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Analysis of mass spectrometry data

Due to the wide diversity of mass spectrometers, samples and research questions, data analysis procedures and choice of software are often tailored to specific analyses. For data-intensive analytical workflows, particularly the -omics applications, reliable data analysis pipelines are essential. The IMSC makes use of a set of software tools, both commercial, open source and in-house developed tools.

Proteomics data analysis

For protein identification (LC-MS/MS shotgun proteomics), the IMSC makes use of PEAKS software (current version 7.5). This software runs on local servers (2 licences available) at the IMSC and processed data may be viewed on any Windows PC user PEAKS in viewer mode. PEAKS can be downloaded here.

PEAKS screenshot (click to enlarge):
PEAKS example1

Protein quantitation can be performed in a variety of ways, depending on the experimental design. Quantitation of untargeted data recorded with data dependent acquisition (LC-MS/MS) can be performed with PEAKS Q software, or with MaxQuant, both available on the IMSC data analysis servers.

Metabolomics data analysis

For metabolomics data analysis, Progenesis QI is available on a server at the IMSC. This powerful software package can be used both for relative quantitation and metabolite identification. Data from Progenesis QI can only be viewed on the server PC.

Progenesis QI screenshot (click to enlarge):
Hjalmar Permentier

Useful open source software