protrusionproteome is a package that contains a number of functions to perform basic analysis of TMT-labelled samples (cell bodies and protrusions) for proteomic experiments published by Dermit et al 2020. Protein, peptide and evidence data output of MaxQuant is contained within the package. Data is handled as SummarizedExperiment object and functions for filtering, log2 transformations, calculating TMT ratios and median substation are included. Vizualization tools for QC checks of protrusion purification efficiency, protease efficiency and TMT incorporation are provided. It is also includes tools for statistical testing of significantly enriched protein categories in cell protrusions.

### Install

Once installed, load the package by writing in the console

library(protrusionproteome)

### Datasets for analysis

Mass-spectrometry derived TMT-datasets available in protrusionproteome are:

Data Description
prot.raw TMT quantitative proteomics analysis of protrusions and cells bodies of MDA-MB231 cells collected after 0.5, 1, 2, 4, & 8 hrs post protrusion induction (proteinGroups.txt)
peptides.raw TMT quantitative peptide analysis of protrusions and cells bodies of MDA-MB231 cells collected after 0.5, 1, 2, 4, & 8 hrs post protrusion induction (peptides.txt)
evidence.raw Information about the identified peptides for TMT quantitative peptide analysis of protrusions and cells bodies of MDA-MB231 cells collected after 0.5, 1, 2, 4, & 8 hrs post protrusion induction (evidence.txt)