Software for the Analysis of Mass Spectrometry Data
A major effort of our laboratory has and continues to be the development of novel and practical tools for the analysis of mass spectrometry data. Check this page frequently since we are routinely making additions to our available toolset.
RelEx (Relative Expression):
A program for quantitative proteomics available through a software transfer agreement from The Scripps Research Institute, La Jolla, CA. Contact Mike MacCoss with questions, feature requests, and bugs.
MakeMS2:
A windows client program used to produce compact and easily parsed text based file formats for shotgun proteomic spectra and indentifications. The format of these files have been publised in McDonald et al. Rapid Commun. Mass Spectrom. 18, 2162-2168 (2004).
BiblioSpec:
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.
Hardklör:
A computer program for the analysis of high resolution mass spectrometry data. Hardklör will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions.
Percolator:
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.
Percolator was just released as a fully open source project. The latest build and source code is available here.
MScout:
MScout is a program that we have used for assessing LC-MS data quality.
P3 Predictor:
A obsolete program to aide in establishing SRM transitions for targeted proteomics. Please use Skyline instead.
IDCalc:
An implementation of the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions.
Skyline:
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.
PAnDA:
An acronym for Post Analysis Data Acquisition. PAnDA uses the Hardklor feature finder to define the molecular species in an LC-MS analysis and then uses this information to automatically construct new methods to specifically target features that were missed in subsequent analyses. PAnDA is particularly powerful when running technical and biological replicates to increase the fraction of the features that can be assigned a peptide identity.
Topograph:
Topograph is an advanced program for the analysis of proteomics data using stable isotope labeling. This software is still in the early stages of development. Improvements are added regularly.
MSDaPI:
Our laboratory's data repository for storing, visualizing, and disseminating proteomics results. (You will be prompted for a password)
Recent News & Updates
Sept 24, 2009Skyline v0.5 Released
The latest release of our popular software tool for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) methods and analyzing the resulting mass spectrometer data. More ...
May 2009Interview by Environmental Health Perspective
Discussion on the use of targeted proteomics for the analysis of environmental toxicants on proteins. More ...
Feb 26, 2009MacCoss honored at UW Early Career Award Recognition
Four Assistant Professors recognized for winning national awards. More ...
Dec 19, 2008Mike MacCoss wins 2007 PECASE Award
The Presidential Early Career Award for Scientists and Engineers is the nation's highest honor for scientists at the onset of their careers.
NIH Press ReleaseUW Press Release