Peptide correlation analysis (PeCorA)

PeCorA is short for "Peptide Correlation Analysis", which is an R package that enables detection of discordant peptide quantities in shotgun proteomics data. The package also contains a number of published proteomics datasets processed with different processing tools to demonstrate the workflow.

Please find the relevant preprint here: https://doi.org/10.1101/2020.08.21.261818

Install

You can install PeCorA from github downloading the package by cloning the repository.

$ git clone https://github.com/jessegmeyerlab/PeCorA.git

$ R CMD INSTALL PeCorA-master

Alternatively you can install PeCorA directly from R using devtools:

library(devtools)
install_github("jessegmeyerlab/PeCorA")

Or you can installPeCorA from CRAN by typing in R: install.packages(“PeCorA”)

Once installed, load the package by writing in the console

library(PeCorA)

Available datasets

Currently, there are three datasets available in PeCorA.

Data	Description
PeCorA_noZ	Primary mouse microglia dataset (PXD014466)
input.dda.iprg.pg	BRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of Differentially Abundant Proteins in Label-Free Quantitative LC-MS/MS Experiments
Covid_peptides	Large-scale proteomic Analysis of COVID-19 Severity

Loading data

Data available in the package is loaded into the R session using the load function; for instance, to get the DDA iPRG data from Choi et al 2017:

data("input.dda.iprg.pg")

To get more information about a dataset, see its manual page.

?input.dda.iprg.pg

How to use

PeCorA requires a filename.csv file containing table in long format of peptides, their quantities, and the proteins they belong to. This file must at least contain the following columns (check spelling and letter case):

“Condition” - group labels of the conditions. Can be more than 2 but must be at least 2. “Peptide.Modified.Sequence” - peptide sequence including any modifications “BioReplicate” - numbering for biological replicates “Protein” - protein membership for each peptide

You may need to transform your data into PeCorA-ready format. For example ransform peptides.txt output of MaxQuant into t use function import_preprocessed_for_PeCorA.

Functions

The main function of the package is called PeCorA, which fits a linear model with interaction between peptides and biological treatment groups.

Vignette

See Vignette for complete workflow.

Contact

If you have any questions or suggestions please contact us:

Maria Dermit : maria.dermit at qmul.ac.uk

Jesse Meyer: jesmeyer at mcw.edu