Service – Data Analysis
We offer a wide variety of data analysis services, including de novo protein and peptide sequencing, protein identification, small molecule ID and quantification, bioinformatics workflows for untargeted metabolomics and proteomics analysis, structural proteomics analysis- including HD-exchange analysis and cross-linking protein MS analysis and modelling.
We encourage the involvement of faculty, staff, and students in the data analysis stage of any mass spectrometry projects. Student training on proteomics, metabolomics, targeted metabolic, and HD-exchange analysis is available. Licensed software used for data analysis is housed on two dedicated computers in the core facilities and can be used for training purposes under the supervision of core facilities staff.
This software includes:
- ProteomeDiscover 2.5 (ThermoFisher)
- MarkerView (SciEX)
- PeakView (SciEX)
- MassLynx (Waters)
- TargetLynx (Waters)
- ProteinGlobalLynxServer (PGLS; Waters)
- DynamX (Waters)
Additional software routinely used for MS data analysis and visualization housed in the core facilities are:
- FragPipe (https://fragpipe.nesvilab.org/)
- MaxQuant (https://www.maxquant.org/)
- MZmine 3 (http://mzmine.github.io/)
- Proteowizard/msconvert (https://proteowizard.sourceforge.io/download.html)
- Skyline (https://skyline.ms/wiki/home/page.view?name=default)
- SPSS (https://www.ibm.com/products/spss-statistics)
- Mass Spec Studio (https://www.msstudio.ca/)
- Rstudio (now posit, https://posit.co/)
- Python 3 (https://www.python.org/downloads/)
