Additional data from publication:
New light on the HLA-DR immunopeptidomic landscape
Emilie Egholm Bruun Jensen, Birkir Reynisson, Carolina Barra, and Morten Nielsen
Overview of the includes MS samples (samples.tsv)
In the format
sampleID #ligs HLA_typing 144.1 4382 DRB1_0101,DRB1_0301,DRB3_0101 144.2 3975 DRB1_0101,DRB1_0301,DRB3_0101 183.1 3929 DRB1_0801,DRB1_1501,DRB5_0101 ..
File with the complete annotated data set (ANNOTATED_DATA.tsc)
In the format
Clus_ID+DonorID Clus_ID Peptide HLA Rank Core ProtID SampleID DeepLoc DonorID Best_Rnk Nclus
AAAAFNKDALLNWLK+158 AAAAFNKDALLNWLK AAAAFNKDALLNWLK DRB3_0101 6.5508117676 FNKDALLNW P42338.1 158.2 Dual 158 6.5508117676 1
AAAAVRQMNPHIRVT+978 AAAAVRQMNPHIRVT AAAAVRQMNPHIRVT DRB5_0202 0.5007802844 VRQMNPHIR P22314.3 978.1 Cyto 978 0.5007802844 1
AAADDIKPCPRCAAY+154 AAADDIKPCPRCAAY AAADDIKPCPRCAAY DRB1_0404 38.7160453796 IKPCPRCAA Q9NV58.3 154.3 Endo 154 38.7160453796 1
AAADDIKPCPRCAAYIIKMND+786 AAADDIKPCPRCAAYIIKMND AAADDIKPCPRCAAYIIKMND DRB1_1302 52.2107086182 IKPCPRCAA Q9NV58.3 786.1 Endo 786 52.2107086182 1
...
where Clus_ID+DonorID: The unique cluster ID Clus_ID: The peptide definting the cluster Peptide: The peptide member of the cluster HLA: The predicted HLA restriction Rank: The predicted percentile rank score of the peptide Core: The predicted binding core ProtID: Protein ID SampleID: Sample ID DeepLoc: DeepLoc subcellular prediction [Cyto, Endo or Dual] DonorID: Donor ID Best_Rnk: Lowest rank of all peptides within the cluster Nclus: Number of peptides within the cluster (1 indicates singletons)
Here we find the 11 of the 21 (52%) proteins have an Average Spectral Count value beyond 3. In comparision, this is only the case for 2329 of the 21935 unique entries in the Single Step Epitope tag CRAPome database. This result thus strongly indicating that the identified proteins have a high propensity to be a contaminant.