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

A library for QC report based on MultiQC framework

Library for mass spectrometry projects

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

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

A unifying bioinformatics framework for organelle proteomics

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

MaxQuant and Perseus Bug Reporting

Github repository for nanoSPLITS manuscript data and R scripts

Feature extraction from .pdb files

DeltaMass: view and interrogate open proteomics search data

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

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).

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

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

ProXI: Schema definitions for the Proteomics eXpression Interface

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

List of online databases and resources for Mycobacterium Tuberculosis

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

Prediction of molecular subtypes of Breast Cancer based on TCGA proteomic data

A python-based program to optimise mass spectrometer collision energies for peptides in HDX-MS experiments

Custom analysis of in vitro circadian proteomics and phosphoproteomics using multiple sets of 10plex TMT with two genotypes

ASDParser

Mass spectrometry Perseus Data analysis

protGear is a package for protein microarray data processing just before the main analysis.

Data for proteomics data analysis course

Differential Abundance Analysis for Peptide Data