What search engines and databases are supported?
Progenesis LC-MS 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 |
|---|---|
| Mascot | Provided as standard |
| PEAKS Studio |  |
| Phenyx | Provided as standard |
| PLGS v2.3 | |
| PLGS v2.4 and v2.5 | |
| Proteome Discoverer (.xls) | |
| 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) | |
| 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.