Mass spectrometry of proteins is a field that has evolved very dynamically over the last 25 years. New types of mass spectrometers, mainly MALDI-MS and LC-ESI-MS, have been developed and continuously improved with respect to sensitivity, mass accuracy and resolution.

This has revolutionized the field of protein research and enabled the development of biologics as drugs. In parallel, the amount of data that is produced by mass spectrometers has steadily increased. Completely new algorithms have been developed in order to cope with the increasing data size and complexity.

Today, even though many sophisticated algorithms are available on the market, bioinformatics expertise is still needed to fully interpret mass spectrometry data sets.

Protagen Protein Services GmbH offer a full range of bioinformatics-expertise that can be applied for:

Quality Control

Assessing the quality of a mass spectrometry data set or the results of a protein identification can be performed by experienced bioinformaticians. The quality can be determined concerning sample preparation (were the sample affected by this?), protein or peptide separation by HPLC (were there retention time shifts between the runs?), the mass spectrometry data themselves (Was the calibration OK, was the sensitivity good?) and the results of the protein identification (were all MS/MS data sets identified? Are there impurities that were detected/not detected so far).

Protein Identification

Bioinformatics expertise is needed to identify proteins, especially impurities at low concentrations, and to possibly quantify these. The quality of the protein identification results in terms of reliability and sequence coverage can vastly be improved by further bioinformatics analysis of data sets. As the usual software packages will only identify what is already known or assumed to be contained in a sample, many MS/MS data sets are not interpreted correctly or not at all. The application of in-house developed algorithms and bioinformatics expertise can improve the protein identification results.

Data Processing

Our ability to directly access the raw data of virtually any mass spectrometer allows us to process the data files with the best accuracy and to perform data processing that will enable us to gain the best possible insight from al mass spectrometry data sets.

Software Development

We have a long standing experience in the development of new algorithms and software packages for the life science industry. This goes far beyond the implementation of new algorithms for mass spectrometry and also encompasses e.g. the development of image analysis software, LIMS-systems or processing of chromatographic data.

Your contact for Bio-IT in Mass Spectrometry at Protagen Protein Services GmbH

burkhard fleckenstein

Dr Burkhard Fleckenstein

Director Operations 
Our business development team will be happy to assist you with your project.

Phone: +49 (0) 231 9742-6100