Base Classes and Functions for Mass Spectrometry and Proteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

RawTools is an open-source and freely available package designed to perform scan data parsing and quantification, and quality control analysis of Thermo Orbitrap raw mass spectrometer files from data-dependent acquisition experiments.

Ursgal - universal Python module combining common bottom-up proteomics tools for large-scale analysis

Library for mass spectrometry projects

Examples of TMT data analyses using R. Links to notebooks and repositories. Also a few spectral counting analyses.

An exploration of internal reference scaling (IRS) normalization in isobaric tagging proteomics experiments.

A unifying bioinformatics framework for organelle proteomics

Proteomic Data Manager is a Web-based integrated plateform to combine data storage/backup, process and visualization of MS-based Proteomics data.

DeltaMass: view and interrogate open proteomics search data

MaxQuant and Perseus Bug Reporting

Protein Cluster Quant is a Java software for the analysis of complex proteomics samples (quantitative or not). It helps to reduce the redundancy of the peptide-to-protein relationship and to visualize the results in a bipartite network (Cytoscape).

Molecular biology experiments, mass spectrometry-based proteomics, and reproducible data analysis in R

PACOM (Proteomics Assay COMparator) is a Java stand alone tool for visualize and compare large proteomics datasets

Simple workflows for the isobaric-labeling proteomic data from Proteome Discoverer with ANOVA, t-testing, DEqMS/limma and annotation via fgsea

Feature extraction from .pdb files

ProXI: Schema definitions for the Proteomics eXpression Interface

Github repository for nanoSPLITS manuscript data and R scripts

Tool to automatically upload result file to Proteomics Data Manager (mainly for MS based proteomics)

Smart, light, easy and robust Thermo RAW files backup program