Abstract
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.
Highlights
Mass spectrometry (MS)-based proteomics has become an increasingly prominent field in the last decade, allowing the identification, quantification and characterization of peptides and proteins in biological samples [1,2]
Previous reviews addressed the advances in the field of software tools and bioinformatics applications for proteomics MS experiments [18,19,21,22,23], but open-source frameworks and libraries were not evaluated in detail
The framework contains a set of components such as: (i) the mzGraph Browser library, for visualizing MS spectra, chromatograms and MS/MS spectrum annotation; (ii) the QualityChart library provides a number of charts for performing a quick quality assessment of the MS experiments; (iii) several application programming interface (API) for parsing standard data proteomics formats such as mzML, mzIdentML, mzTab and PRoteomics IDEntifications (PRIDE) XML; (iv) the XXIndex library enables the fast indexing of large XML files; (v) the PRIDE Utilities library contains classes with some functionality shared by many of the PRIDE related tools; and (vi) the PRIDE core library, for general data management
Summary
Mass spectrometry (MS)-based proteomics has become an increasingly prominent field in the last decade, allowing the identification, quantification and characterization of peptides and proteins in biological samples [1,2]. There is an increasing demand for high-performance bioinformatics solutions that can help to address the various data processing and data interpretation challenges in the field [18,19,20] While these tools can vary substantially, a basic set of features can be shared between many of them. The number of available open-source software libraries and frameworks has increased significantly in recent years These platforms provide common software infrastructures, features and algorithms that can help in the development of new applications and tools. Previous reviews addressed the advances in the field of software tools and bioinformatics applications for proteomics MS experiments [18,19,21,22,23], but open-source frameworks and libraries were not evaluated in detail. We will mention some tools that are specific for targeted proteomics approaches (SRM)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
