IMMUNO RESOURCES

Search Page

1) Search Filters

Use the Search Filters to query peptides by Canonical / Non-Canonical, HLA Type, Genomic Event, HLA Allele, Gene Name, and Peptide Sequence. Click Apply (bottom-right) to run, and Reset (bottom-left) to clear all filters.

TIP. You can type a partial peptide sequence in Peptide Sequence to match prefixes or substrings, depending on your configuration.

2) Search Results

The Search Results panel shows peptides matching your filters. Use Download CSV to export the current list to your computer.

Peptide Sequence	Gene Name	HLA Type	Event	Tissue / Cell line	Disease	Canonical/Non-canonical	HLA Allele
IVDVKMVSGFIPLKP	A2M	HLA-Class I	PC	Ovary (Tissue)	Ovarian Cancer	Canonical	HLA-A03:01, HLA-A66:01, HLA-B07:02, HLA-B14:01, HLA-C07:02, HLA-C08:02

Below Download CSV, you’ll find toggle buttons to enable/disable per-column visualizations for Search Results — handy when you want to focus on specific attributes. To view PSM (Peptide-Spectrum Match) details for a peptide, click its row.

TIP. Export filtered results on the Search page using Download CSV.

Events Tab

Event abbreviations:

PC: Protein Coding
FS: Frameshift
ncRNA: Noncoding RNA
5'-UTR: 5' Untranslated Region
3'-UTR: 3' Untranslated Region
IR: Intron Retention
IGR: Intergenic Region
asRNA: Antisense RNA
AS: Alternative Splicing

Search filters and results overview — Search - Filtered peptide list

3) Navigating to Peptide Details

Clicking a peptide row opens the details page. The peptide’s PSM list is visualized; press the + button on a PSM row to expand and see more.

Navigate to peptide details — Search - List of all PSMs associated with the peptide

4) Details: MS / Sample / Genomic Information

The details page includes MS (spectrum), sample, and genomic information. Under Sample Information, RNA Resource and MS Resource link out to public repositories for raw files. The spectrum graph (bottom-left) visualizes the matching between the experimental and theoretical MS2 spectra for the peptide. The Binding Information panel (bottom-right) shows predicted HLA alleles and scores from three tools.

NOTE. Binder thresholds: netMHCpan ≤ 2.0, STMHCpan ≥ 0.5, TransPHLA ≥ 0.5.

5) JBrowse Genome View

The JBrowse panel visualizes the genomic locus. The region identified by pXg is highlighted in orange. Below, Total reads (all RNA-seq alignments) and Mapped reads (reads mapped to the peptide) tracks are shown. You can pan/zoom interactively, but note that the read tracks cover only the initially loaded range.

Details: spectrum, binding, and genome view — Search – PSM information including MS, Sample, and Genomic annotation

Browse Page

1) Quick Search & Row Navigation

In Browse, you can filter rows by typing a partial peptide sequence in the quick search box. Click a peptide row to see its PSM list and details. The subsequent steps mirror Search 3 and Search 4 above.

Browse page — Browse – scan through the dataset and open details with a row click.

Usage