Proline: an efficient and user-friendly software suite for large-scale proteomics
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 processi...
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| Published in | Bioinformatics Vol. 36; no. 10; pp. 3148 - 3155 |
|---|---|
| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.05.2020
Oxford University Press (OUP) |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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. |
|---|---|
| AbstractList | 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.
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.
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 data are available at Bioinformatics online. 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. 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.MOTIVATIONThe 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.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.RESULTSHere, 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.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.AVAILABILITY AND IMPLEMENTATIONProline 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 data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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. |
| Author | Hesse, Anne-Marie Bouyssié, David Burlet-Schiltz, Odile Garin, Jerome Rompais, Magali Carapito, Christine Couté, Yohann Cianférani, Sarah Kalaitzakis, Andrea Mouton-Barbosa, Emmanuelle Gonzalez de Peredo, Anne Romdhani, Aymen Burel, Alexandre Dupierris, Véronique Macron, Charlotte Menetrey, Jean-Philippe Poisat, Julie Bruley, Christophe |
| AuthorAffiliation | b3 Laboratoire de Spectrométrie de Masse BioOrganique , Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France b1 Institut de Pharmacologie et de Biologie Structurale (IPBS) , Université de Toulouse, CNRS, UPS, Toulouse, France b2 Université Grenoble Alpes , Inserm, CEA, IRIG, BGE, Grenoble 38000, France |
| AuthorAffiliation_xml | – name: b2 Université Grenoble Alpes , Inserm, CEA, IRIG, BGE, Grenoble 38000, France – name: b3 Laboratoire de Spectrométrie de Masse BioOrganique , Université de Strasbourg, CNRS, IPHC, Strasbourg 67087, UMR 7178, France – name: b1 Institut de Pharmacologie et de Biologie Structurale (IPBS) , Université de Toulouse, CNRS, UPS, Toulouse, France |
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| PublicationPlace_xml | – name: England |
| PublicationTitle | Bioinformatics |
| PublicationTitleAlternate | Bioinformatics |
| PublicationYear | 2020 |
| Publisher | Oxford University Press Oxford University Press (OUP) |
| Publisher_xml | – name: Oxford University Press – name: Oxford University Press (OUP) |
| References | Mann (2023013112032326100_btaa118-B13) 2013; 49 Mueller (2023013112032326100_btaa118-B14) 2008; 7 Nahnsen (2023013112032326100_btaa118-B15) 2013; 12 America (2023013112032326100_btaa118-B2) 2008; 8 Nesvizhskii (2023013112032326100_btaa118-B18) 2003; 75 Vizcaíno (2023013112032326100_btaa118-B25) 2014; 32 Vaudel (2023013112032326100_btaa118-B23) 2015; 33 Vizcaíno (2023013112032326100_btaa118-B24) 2009; 9 Choi (2023013112032326100_btaa118-B5) 2017; 16 Shteynberg (2023013112032326100_btaa118-B22) 2013; 12 Cox (2023013112032326100_btaa118-B6) 2008; 26 Rieckmann (2023013112032326100_btaa118-B20) 2017; 18 Cox (2023013112032326100_btaa118-B8) 2014; 13 Handy (2023013112032326100_btaa118-B11) 2017; 12 Neuhauser (2023013112032326100_btaa118-B2225716) 2013 Savitski (2023013112032326100_btaa118-B21) 2011; 10 Doll (2023013112032326100_btaa118-B10) 2017; 8, 1469 Hesse (2023013112032326100_btaa118-B12) 2016; 15 Andreev (2023013112032326100_btaa118-B3) 2007; 6 Aebersold (2023013112032326100_btaa118-B1) 2016; 537 Bouyssié (2023013112032326100_btaa118-B4) 2015; 14 Deutsch (2023013112032326100_btaa118-B9) 2008; 33 Ramus (2023013112032326100_btaa118-B19) 2016; 132 Nesvizhskii (2023013112032326100_btaa118-B17) 2005; 4 |
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Motivation
The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results.... The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results. Although many tools... Motivation: The proteomics field requires the production and publication of reliable mass spectrometry-based identification and quantification results.... |
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| SubjectTerms | Biochemistry, Molecular Biology Computer Science Genomics Life Sciences Original Papers |
| Title | Proline: an efficient and user-friendly software suite for large-scale proteomics |
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