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López-Fernández H, Araújo JE, Jorge S, Glez-Peña D, Reboiro-Jato M, Santos HM, Fdez-Riverola F, Capelo JL. S2P: A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2018; 155:1-9. [PMID: 29512488 DOI: 10.1016/j.cmpb.2017.11.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 06/08/2023]
Abstract
BACKGROUND AND OBJECTIVE 2D-gel electrophoresis is widely used in combination with MALDI-TOF mass spectrometry in order to analyze the proteome of biological samples. For instance, it can be used to discover proteins that are differentially expressed between two groups (e.g. two disease conditions, case vs. control, etc.) thus obtaining a set of potential biomarkers. This procedure requires a great deal of data processing in order to prepare data for analysis or to merge and integrate data from different sources. This kind of work is usually done manually (e.g. copying and pasting data into spreadsheet files), which is highly time consuming and distracts the researcher from other important, core tasks. Moreover, engaging in a repetitive process in a non-automated, handling-based manner is prone to error, thus threatening reliability and reproducibility. The objective of this paper is to present S2P, an open source software to overcome these drawbacks. METHODS S2P is implemented in Java on top of the AIBench framework, and relies on well-established open source libraries to accomplish different tasks. RESULTS S2P is an AIBench based desktop multiplatform application, specifically aimed to process 2D-gel and MALDI-mass spectrometry protein identification-based data in a computer-aided, reproducible manner. Different case studies are presented in order to show the usefulness of S2P. CONCLUSIONS S2P is open source and free to all users at http://www.sing-group.org/s2p. Through its user-friendly GUI interface, S2P dramatically reduces the time that researchers need to invest in order to prepare data for analysis.
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Affiliation(s)
- Hugo López-Fernández
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain; UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal.
| | - José E Araújo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Susana Jorge
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Daniel Glez-Peña
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Miguel Reboiro-Jato
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - Hugo M Santos
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Florentino Fdez-Riverola
- ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, Universidad de Vigo, 32004 Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
| | - José L Capelo
- UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Portugal; ProteoMass Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
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