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TermineR: extracting information on proteolytic processing from shotgun proteomics data

ABSTRACT: TermineR is a data analysis approach for the analysis of proteolytic processing from shotgun proteomics data, wrapped up in an R package currently available on Github. This repo contains raw data used to showcase this approach. We used a model of polycystic kidney disease (PKD) in mice to showcase this approach (KO -> PKD, vs WT). After protein extraction and reductive alkylation, samples were treated with TMT16plex for labelling of protein N-termini and cleavage events; then digested with trypsin. Measurements of this experiment were performed via Q-Exactive plus and searched using FragPipe. To evaluate the potential effect of protein extraction methods on the identification of cleavage events, we performed a pilot experiment with samples from the same PKD model. Tissues from 3 mice for each condition (KO or WT) were subjected to protein extraction using beat beating, and two sonication approaches. Then processed with trypsin and measured in label-free DIA model in a timsTOF flex and searched in Spectronaut.

INSTRUMENT(S): Q Exactive Plus, timsTOF fleX

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Prof. Oliver Schilling

PROVIDER: MSV000094661 | MassIVE | Thu May 02 04:37:00 BST 2024

SECONDARY ACCESSION(S): PXD051940

REPOSITORIES: MassIVE

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