TY - JOUR
T1 - S2P
T2 - A software tool to quickly carry out reproducible biomedical research projects involving 2D-gel and MALDI-TOF MS protein data
AU - López-Fernández, Hugo
AU - Jorge, Susana
AU - Araújo, José E.
AU - Glez-Peña, Daniel
AU - Reboiro-Jato, Miguel
AU - Santos, Hugo M.
AU - Fdez-Riverola, Florentino
AU - Capelo, José L.
N1 - info:eu-repo/grantAgreement/FCT/5876/147258/PT#
info:eu-repo/grantAgreement/FCT/5876/147218/PT#
This work has been partially funded by: (i) the "Platform of integration of intelligent techniques for analysis of biomedical information" project (TIN2013-47153-C3-3-R) from Spanish Ministry of Economy and Competitiveness; (ii) the "Discovery of biomarkers for bladder carcinoma diagnosis" project from Nova Medical School (Nova Health Project Pilot 01); (iii) the "Biomarkers for rheumatic inflammatory diseases diagnosis" project from Nova Medical School (Nova Health Project Pilot 02); (iv) the UCIBIO (Unidade de Ciencias Biomoleculares Aplicadas), which is financed by national funds from FCT/MEC (UID/Multi/04378/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007728); (v) the Associate Laboratory for Green Chemistry LAQV,which is financed by national funds from FCT/MEC (UID/QUI/50006/2013) and co-financed by the ERDF under the PT2020 Partnership Agreement (POCI-01-0145-FEDER-007265); and (vi) Conselleria de Cultura, Educacion e Ordenacion Universitaria (Xunta de Galicia) and FEDER (European Union). The Proteomass Scientific Society is acknowledged for the funding provided to the Isabel Moura biological mass spectrometry laboratory. H. Lopez-Fernandez is supported by a post-doctoral fellowship from Xunta de Galicia. H. M. Santos is funded by the FCT 2015 Investigator Program (IF/00007/2015). J.E. Araujo and S. Jorge are supported by the Portuguese Foundation for Science and Technology under doctoral grant numbers SFRH/BD/109201/2015 and SFRH/BD/120537/2016, respectively.
PY - 2018/3/1
Y1 - 2018/3/1
N2 - 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.
AB - 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.
KW - 2D-gel
KW - Data processing
KW - emPAI
KW - LC-MS/MS
KW - MALDI-TOF-MS
KW - Protein identification
UR - http://www.scopus.com/inward/record.url?scp=85036478641&partnerID=8YFLogxK
U2 - 10.1016/j.cmpb.2017.11.024
DO - 10.1016/j.cmpb.2017.11.024
M3 - Article
C2 - 29512488
AN - SCOPUS:85036478641
SN - 0169-2607
VL - 155
SP - 1
EP - 9
JO - Computer Methods and Programs in Biomedicine
JF - Computer Methods and Programs in Biomedicine
ER -