Thermo Scientific Software available on the analysis computers in the CMS:
- Proteome Discoverer 2.4 – a comprehensive package for the qualitative and quantitative analysis of large Proteomics data sets with incorporated statistical and visualization nodes (some helpful video tutorials, as well as answers to some FAQ on terminology)
- Compound Discoverer 2.3 – a comprehensive package for the qualitative and quantitative analysis of metabolomics and other small molecule data sets data sets with incorporated statistical and visualization nodes. Particularly suited for tandem integration of DIA quantitation with DDA fragmentation patterns.
- Trace Finder- A package for development of streamlined targeted small molecule quantitation using MRM and PRM methods.
- BioPharma Finder -intact protein analysis of LC/MS data and peptide mapping analysis of LC/MS2 data for identification and relative quantitation of proteins, sequence variants, and low-level post-translational modifications (PTMs) (some helpful video tutorials)
- ProSightPC – top-down proteomics analysis
Freeware packages for Proteomics:
- MaxQuant – a quantitative proteomics software package designed for analyzing large-scale mass-spectrometric data sets
- Perseus – a computational platform for analysis of proteomics data
- (Helpful lectures and tutorials for both on the MaxQuant channel)
Open Source Metabolomics Software:
- MPACT – An open source data processing platform for filtering, management of hierarchal replication, and data visualization of untargeted metabolomics datasets.
- MS-DIAL – A raw data processing tool for peak picking and spectral deconvolution for metabolomics, lipidomics, and now proteomics, datasets.
- MetaboAnalyst – A post processing platform for metabolomics featuring many statistical tools