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Fragpipe & MSFragger

FragPipe is a comprehensive computational platform designed for the analysis of mass spectrometry-based proteomics data. The software is basically a graphical user interface that integrates several very potent analysis tools (MSFRagger, DIA-NN, IonQuant, Philosopher). The scope of the software is comparable to MaxQuant. We like the software particularly for the integration of MSFragger and the possibility to do open searches. Another plus: the software is super fast. 

Mascot

Industry standard for matching peptide spectra to a database. We like to use Mascot for QC and for the identification of unexpected modifications (error tolerant search).

MaxQuant

MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. The software is easy to use and can handle as many experiments as you like in one sitting. It has a couple of features, which makes it ideally suited for our purposes. Just to name a few: label-free quantification, match-between-runs, automatic recalibration of masses and retention times … drawback: it is very slow.

MeroX

MeroX is a software for the identification of cross-linked peptides. The nice thing about MeroX … you can program it to analyze almost any kind of cross-linker be that cleavable or non-cleavable.

MetaMorpheus

MetaMorpheus is a bottom-up proteomics database search software with integrated post-translational modification (PTM) discovery capability. We use the software primarily for the analysis of cross-likning experiments. 

Perseus

The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data. We use the software primarily for the statistical evaluation of MaxQuant and MSFragger results.

Proteome Discoverer

PD is a framework for the analysis of mass spectrometry based data. It integrates several search engines (MS Amanda, Sequest HT, Mascot) and is also able to do MS1 based quantification (Minora Node). We use it primarily for QC and for the analysis of CL-MS experiments with cleavable cross-linkers (XlinkX).

ProXL Server

The Proxl Server is a free, publicly-available, and fully functional server where you may upload, analyze, and share your protein cross-linking data. We installed this server in-house and use it extensively to share data from cross-linking experiments with our collaborators. 

Skyline

Very potent software tool that can handle data from SRM/MRM, PRM, DIA/SWATH and DDA experiments. We currently use Skyline for the analysis of AQUA experiments and for QC.

XlinkX

This is a software tool for the analysis of cross linking experiments. It works best with cleavable cross-linkers. It is integrated in Proteome Discoverer.