Proteome Discoverer (Thermo Fisher, Inc,).

CMSP utilizes the Proteome Discoverer software package for analysis MS-based proteomics data. Users are able to view results using the free Proteome Discoverer viewer.

Help documentation can be found within the free viewer.

PEAKS (Bioinformatics Solutions, Inc).

CMSP has access to the PEAKS software for analysis of MS-based proteomics data. Users can view results using the free PEAKS viewer. Instructions for opening results in the PEAKS viewer are also available.

PEAKS help document

Scaffold (Proteome Software, Inc).

CMSP can use the Scaffold software to organize and generate results from MS-proteomics data. Users can view results using the free Scaffold viewer

Scaffold help document is also available.

MZmine (

MZmine enables analysis of MS-based metabolomic and proteomic data. It is freeware available at

MZmine documentation

MassHunter and MassProfiler (Agilent, Inc).

For targeted MS-based metabolomics data generated on our Agilent instrumentation, we have access to compatible software packages for analysis of generated data. More information can be found at:

MultiQuant software (Sciex, Inc.).

For targeted MS-based metabolomics and proteomics data generated on Sciex Qtrap instruments, we utilize the MultiQuant software compatible with this data.

Progenesis QI (Waters, Inc.).

For untargeted MS-based metabolomics data, the CMSP has access to Progenesis QI for alignment and quantification of detected metabolites. More information on Progenesis QI is available here.

Skyline (

CMSP utilizes the freely available Skyline software platform from the MaCoss laboratory for analysis of MS data. More information on Skyline is available at

MSSEARCH/AMDIS (National Institutes of Standards and Technology, NIST).

CMSP staff have experience with the freely available tools from NIST for analysis of untargeted MS-based metabolomics data. More information on these tools can be found here.