Mass spectrometry, Protein Chemistry Facility
Research Institute of Molecular Pathology (IMP)
Institute of molecular biotechnology of the Austrian Academy of Sciences (IMBA)
Gregor Mendel Institute of Molecular Plant Biology (GMI)

PD-Nodes SimpatiQCo Software Tools Publications

SimpatiQCo About Download Installation Manual FAQ's

Publication: PDF

SimpatiQCo is a free software suite running on a local server for your research group or service facility. Through a web interface, it allows everyone to upload raw or wiff files (please see list of supported instruments below), stemming from a Thermo mass spectrometer or an ABI Sciex mass spectrometer respectively. The software will then analyse the raw file, extract data (Ion injection times, Scan times,...) and will also do a Mascot search if a Mascot-server is available. All data (from the raw file and search results) is then stored in a database, which is accessable through the web interface to view several values and graphs for the current run, but also to view long-term data over a time course. It is therefore easy to plot e.g. PSMs vs. retention time, to plot the lock mass deviation over a whole run, or to create a plot viewing the sequence coverage of a certain protein over a long time period.

Features: Supported and tested instruments:
Rawfile parameters and Mascot search: Rawfile parameters only (no Mascot search):

Basic start screen, showing the values and search results of a raw file after picking it from the list of previously uploaded files.

One of many detailded graphs obtained from the raw file data. Currently showing the injection times filterd for MS1 scans.

This graph concerns the mascot search results and shows the number of PSMs per minute of the run time.

Time course monitoring of certain parameters made easy.

Simpatiqco was invented and coded by Michael Mazanek, and inspired by Peter Pichler, Christoph Stingl, Werner Straube, Thomas Köcher and Karl Mechtler.

For technical questions please contact Florian Stanek (