Label free analysis

Proteios have beta functionality for label-free quantification using precursor intensities for quantification.

1. upload peak lists and perform peptide identification.

1. Import the results to the hits report

1. Make a combined hits report to obtain combined FDR values for the peptide identifications

1. Perform feature finding using msInspect. Upload the .peptides.tsv files, and the mzML or mzXML files.

1. Select all the peptides.tsv files and do extensions->import file[s]->msInspect feature importer.

1. Open up the Feature report (PROJECT_NAME->reports->Features

1. Match features with identifications. Press the 'Match-Feature-Hits' button at the bottom of the report.

1. 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.