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.
[doi:10.25345/C50P0X26C]
[dataset license: CC0 1.0 Universal (CC0 1.0)]
Keywords: proteolysis ; terminomics ; data processing ; polycystic kidney disease
Principal Investigators: (in alphabetical order) |
Prof. Oliver Schilling, Institute for Surgical Pathology, University Medical Center Freiburg, Germany |
Submitting User: | miguelcos |
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Owner | Reanalyses | |
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Experimental Design | ||
Conditions:
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Biological Replicates:
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Technical Replicates:
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Identification Results | ||
Proteins (Human, Remapped):
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Proteins (Reported):
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Peptides:
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Variant Peptides:
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PSMs:
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Quantification Results | ||
Differential Proteins:
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Quantified Proteins:
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Browse Dataset Files | |
FTP Download Link (click to copy):
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