Python Package for the downstream analysis of mass-spectrometry-based proteomics data

A Quality Control (QC) pipeline for Proteomics (PTX) results generated by MaxQuant

SDRF official validator and converts SDRF to pipeline configuration files

amica: an interactive and user-friendly web-based platform for the analysis of proteomics data

R package for easy interop between Perseus and R

Package to analyze Mass Spec Data

Integration between Perseus and Python

Enables working with external scripts and tools from within Perseus

Functionality for processing and analysing HeLa data quality control (QC) and maintenance (MNT) samples processed by MaxQuant

R package and Shiny app for the dowstream analysis of quantitative proteomic data

Quality Control Pipeline Server for Large-Cohort Quantitative Proteomics (TMT)

The hero we all need to defeat the kraken that is Go module dependency graphs

Compares PAW and MQ for a 7-channel TMT experiment; compares edgeR to two-sample t-test

Tools for preprocessing and normalizing results of MaxQuant experiments and their respective controls from a run by normalizing data from the output peptides.txt file.

Developing mouse lens done with MQ

R package that visualizes MaxQuant output of activity-based protein profiling experiments.

Automated Proteomics quality control package

R-script to check incorporation level of heavy SILAC amino acids

Reanalysis of Phaeodactylum tricornutum nitrogen-starvation proteome (PRIDE PXD033328, MaxQuant LFQ): cleaning + Perseus imputation, PCA/PLS-DA, differential proteins, on/off switch theme. Full R.

A lightweight PowerShell 7 scheduler for running multiple MaxQuant jobs in parallel on Windows, using a queue-based submission model, CPU affinity, and robust success/failure classification.