To investigate whether low input samples benefit from rescoring, we rescored a timsTOF SCP dataset. For detailed information on data acquisition, please refer to the original publication by Phulphagar et al. (PXD040740). In brief, HLA-I peptides were directly enriched from 1 million to 40 million A-375 cell equivalents by single shot injections on timsTOF SCP. Each sample was measured in technical triplicate (four technical replicates for the 40 million sample).
Individual spectrum peak files were searched against a compiled database consisting of the human reference proteome, common laboratory contaminants, curated small open reading frames (ORFs), and novel unannotated ORFs (nuORFs) supported by ribosomal profiling. All proposed PSMs by MaxQuant (version 2.0.3.1) were subsequently rescored using Oktoberfest (https://github.com/wilhelm-lab/oktoberfest) and the new timsTOF Prosit 2023 model. The results showed an average increase in identified HLA-I ligands across different cell input sizes, ranging from 1.3-fold at 1 million cell equivalents to 1.9-fold at 40 million cell equivalents. In addition, we were able to almost double the identifications of immunopeptides from unique nuORF source proteins, which hold the potential to serve as valuable targets for immunotherapy.
[doi:10.25345/C5NP1WV33]
[See
results attachment job
for details]
Keywords: timsTOF ; Prosit ; Immunopeptidomics
Number of Files: | |
Total Size: | |
Experimental Design | |
Conditions:
|
|
Biological Replicates:
|
|
Technical Replicates:
|
|
Identification Results | |
Proteins (Human, Remapped):
|
|
Proteins (Reported):
|
|
Peptides:
|
|
Variant Peptides:
|
|
PSMs:
|
|
Quantification Results | |
Differential Proteins:
|
|
Quantified Proteins:
|
|
Browse Reanalysis Files | |
FTP Download Link (click to copy):
|