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

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

DeltaMass: view and interrogate open proteomics search data

Github repository for nanoSPLITS manuscript data and R scripts

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

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