miguelcos/fragterminomics

Annotation and processing of peptides from FragPipe search results

Fragterminomics

A data analysis approach for extracting information related to proteolytic activity (N-terminomics) from shotgun proteomics data. Some of the processing functions were optimzed for FragPipe search results.

Installation

You can install the development version of Fragterminomics by typing:

devtools::install_github("MiguelCos/Fragterminomics")

Usability example:

You can find an use case of this workflow, together with experimental and data analysis description in the following link here

fragterminomics's Issues

annotate_peptides function does not show error for mismatching identifiers

The for loop in the function will stop if it doesn't find a match between protein identifiers and the fasta file.

It doesn't show an error if this is the case. This should be corrected.

The annotate_peptides function generate character columns for the positional info of the peptides

The peptide location columns need to be numeric.

annotate_peptides function does not properly label specificity as 'unspecific'.

The function categorize_nterm needs to be checked

A progress bar would be useful for the annotate_peptides function

enrichplot::dotplot does not accept ggplot aesthetics in 4.1.0

Check that

annotate_peptides and annotate_nterm functions - need correction

The N-terminal or C-terminal semi-specific peptides (comining from proteolysis) need to be better annotated.

Add info in the tutorial regarding the required packages to reproduce the analysis

function nterm_annot needs to work with the psm.tsv file instead of the peptide.tsv

feature_fdr_correction function only working with Fragpipe-specific columns

The function needs to be generalized so it wont depend on the presence of an index column in the features table

annotate_nterm function would not work with identified TMT modification is 304.2071

New feature: implement heatmap visualization of amino acid counts

We need a function to quickly process and visualize the amino acid usage around the differentially abundant cleavage areas.

Set a general `theme` for all plots

To decreased the amount of code and consistency, set the general ggplot theme for all plots in the reproducible reports at the beggining of the 'tutorial' without echoing.

feature_fdr_correction function