$ library(devtools) $ install_github("shaowenguang/PIN")
Needs to wait for the official release...
This document describes a computational method, namely PIN (proteome integrity number), to assess a quantitative measure of protein stability directly from bottom-up proteomic datasets.
By quantifying the relative abundance of semi-tryptic peptides (i.e. the likely products of protein degradation), an individual protein integrity score (iPIS) was first calculated for each measured protein. A per-sample PIN was then derived to summarize a proteome-wide measurement indicating the level of protein degradation.
This method has been used in a clinical cohort of prostate tissue samples, in which degradation is usually inevitable during the sample preparation.
First: to load the package.
Second: to extract the peptide list, together with their quantities, from OpenSWATH outputs.
$ peptides <- generate_peptide_table(search_results="./openswath_search_results.tsv", sample_annotation="./sample_annotation_table", sptxt="./spectral_library.sptxt")
Third: to perform PIN analysis.
| File Name | Description | | ------ | ------ | | PIN.tsv | PINs and their p-values, for each sample | | iPIS.tsv | individual Protein Integrity Score, for each individual proteins | | lib_peptide.tsv | a temp file that records the assay library information |
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