Peptide Length Distribution
The above histogram demonstrates the peptide length distribution of the sample(s) uploaded.
Peptides labelled with #CONTAM or #DECOY in the accession column have been filtered out.
Peptides with the length between 5 to 30 residues have been selected. The error bar in case of replicates
represents the standard deviation of the number of specifc n-mers across replicates. The switch button above can be used to switch between the distributions presented in percentage and absolute numbers. Click the tool icons at the top right corner
for more operations.
Peptide Overlap (Click bars to download)
The UpSet plot depicts peptides after pre-processing: peptides labeled with #CONTAM or #DECOY are removed, as well as those with post-translational modifications (PTMs) and any resulting duplicates. For class I analysis, 8–14-mers are shown; for class II, 12–20-mers are shown.
📥 Click any bar to download a list of overlapping peptides (as a .txt file).
Peptide consensus binding motif analysis
The Seq2Logo depicts peptides after pre-processing (Peptides labelled with #CONTAM or #DECOY peptides removed, PTM and resulting duplicates removed). For class I analysis, either 8-mers or 9-mers are used based on the user's choice. Class II analysis uses 9-mer cores predicted by netMHCIIpan-4.3.
Peptide sequence analysis
Liver
Skin
Skin_Set1_DDA
Spleen
Spleen_Set1_DDA
Gibbs Clustering has been applied to peptides after removal of peptides labelled as #CONTAM or #DECOY, PTMs and resulting duplicates. For class I based on 8-14-mers, for class II based on 12-20-mers (duplicates removed). Each logo is labeled with the predicted allele and PCC (Pearson Correlation Coefficient) value, as determined by MHC-TP.
MHC-TP (MHC Typing Prediction)
Spleen
Liver
Skin
A novel algorithm, MHC-TP, predict MHC I alleles based on peptide clustering results, allowing in silico MHC typing of datasets, where genetic MHC typing is unavailable, ethically restricted, or cost-prohibitive for large-scale datasets.
Peptide-HLA binding affinity prediction
Binding prediction has been applied to a peptide list after removal of eptides labelled as #CONTAM or #DECOY, PTMs (For e.g., “A[+28.03]TFGVDESNAK” or “A(+28.03)TFGVDESNAK” will be treated as “ATFGVDESNAK”) and resulting duplicates. For class I based on 8-14-mers were used as input whereas for class II 12-20-mers were used. Seq2Logos are generated based on 9-mer cores (duplicates removed) predicted by binding prediction tools.
Download data files used to generate report (ZIP) Download binders
Spleen
| Alleles | MHCflurry | MixMHCpred | NetMHCpan | Majority Voted |
|---|---|---|---|---|
| H-2Db |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
| H-2Kb |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
Spleen_Set1_DDA |
Liver
| Alleles | MHCflurry | MixMHCpred | NetMHCpan | Majority Voted |
|---|---|---|---|---|
| H-2Db |
Liver_Set1_DDA |
Liver_Set1_DDA |
Liver_Set1_DDA |
Liver_Set1_DDA |
| H-2Kb |
Liver_Set1_DDA |
Liver_Set1_DDA |
Liver_Set1_DDA |
Liver_Set1_DDA |
Skin
| Alleles | MHCflurry | MixMHCpred | NetMHCpan | Majority Voted |
|---|---|---|---|---|
| H-2Db |
Skin_Set1_DDA |
Skin_Set1_DDA |
Skin_Set1_DDA |
Skin_Set1_DDA |
| H-2Kb |
Skin_Set1_DDA |
Skin_Set1_DDA |
Skin_Set1_DDA |
Skin_Set1_DDA |
Above table for each uploaded sample contains the information for predicted binders for each selected allele. The information is presented for every combination of alleles vs prediction tools. The information about binders is stored in csv files which can be downloaded by clicking the specific icon. Among others, the csv file contains three columns including 'Peptide', 'Binding Level' and 'Control'. The 'Peptide' column contains the binder sequence. The 'Binding Level' column demonstrates the binder type (i.e., a strong or weak binder). And the 'Control' column specifies whether the peptide is also present in the control group, if uploaded. The binders in the downloadable csv files are sorted by their predicted binding affinity.
Binding motif
download