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ProSightPC

Software suit primarily used to analyze Top Down Proteomics experiments.

Delta2D

Delta2D is a very intuitive software that we use to analyze and compare 2D Gel electrophoresis gels. It is especially powerful when it comes to analyze 2D DIGE experiments.

MaxQuant

This is our analysis workhorse. 90% of our projects are analyzed with this software. 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 …

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.

Perseus

Analysis software primarily used for the statistical evaluation of MaxQuant results.

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.

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.

Proteome Discoverer

PD is a framework for the analysis of mass spectrometry based data. It integrates several search engines (MS Amanda, Sequest HT, MS Fragger, 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).

Protein deconvolution

This software can deconvolute MS sepctra of large scale protein complexes. We use it primarily in native MS experiments.

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).