Speeding up the screening of steroids in urine: development of a user-friendly library

Sample Preparation Techniques for Growth-Promoting Agents in Various Mammalian Specimen Preceding MS-Analytics

The misuse of growth-promoting drugs such as beta-2 agonists and steroids is a known problem in farming and sports competitions. Prior to the analysis of biological samples via liquid chromatography (LC)-mass spectrometry (MS) or gas chromatography (GC)-MS, sufficient sample preparation is required to reliably identify or determine the residues of drugs. In practice, broad screening methods are often used to save time and analyze as many compounds as possible. This review was conceptualized to analyze the literature from 2018 until October 2023 for sample preparation procedures applied to animal specimens before LC- or GC-MS analysis. The animals were either used in farming or sports. In the present review, solid phase extraction (SPE) was observed as the dominant sample clean-up technique for beta-2 agonists and steroids, followed by protein precipitation. For the extraction of beta-2 agonists, mixed-mode cation exchanger-based SPE phases were preferably applied, while for the steroids, various types of SPE materials were reported. Furthermore, dispersive SPE-based QuEChERs were utilized. Combinatory use of SPE and liquid-liquid extraction (LLE) was observed to cover further drug classes in addition to beta-2 agonists in broader screening methods.

Sterolomics in biology, biochemistry, medicine

In mammalian systems "sterolomics" can be regarded as the quantitative or semi-quantitative profiling of all metabolites derived from cholesterol and its cyclic precursors. The system can be further complicated by metabolites derived from ingested phytosterols or pharmaceuticals, but this is beyond the scope of this article. "Sterolomics" can be performed on either an unbiased global format, or more usually, exploiting a targeted format. Here we discuss the different mass spectrometry-based analytical techniques used in "sterolomics" giving specific examples in the context of neurodegenerative disease and for the diagnosis of inborn errors of metabolism. We pay particular attention to the profiling of cholesterol metabolites in the bile acid biosynthesis pathways, although the analytical techniques discussed are also appropriate for analysis of hormonal steroids.

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4s.

The Artificial Intelligence Workbench: a retrospective review

Last decade, biomedical and bioinformatics researchers have been demanding advanced and user-friendly applications for real use in practice. In this context, the Artificial Intelligence Workbench, an open-source Java desktop application framework for scientific software development, emerged with the goal of provid-ing support to both fundamental and applied research in the domain of transla-tional biomedicine and bioinformatics. AIBench automatically provides function-alities that are common to scientific applications, such as user parameter defini-tion, logging facilities, multi-threading execution, experiment repeatability, work-flow management, and fast user interface development, among others. Moreover, AIBench promotes a reusable component based architecture, which also allows assembling new applications by the reuse of libraries from existing projects or third-party software. Ten years have passed since the first release of AIBench, so it is time to look back and check if it has fulfilled the purposes for which it was conceived to and how it evolved over time.

Mass-Up: an all-in-one open software application for MALDI-TOF mass spectrometry knowledge discovery

BACKGROUND

Mass spectrometry is one of the most important techniques in the field of proteomics. MALDI-TOF mass spectrometry has become popular during the last decade due to its high speed and sensitivity for detecting proteins and peptides. MALDI-TOF-MS can be also used in combination with Machine Learning techniques and statistical methods for knowledge discovery. Although there are many software libraries and tools that can be combined for these kind of analysis, there is still a need for all-in-one solutions with graphical user-friendly interfaces and avoiding the need of programming skills.

RESULTS

Mass-Up, an open software multiplatform application for MALDI-TOF-MS knowledge discovery is herein presented. Mass-Up software allows data preprocessing, as well as subsequent analysis including (i) biomarker discovery, (ii) clustering, (iii) biclustering, (iv) three-dimensional PCA visualization and (v) classification of large sets of spectra data.

CONCLUSIONS

Mass-Up brings knowledge discovery within reach of MALDI-TOF-MS researchers. Mass-Up is distributed under license GPLv3 and it is open and free to all users at http://sing.ei.uvigo.es/mass-up.