MassIVE MSV000092631

Partial Public PXD044463

Digestion of protein substrates by 20S proteasomes

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Description

The proteasome is the central protease in generating peptide repertoires for antigen presentation on human leukocyte antigen class I (HLA-I). Proteasomes not only can catalyze peptide hydrolysis but are also capable of mediating transpeptidation, resulting in spliced peptides generation, a process known as proteasome-catalyzed peptide splicing (PCPS). Despite its immunological importance, it is still unclear what are the determinants of PCPS that favor transpeptidation over hydrolysis. Hence, we sought to characterize the processing of many protein substrates and their peptide products by using a simplistic in vitro antigen processing system and analyzed by mass spectrometry followed by a refined downstream data analysis pipeline. [doi:10.25345/C5X921V5S] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Mass Spectrometry ; antigen processing ; 20S proteasomes ; MHC-I presentation

Contact

Principal Investigators:
(in alphabetical order) 		Dr. Juliane Liepe, Max Planck Institute for Multidisciplinary Sciences, Germany
Michele Mishto, King's College London and the Francis Crick Institute, United Kingdom
Submitting User: waitucksoh

Publications

Wai Tuck Soh, Hanna P. Roetschke, John A. Cormican, Bei Fang Teo, Nyet Cheng Chiam, Monika Raabe, Ralf Pflanz, Fabian Henneberg, Stefan Becker, Ashwin Chari, Haiyan Liu, Henning Urlaub, Juliane Liepe & Michele Mishto.
Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing.
Soh, W.T., Roetschke, H.P., Cormican, J.A. et al. Protein degradation by human 20S proteasomes elucidates the interplay between peptide hydrolysis and splicing. Nat Commun 15, 1147 (2024). https://doi.org/10.1038/s41467-024-45339-3.

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Identification Results
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Quantification Results
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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

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

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

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

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

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

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Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

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Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

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

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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 dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.