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Software for the Analysis of Mass Spectrometry Data


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.

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.


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.


EncyclopeDIA is a library search engine comprised of several algorithms for DIA data analysis and can search for peptides using either DDA-based spectrum libraries or DIA-based chromatogram libraries. Check out our manuscript describing EncyclopeDIA on bioRxiv at doi:10.1101/277822 for more information. EncyclopeDIA contains Walnut, an implementation of the PECAN (Ting et al, 2017) scoring system to enable chromatogram library generation from FASTA protein sequence databases when spectrum libraries are unavailable.

Looking for older software?

The previous incarnation of the MacCoss lab website, which still has links to some of our older, no longer supported software, can be found HERE.

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