Figure 4.

Explore page in the SysteMHC Atlas web-based interface. HLA allele-specific peptide spectral libraries can be downloaded here. The web interface can also be used to query the SysteMHC Atlas and find specific information. (A) As an example the source protein BIRC6 was searched and the Atlas returned back all HLA-associated peptides originating from this protein as well as the context (i.e. SysteMHC ID, Sample ID, iProphet score, HLA annotation score, spectral counts, assigned HLA type and class) in which this peptide was observed. Then, the user can click on a specific Sample ID hyperlink and be redirected to the corresponding raw MS files and metadata (e.g. tissue type, cell type, culture condition, purification method, antibody used, mass spectrometer used etc). (B) The peptide RLLDYVATV was searched and the Atlas returned back the datasets in which this peptide was observed. By clicking on the peptide sequence hyperlink, the user is redirected to a new page in which the LibID information is available for MS/MS spectra visualization. Information can be downloaded as .csv files for further analysis.