Analysis validation

Search result data associated with an Analysis must be validated before being accessible by end-user for further interpretation. Data processing of Analysis data is a multi-step process.

Analyses icons are color-coded based on their data processing status to help users to easily determine the validation level of each of them:
  • validation_not_completed : Protein annotation import not yet completed.
  • validation_not_validated : Data not yet validated.
  • validation_partially_validated : Data partially validated.
  • validation_validated : Data validated and reported.


Protein annotation import from the databank file(s) is not part of the validation process. It is triggered as a background task immediately after search result data import. This process can take several minutes depending on the number of proteins identified. However, validated data cannot be reported (see the Reporting section below for more details) before protein annotation data import has been completed.

Automated peptide/protein validation

FDR (False discovery rate) - based validation

FDR-based validation is initiated at the data import step to filter out data below the corresponding threshold score (see Analysis import).

Qualitative validation

Comparative validation

Validation templates

Manual peptide/protein validation

Peptides selection/exclusion

Protein exclusion and filtering

Lower-scoring peptides activation

Clear peptide/protein selections

Sequence modification validation

Phosphorylation sites validation with PhosphoRS

PhosphoRS [1] is an algorithm used to determine phosphorylation positions on a peptide, based on its sequence and MS2 fragmentation spectrum. This tool is included into myProMS and can be used to correct imported phosphorylation data. From “Process analyses” menu, select Peptide/Protein Selection process type, and click on Start PhosphoRS analysis.

The following form is then displayed:

<Figure phosphoRS form>

PhosphoRS parameters can be set in PhosphoRS Analysis Rules section: - : - Activation type: select the fragmentation mechanism of the analysis instrument. PhosphoRS is optimized for each activation type. - Mass Deviation: mass error tolerance when PhosphoRS matches experimental spectra with theoretical spectra.

Manual validation of modifications

Validation traceability