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Proline: an efficient and user-friendly software suite for large-scale proteomics
- Source :
- Bioinformatics, Bioinformatics, 2020, 36 (10), pp.3148-3155. ⟨10.1093/bioinformatics/btaa118⟩, Bioinformatics, Oxford University Press (OUP), 2020, 36 (10), pp.3148-3155. ⟨10.1093/bioinformatics/btaa118⟩
- Publication Year :
- 2020
- Publisher :
- HAL CCSD, 2020.
-
Abstract
- 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.
- Subjects :
- Statistics and Probability
Proteomics
Proline
Computer science
Data management
Interface (computing)
Gene Expression
[INFO] Computer Science [cs]
Mass spectrometry
computer.software_genre
Biochemistry
Mass Spectrometry
03 medical and health sciences
0302 clinical medicine
Software
[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
[INFO]Computer Science [cs]
Molecular Biology
030304 developmental biology
0303 health sciences
Software suite
Data curation
business.industry
Original Papers
Computer Science Applications
Visualization
Computational Mathematics
Workflow
Computational Theory and Mathematics
[SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN]
Data mining
business
computer
030217 neurology & neurosurgery
Algorithms
Subjects
Details
- Language :
- English
- ISSN :
- 13674803 and 13674811
- Database :
- OpenAIRE
- Journal :
- Bioinformatics, Bioinformatics, 2020, 36 (10), pp.3148-3155. ⟨10.1093/bioinformatics/btaa118⟩, Bioinformatics, Oxford University Press (OUP), 2020, 36 (10), pp.3148-3155. ⟨10.1093/bioinformatics/btaa118⟩
- Accession number :
- edsair.doi.dedup.....976f639cc6b39bbf0dc78b59cde88798