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.
One of the major bottlenecks in the proteomics field today resides in the computational interpretation of the massive data generated by the latest generation of high-throughput MS instruments. MS/MS datasets are constantly increasing in size and complexity and it becomes challenging to comprehensively process such huge datasets and afterwards deduce most relevant biological information. The Mass Spectrometry Data Analysis (MSDA, https://msda.unistra.fr) online software suite provides a series of modules for in-depth MS/MS data analysis. It includes a custom databases generation toolbox, modules for filtering and extracting high-quality spectra, for running high-performance database and de novo searches, and for extracting modified peptides spectra and functional annotations. Additionally, MSDA enables running the most computationally intensive steps, namely database and de novo searches, on a computer grid thus providing a net time gain of up to 99% for data processing.
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