares fragment ions against the MS/MS spectrum, and generates a preliminary score for each amino acid sequence. A cross correlation analysis is then performed on the top 500 preliminary scoring peptides by correlating theoretical, reconstructed spectra against the experimental spectrum. Output results are displayed accordingly.

An advanced windows program for building methods and analyzing data from SRM/MRM targeted proteomics experiments. New release of v0.5 and several videos demonstrating the capabilities and how to use the software.

Philius uses Hidden Markov Models (HMM) to predict transmembrane protein topology and signal peptide position.

Rosetta is a molecular modeling software package for understanding protein structures, protein design, protein docking, protein-DNA and protein-protein interactions. The Rosetta software contains multiple functional modules, including Rosetta ab initio, RosettaNMR, RosettaDesign, RosettaDock, Rosetta Fragment Selection, Rosetta Nucleic Acids, RosettaLigand, and more.

FRETSCAL screens images of cells that contain CFP and YFP tagged proteins in order to determine the extent of energy transfer(FRET)between the two fluorophores. The graphical user interface (GUI) of FRETSCAL allows the user to specify criteria that are used to identify areas of interest (AOIs) in the images.

qvality performs nonparametric estimation of posterior error probabilities.

JobCenter is a novel client/server architecture for distributing and executing computing jobs across heterogeneous computing environments, such as those typically found in research laboratories.

Mason is a portable web site module designed to visualize and compare annotated features of one or more nucleotide or protein sequence.

SnipViz is a client-side software tool designed to disseminate multiple versions of related gene and protein sequences on web sites.