Waters | Nonlinear Dynamics

Progenesis QI for proteomics

The next generation in LC-MS proteomics data analysis software.
Discover the significantly changing proteins in your samples.

What search engines and databases are supported?

Progenesis QI for proteomics supports many of the most common data formats used by search engines and databases as standard. It also offers an extension mechanism by which new formats can be supported.

The following table gives the various file formats currently supported, both those that are pre-packaged with the software and others that can be downloaded to extend your existing software:

Peptide search method Download the plugin
Byonic Download Byonic
EasyProt Download EasyProt
Mascot Provided as standard
PEAKS Studio Download PEAKS Studio
PEAKS Studio (pepXml import only) Download PEAKS Studio (pepXml import only)
Phenyx Provided as standard
PLGS v2.3 and v3.0 Download PLGS v2.3 and v3.0
PLGS v2.4 and v2.5 Download PLGS v2.4 and v2.5
ProteinPilot (group2xml) Download ProteinPilot (group2xml)
Proteome Discoverer (pepXML) Download Proteome Discoverer (pepXML)
Proteome Discoverer 1.3 (.xls) Download Proteome Discoverer 1.3 (.xls)
Scaffold v3.0 and v4.0 Download Scaffold v3.0 and v4.0
SEQUEST (dta and out files) Provided as standard
SEQUEST (dta and pepXml files) Provided as standard
SEQUEST (sqt and ms2 files) Download SEQUEST (sqt and ms2 files)
Spectrum Mill Download Spectrum Mill

Note: after installing any of the plugins above, you will need to restart Progenesis before they are available for use.

Custom development

We're happy to work with you to develop custom plugins that support other search engines you may prefer to use. If you're interested in this option, please email support_nld@waters.com and one of our development team will contact you to discuss your needs and how we might help.