The Analytical Proteomics Lab provides several options for data analysis.

Applied Biosystems

Data Explorer
Individual MALDI mass spectra can be viewed and processed by Data Explorer


Thermo ScientificXCalibur & Proteome Discoverer
The easy-to-use interface enables quick and efficient acquisition, data processing and results delivery. Xcalibur integrates instrument setup, acquisition, data processing and reporting. Results can be quickly reviewed with the Qual, Quan and Library Browsers. Proteome Discoverer software is a flexible, expandable platform for the analysis of qualitative and quantitative proteomics data.  Proteome Discoverer offers a wide array of bio-software tools and customizable workflows for every proteomics experiment.

MassLynx and Protein Lynx Global Servier

MassLynx & ProteinLynx Global SERVER (PLGS)
This fundamental platform is designed to acquire, analyze, manage, and share mass spectrometry information. ProteinLynx Global SERVER™ (PLGS) is a fully integrated Mass-Informatics™ platform for quantitative and qualitative proteomics research.

Matrix Science

Mascot Search Engine Server
Mascot software uses mass spectrometry data to identify proteins from primary sequence databases.



PEAKS allows protein identification, analysis of protein post-translational modifications (PTM) and mutations by using de novo sequencing algorithm. Its SPIDER feature is a sequence tag based search tool, which can be used to identify peptides that traditional tandem mass spectrometry ion search engines will miss.


Scaffold software

This piece of software combines and validates results from multiple search engines (Sequest, Mascot and X!Tandem) to increase coverage and confidence, to visually compare results across an entire experiment. Scaffold also allows the organization and sharing of significant MS/MS data with clients and colleagues. Scaffold viewer allows viewing of any data loaded and analyzed by Scaffold.




sample submission

authorship guidelines

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