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S2P: A Desktop Application for Fast and Easy
Processing of 2D-Gel and MALDI-Based Mass
Spectrometry Protein Data
Hugo López-Fernández
1,2,3
(
✉
)
, Jose E. Araújo
3
, Daniel Glez-Peña
1,2
,
Miguel Reboiro-Jato
1,2
, Florentino Fdez-Riverola
1,2
, and José L. Capelo-Martínez
3
1
ESEI - Escuela Superior de Ingeniería Informática, Edificio Politécnico, Universidad de Vigo,
Campus Universitario As Lagoas s/n, 32004 Ourense, Spain
{hlfernandez,dgpena,mrjato,riverola}@uvigo.es
2
CINBIO - Centro de Investigaciones Biomédicas, University of Vigo,
Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
3
UCIBIO-REQUIMTE, Departamento de Química, Faculdade de Ciências e Tecnologia,
Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
{jeduardoaraujo,jlcapelom}@bioscopegroup.org
Abstract. 2D-gel electrophoresis is widely used in combination with MALDI-
TOF mass spectrometry in order to analyse the proteome of biological samples.
It can be used to discover proteins that are
differentially
expressed between two
groups (e.g. two disease conditions) obtaining thus a set of potential biomarkers.
Biomarker discovery requires a lot of data processing in order to prepare data for
analysis or in order to merge data from different sources. This kind of work is
usually done manually, being highly time consuming and distracting the operator
or researcher from other important tasks. Moreover, doing this repetitive process
in a non-automated, handling-based manner is error-prone, affecting reliability
and reproducibility. To overcome these drawbacks, the S2P, an AIBench based
desktop multiplatform application, has been specifically created to process 2D-
gel and MALDI-mass spectrometry protein identification-based data in a
computer-aided manner. S2P is open source and free to all users at http://www.
sing-group.org/s2p.
Keywords: Protein identification · Data processing · Bioinformatics tools · Open
source · 2D-gel · MALDI-TOF-MS · Protein data · Mascot identifications
1 Introduction
2D-gel electrophoresis and mass spectrometry using matrix assisted laser desorption
ionization coupled to time of flight analysers, MALDI-TOF-MS, are widely used in
conjunction in order to perform proteome analysis [1, 2]. In brief, while the comparison
of 2D-gels allows obtaining a set of differentially expressed spots, MALDI-TOF-MS
allows to identify the proteins separated in such spots.
© Springer International Publishing AG 2017
F. Fdez-Riverola et al. (eds.), 11th International Conference on Practical
Applications of Computational Biology & Bioinformatics, Advances in Intelligent
Systems and Computing 616, DOI 10.1007/978-3-319-60816-7_1