Software Resources and Downloads

Title Description Category Tags
MAGMA Multiobjective Analyzer for Genetic Marker Acquisition

A genetic mapping project, typically implemented during a search for genes responsible for a disease, requires the acquisition of a set of data from each of a large number of individuals. This data set includes the values of multiple genetic markers.

miRvestigator Framework

The miRvestigator framework is designed to take as input a list of co-expressed genes and will return the most likely miRNA regulating these genes.

Software Integration Framework Database, Software
mspecLINE Web Application Integration, Literature, MS/MS
PASSEL (PeptideAtlas SRM Experiment Library)

The PeptideAtlas SRM Experiment Library (PASSEL) is a component of the PeptideAtlas project that is designed to enable submission, dissemination, and reuse of SRM experimental results from analysis of biological samples.

Information Resource Database, Proteomics, Public Resource, SRM, Transitions

PeptideAtlas is a multi-organism, publicly accessible compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments.

Information Resource Database, MS/MS, Proteomics, Public Resource

PeptideProphet is a tool for generating statistical validation of MS/MS search engines' spectra-to-peptide sequence assignments. This tool was orginally develped at the SPC, part of the ISB. PeptideProphet is now a core part of the Trans-Proteomic Pipeline software distrubtion.

Analysis Software C++, MS/MS, Proteomics, PSM, TPP, Validation

It has been noted [1] that only a handful of a protein’s possible tryptic peptides are consistently observed in proteomics experiments. We denote these consistently observed peptides to be proteotypic peptides.

Analysis Software MS/MS, Peptides, Proteomics, Proteotypic

PhospoPep version 2.0 is a project to support systems biology signaling research by providing interactive interrogation of MS-derived phosphorylation data from 4 different organisms.

Information Resource Database, MS/MS, Phosphoproteomics, Proteomics, Public Resource
PIPE2 (Protein Information and Property Explorer) Web Application GO, Protein list, Visualization

ProbTF is a web server that enables the analysis of DNA sequences using mouse-specific position weight matrices from the TRANSFAC™ database.

Web Application

ProteinProphet is a tool for generating probablities for protein identifications based on MS/MS data. ProteinProphet makes use of results from PeptideProphet, which produces validation results for peptide sequence identifications.

Analysis Software C++, MS/MS, Proteins, Proteomics, TPP, Validation
Proteomics Toolkit Web Application Java, MS/MS, Proteomics

Pubcrawl is an application that combines literature based semantic distances with protein domain interactions to dynamically create network topologies of terms.

Web Application

RF-ACE is an efficient implementation of a robust machine learning algorithm for uncovering multivariate associations from large and diverse data sets.

SBEAMS (Systems Biology Experiment Analysis Manangement System)

In order to better support the data being generated by local microarray, proteomics, macroarray, and other experiments, we are developing and using SBEAMS (Systems Biology Experiment Analysis Management System), a framework for collecting, storing, and accessing data produced by these and

Data Management LIMS, Multi-Omics, Perl

SpectraST (short for "Spectra Search Tool" and rhymes with "contrast") is a spectral library building and searching tool designed primarily for shotgun proteomics applications.

Analysis Software C++, MS/MS, Proteomics, Spectral library search, TPP

 The SRMAtlas is a compendium of targeted proteomics assays to detect and quantify proteins in complex proteome digests by mass spectrometry.

Information Resource Database, Proteomics, Public Resource, SRM, Transitions
The GESTALT Workbench

Large amounts of 'raw' genomic sequence data already exist and continue to grow exponentially. Many tools are available for automated analysis of these data by comparison to known sequences or by pattern recognition.

Analysis Software Analysis, Modeling
Trans-Proteomic Pipeline

The Trans-Proteomic Pipeline (TPP) is a collection of integrated tools for MS/MS proteomics, developed at the SPC.

Analysis Software C++, MS/MS, Proteomics, TPP, Validation

Unipep is a project to provide access to proteomics data from the Serum Biomarker group at the Swiss Federal Institute of Technology (ETH) in Zurich Switzerland, and the Institute for Systems Biology (

Information Resource Database, MS/MS, N-glycocapture, Proteomics, Public Resource