MaxQuant

Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol, 2008, 26, pp 1367-72. Note that the paper has a large supplement containing in-depth descriptions of algorithms.

MaxQuant is a cutting-edge proteomics software that allows for the identification, quantification, and analysis of large-scale proteomics data. This user-friendly tool utilizes state-of-the-art algorithms and statistical models to provide accurate and reliable results. It is designed to handle complex data sets and can accommodate a wide range of experimental designs, including label-free and isobaric labeling approaches.

The software offers a wide range of features, including peptide and protein identification, quantification of label-free and labeled samples, protein quantification across multiple samples, and advanced statistical analysis. The software also supports a variety of data formats and integrates seamlessly with other popular proteomics software tools.

MaxQuant's user-friendly interface and powerful algorithms make it an indispensable tool for proteomics researchers. Whether you are performing targeted or exploratory analysis, MaxQuant provides accurate and reliable results that enable you to draw meaningful conclusions from your data. With MaxQuant, you can unlock the full potential of your proteomics data and accelerate your research.

The ProteomicsQC pipeline uses MaxQuant to process individual and independent ThermoFisher RAW files. To generate an input parameter file for the ProteomicsQC, a local installation of MaxQuant must be installed and setup with an example RAW files and the desired search parameters. Only one RAW file should be used to do so. Then the search parameters must be exported and can be uploaded to ProteomicsQC.