The application for mass spectrometry perfectionists with deadlines. MSQuant is a high-level application that encourages manual inspection of mass spectrometry data and at the same enables one automation.

What is MSQuant?

MSQuant is a tool for quantitative proteomics/mass spectrometry and processes spectra and LC runs to find quantitative information about proteins and peptides. Though automated it also allows manual inspection and change.

Developed and used over many years by the CEBI research group at University of Southern Denmark (SDU), MSQuant was designed to handle two challenges: the intensive dynamics of changing requirements and the support for new mass spectrometers and the stringent requirements of the experienced mass spectrometrists. It lets you process data quickly.

MSQuant both focuses on automating as much as possible and at the same time allow fine-grained control of the processing.

When you're ready to process data, read the installation guide.

The MSQuant ecosystem


Quantitate isotope labelled samples. E.g. SILAC or N15.

Use quantitation modes with any number of SILAC dishes, e.g. double, triple and penta encoding.

Support of N15 quantitation (with the help of extra software).

Compute protein quantitation ratios (with standard deviation estimation).

Making sense of Mascot results

Scan Mascot result files, including the modifications.

Peptide identifications

Get much higher confidence by MS3 scoring.

Increase confidence in your peptide identifications by manual inspection of fragmentation patterns.

LC correlation

Correlate LC retention times across several LC runs/files.


Define your own modifications and quantitation modes.

Define your own ion series and associated rules. E.g. with -98 Da and -196 Da loss ion series if the peptide is phosphorylated.


Display of LC profiles.

Marking of fragment ions for identified peptides.

Inspect systematic and random precursor mass errors to optimise the Mascot mass tolerance.

It is open and allow you to publish!

Do one-step documentation of peptide fragment spectra. E.g. required by MCP (Molecular & Cellular Proteomics, published by the American Society for Biochemistry and Molecular Biology publishes). Sample, early version. As PDF.

Export results to files, Open Office Calc, Excel and to databases.

Enjoy support of 3 different mass spectrometers: QSTAR; vendor MDS/Sciex; software package Analyst (.wiff files), LTQ-FT; vendor Thermo Electron/Finnigan; software package XCalibur (.raw files), Qtof; vendor Waters/Micromass; software package MassLynx (.dat files).

Work effectively - use the bundled helper applications

Retrieve large and small Mascot result files in a single very fast step with Mascot Result Launcher, prepare a large set of RAW files with DTASuperCharge and combine multiple raw files for a single Mascot using MGFcombiner.