README.md

In shaowenguang/PIN: Proteome Integrity Number

PIN

Installation of development version from GitHub

$ library(devtools)
$ install_github("shaowenguang/PIN")

Installation of release version from CRAN

Needs to wait for the official release...

$ install.packages("PIN")

Description

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.

Usage

First: to load the package.

$ library(PIN)

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.

$ perform_PIN_analysis(peptides)

Outputs

| 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 |

Todos

License

shaowenguang/PIN documentation built on May 23, 2019, 4:25 p.m.