Label-free quantitative analysis

Proteios SE has beta functionality for label-free quantification using precursor intensities for quantification. The workflow is:

1. Upload peak lists and perform peptide identification.
2. Import the results to the hits report
3. Create a combined hits report to obtain combined FDR values for the peptide identifications
4. Perform feature finding using msInspect. Upload the .peptides.tsv files, and the mzML or mzXML files. In the case of mzML files, they can be used both for the peptide identification and the quantification.
5. Select all the .peptides.tsv files and do extensions->import file[s]->msInspect feature importer.
6. Open up the Feature report (PROJECT_NAME->reports->Features
7. Match features with identifications. Press the 'Match-Feature-Hits' button at the bottom of the report.
8. Now MS/MS identifications in the Hits report will contain precursor quantity values, and the features will have sequence information where available. There is a log file generated with information about the matching of features and MS/MS identifications.

After these steps, results can be exported from the hits table or feature table for further analysis. It is also possible to compare two samples using the hits comparison report.

In addition, there are old plugins that use msInspect alignement output as input, and will compare groups of samples. It is possible to generate inclusion lists using these plugins.