Wissenschaftsmanagement auf Knopfdruck! Funktioniert das? Die Hochschule Weihenstephan-Triesdorf (HSWT) hat es vor über 10 Jahren gewagt, mit Weih.FIS ein eigenes System zu entwickeln, das über die Anforderungen eines reinen Forschungsinformationssystems (FIS) hinausgeht. Weih.FIS ist das Herz einer zentralen Wissenschaftsmanagementstruktur, in der digitale Workflows, Außendarstellung, Controlling, Steuerung und Strategie aus einem einzelnen System heraus erfolgen. In der täglichen Praxis erprobt, konnten trotz begrenzter Personalkapazitäten im Wissenschaftsmanagement erhebliche Zeit- und Ressourceneinsparungen umgesetzt und schlanke Prozesse für die gesamte Hochschule definiert werden. Die HSWT hat einen pragmatischen Weg beschritten, der mit der Implementierung eines Forschungsinformationssystems begann und als Ziel ein umfassendes Wissenschaftsmanagementsystem (WMS) hat.

(Bio)Informatics plays a major role in (prote)omic research experiments and applications. Analysis of an entire proteome including protein identification, protein quantification, detecting biological pathways, metabolite identification and others is not possible without software solutions for analyzing the resulting huge data sets. In the last decade plenty of software-tools, -platforms and databases have been developed by vendors of analytical hardware, as well as by freeware developers and the open source software community. Some of these software packages are very much specialized for one (omic) topic, as for example genomics, proteomics, interactomics or metabolomics. Other software tools and platforms can be applied in a more general manner, e.g. for generating workflows, or performing data conversion and data management, or statistics. Nowadays the main problem is not to find out a way, how to analyze the experimental data, but to identify the most suitable software for this purpose in the vast software-landscape. This review focuses on the following issue: How complex is the link between biology, analysis and (bio) informatics, and how complex is the variety of software tools to be used for scientific investigations, starting from microorganisms up to the detection of a proteome. Thereby the main emphasis is on the variety in software for (LC) MS(/MS) proteomics. In the World Wide Web sites like ExPASy show extensive lists of proteomics software, leaving it to the user to identify which software actually serves their purposes. First we consider the huge variability of software in the field of proteomics research. Then we take a closer look on the variability of MS data and the incompatibilities of software tools with respect to that. We give an overview over commonly used software technologies and finally end up with the question, whether open source software would not add more value to this field.

Data evaluation of mass spectrometric raw data is an essential step to obtain high-quality results. In our days an exorbitant amount of raw data are produced in analytical (bio)chemistry due to the utilization of sophisticated experimental setups. The recently published free software Achroma has been developed to overcome increasing data processing challenges by providing the possibility of a comprehensive data analysis (http://openmasp.hswt.de/pages/project/achroma.php). To illustrate (a-)typical data evaluation, an online coupled continuous flow system hyphenated with mass spectrometric detection was applied to investigate enzymatic activity changes in the presence of regulatory molecules and alternative substrates. The extended software strategy, the processing as well as evaluation of data is presented in detail based on enzymatic assays of intestinal alkaline phosphatase (iAP) and acetylcholine esterase (AChE). Different Achroma data evaluation modules enabled a high quality analysis. This included the elucidation of enzymatic substrate preferences by means of the calculation of negative and positive peak areas as well as the identification of an inhibitory molecule by comparing different mass spectra with regard to their overall composition. The possibility of an automatically performed validity control to monitor the systems robustness furthermore emphasized the usefulness of Achroma software regarding its applicability in the area of 'functional proteomics' data handling.