Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

Del proteoma humano a la medicina transfuncional personalizada / From human proteome to cross-functional personalized medicine

Actualmente, se ha dado una revolución tecnológica en la medicina personalizada. En esta nueva fase de la proteómica, la prioridad es la apreciación de los valores y virtudes del ser humano. Por esto, no debemos olvidar que las dos razones principales de la medicina personalizada son el reconocimiento de la dignidad de la persona y el diagnóstico y el tratamiento hecho a la medida para cada paciente, se deben tomar en cuenta el trasfondo social y el entorno ambiental a la par de los genes y las proteínas.

Personalized medicine has led the technological revolution in proteomics into a new phase where appreciation of the values and virtues of the human being are paramount. Thus we must not forget that the two main reason for personalized medicine are both acknowledgment of the person's dignity and a tailored diagnosis and treatment of each patient, taking into account not only genes and proteins but also the person's social background and environment.