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) and quantitation, the IMSC makes use of several licensed software packages. The data measured with standard workflow using Data-Independent Acquisition (DIA) is analyzed with Spectronaut software (current version 19), running on a local server at IMSC. The processed data can be viewed on any Windows PC with the viewer version of Spectronaut which can be requested here.
Data measured with in Data-Dependent Acquisition (DDA) is analyzed with PEAKS software (current version 12). This software runs on local servers (multiple 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.
Alternative software options for proteomics data analysis are MaxQuant, DIA-NN, and FragPipe which are also available on the IMSC data analysis servers.
PEAKS screenshot (click to enlarge):
Metabolomics data analysis
For metabolomics data analysis we have various options depending on which instrument the data was acquired with. For Thermo Orbitrap generated metabolomics data, we have a licensed version of Compound Discoverer (current version 3.3 SP3). For Sciex ZenoTOF generated metabolomics data, we have a licensed version of SciexOS (current version 3.3.1) with MarkerView and Molecule Profiler.
Alternative software options for metabolomics data analysis are MS-DIAL, MZmine, and MetaboAnalyst which are also available on the IMSC data analysis servers.
Targeted data analysis
For targeted proteomics and metabolomics data processing Skyline is a good alternative to the vendor-specific software solutions.