MOTIVATION: The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools or algorithms exist, very few consider the importance of combining, in a unique software environment, efficient processing algorithms and a data management system to process and curate hundreds of datasets associated with a single proteomics study. RESULTS: Here, we present Proline, a robust software suite for analysis of MS-based proteomics data, which collects, processes and allows visualization and publication of proteomics datasets. We illustrate its ease of use for various steps in the validation and quantification workflow, its data curation capabilities and its computational efficiency. The DDA label-free quantification workflow efficiency was assessed by comparing results obtained with Proline to those obtained with a widely used software using a spiked-in sample. This assessment demonstrated Proline's ability to provide high quantification accuracy in a user-friendly interface for datasets of any size. AVAILABILITY AND IMPLEMENTATION: Proline is available for Windows and Linux under CECILL open-source license. It can be deployed in client-server mode or in standalone mode at http://proline.profiproteomics.fr/#downloads. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

SUMMARY: VisioProt-MS is designed to summarize and analyze intact protein and top-down proteomics data. It plots the molecular weights of eluting proteins as a function of their retention time, thereby allowing inspection of runs from liquid chromatography coupled to mass spectrometry (LC-MS). It also overlays MS/MS identification results. VisioProt-MS is compatible with outputs from many different top-down dedicated software. To our knowledge, this is the only open source standalone application that allows the dynamic comparison of several MS files, a prerequisite for comparative analysis of different biological conditions. With its dynamic rendering, this user-friendly web application facilitates inspection, comparison and export of publication quality 2 D maps from deconvoluted LC-MS run(s) and top-down proteomics data. AVAILABILITY AND IMPLEMENTATION: The Shiny-based web application VisioProt-MS is suitable for non-R users. It can be found at https://masstools.ipbs.fr/mstools/visioprot-ms/ and the corresponding scripts are downloadable at https://github.com/mlocardpaulet/VisioProt-MS. It is governed by the CeCILL license (http://www.cecill.info).