MassIVE MSV000094661

Partial Public PXD051940

TermineR: extracting information on proteolytic processing from shotgun proteomics data

Description

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

Contact

Principal Investigators:
(in alphabetical order)
Prof. Oliver Schilling, Institute for Surgical Pathology, University Medical Center Freiburg, Germany
Submitting User: miguelcos
Number of Files:
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Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
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Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
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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.

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

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

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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.

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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.

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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.