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.


Skyline is a Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM) and Full-Scan (MS1 and MS/MS) quantitative methods and analyzing the resulting mass spectrometer data. It aims to employ cutting-edge technologies for creating and iteratively refining targeted methods for large-scale proteomics studies.


Panorama is a repository server application for targeted proteomics assays that integrates into a Skyline proteomics workflow. It has been implemented as a module within LabKey Server, an open-source bioinformatics data management platform with extensive support for proteomics data and a security model rich enough to support clinical studies.

The Chorus Project:

Chorus is a new cloud application that provides scientists with the ability to securely store, analyze and share their MS data regardless of the original raw file format. The goal of Chorus is to create a complete catalogue of the world’s mass spectrometric data that can be openly accessed by, and freely accessible to, the global scientific community as well as the general public. Chorus will be invaluable to scientists in all fields that rely on mass spectrometry as a tool for answering the questions: “What is it and how much is there?”.

Chorus is enabled by Amazon Web Services, Inc. a global cloud based computing environment that includes the Amazon Elastic Compute Cloud (Amazon EC2), Amazon Simple Storage Service (Amazon S3), and the Amazon extremely low cost storage service (Amazon Glacier). Chorus provides custom built data analysis tools that convert proprietary data formats to a common MAP Reduce format for processing large data sets with a parallel and distributed algorithms on the cloud. The initial data analysis tools include chromatographic and mass spectral viewers, as well as a database search engine for protein sequence identification. While Chorus’s capabilities have been initially designed to meet the data-intense needs of the proteomics community, Chorus’s chromatographic and spectral analysis tools can be used by anyone conducting MS analyses.
A distinguishing feature of Chorus is that researchers can choose to keep their data sequestered and entirely private, or they can choose to make their data available to select collaborators or put it in the public domain for world-wide access, analysis and discussion. It is the open sharing capability that leads to the name Chorus — a community of shared data voices which together generate new knowledge, new tools, and new understanding.


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.


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. The BiblioSpec library builder is used to build all spectral libraries used in Skyline and Topograph.


An implementation of the method reported by Kubinyi, Analytica Chimica Acta, 247 (1991) 107-119 for the prediction of isotope distributions.


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).


Bullseye takes high resolution accurate masses from full scan spectra and matches these masses to tandem MS scan events. The MS/MS spectra can then be database searched with a narrow precursor ion mass to reduce database search space and improve peptide sequence identification.


A computer program for the analysis of high resolution mass spectrometry data. Hardklor will return monoisotopic m/z and charge states for single or overlapping peptide/protein isotope distributions.


Our laboratory's data repository for storing, visualizing, and disseminating proteomics results. (You will be prompted for a password)


PECAN (PEptide-Centric Analysis) is a tool for peptide detection directly from DIA data without the need of a spectral library. PECAN takes a list of peptide sequences and query each peptide against the DIA data (in centroid mzML format) and reports the best evidence of detection for each peptide.


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.

P3 Predictor:

A obsolete program to aide in establishing SRM transitions for targeted proteomics. Please use Skyline instead.


Software for de novo calibration of low resolution tandem MS/MS data.

Subpages (3): FineTune IDCalc P3 Predictor