MassIVE Reanalysis - RMSV000000693.1

RPXD043845.1

PSM rescoring boosts the identification rate of relevant immunopeptides in low-input samples

Description

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

Reanalyzed Datasets

  • MSV000091456 : Sensitive, high-throughput single-shot HLA-I and HLA-II immunopeptidomics with improved coverage using data dependent parallel accumulation-serial fragmentation mass spectrometry
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Experimental Design
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Identification Results
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Quantification Results
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Browse Reanalysis Files
 
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Species

Instrument

Modifications
Number of distinct conditions analyzed in this reanalysis.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates in this reanalysis.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates in this reanalysis.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed in files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported in this reanalysis.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified in this reanalysis.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this reanalysis.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison in this reanalysis.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this reanalysis.

"N/A" means no results of this type were submitted.