Download S2P - Zenodo

http://www.sing-group.org/s2p
S2P: a desktop application for fast and easy processing of 2Dgel and MALDI-based mass spectrometry protein data
H. López-Fernández, J.E. Araújo, D. Glez-Peña, M. Reboiro-Jato, F. FdezRiverola, J.L. Capelo-Martínez
11th International Conference on
Practical Applications of Computational Biology & Bioinformatics
Outline
1.
Introduction
•
Context
•
Motivation
2.
Implementation
3.
Results
4.
Conclusions and future work
Introduction
Introduction: context

2D-gel electrophoresis (2DE)


Separation of sample proteins into different spots
MALDI-TOF mass spectrometry

Analysis of those spots in order to identify the associated proteins
Why S2P?
Introduction: motivation
…
Spot
Protein
Sample 1
Sample N
100
Protein A
100
200
120
Protein B
100
300
200
Protein C
200
100
240
Protein D
300
450
Protein F
150
250
.
.
.
300
Progenesis
SameSpots
(1 report/sample)
Join
Mascot report
(1 for all samples)
Introduction: motivation
Spot
Sample 1
100
100
120
100
Plate
position
Join
.
.
.
300
150
…
Protein
A1
Protein A
A2
Protein B
B1
Protein C
B2
Protein D
.
.
.
Progenesis SameSpots
(1 report/sample)
E7
MALDI plate
Design
Spot  Plate position
Protein F
Mascot report (1 for all samples)
Introduction: motivation

Why S2P?

2DE and MALDI-TOF-MS analyses produces different data that
must be integrated before analysis

Manual processing of this data is not feasible:

Prone error

Time consuming

Lack of reproducibility
Implementation
Implementation

Java 1.8 and AIBench framework

Graphical User Interface:


Swing and SwingX

GC4S (https://github.com/hlfernandez/GC4S/)
Third party libraries:

JFreeChart

Jsparklines

Charts4j

iText

Apache Commons Mathematics library
Availability


http://www.sing-group.org/s2p/

Installers (Windows, Linux and OS X)

Version history

Tutorials
Source code at GitHub:

https://github.com/sing-group/s2p
Results
Results

S2P v1.0: data processing workflow
Source: H. López-Fernández; J.E. Araújo; D. Glez-Peña; M. Reboiro-Jato; F. Fdez-Riverola; J.L. Capelo-Martínez (2017) S2P: a desktop application for fast and easy processing of 2D-gel and MALDI-based mass spectrometry protein data. 11th
International Conference on Practical Applications of Computational Biology & Bioinformatics: PACBB 2017. Porto, Portugal. 21 - June
Results

S2P v1.0: views and analysis
Results


S2P v1.0 applied to the initial study

Manual processing: about 2 weeks

Using S2P: a few clicks

Error free, reproducible data-processing
Application in other studies

New S2P versions: v1.1 and v1.2

v1.1: new functions to facilitate data handling

v1.2: current development
Results

S2P v1.1 enabled bigger studies


Rats: 9 2DE samples

> 300 spots

9 MALDI plates

18 Mascot protein identification reports
Mice: 9 2DE samples

> 300 spots

3 MALDI plates

6 Mascot protein identification reports
Conclusions and future work
Conclusions and future work

Open source, freely available at http://www.sing-group.org/s2p/

Advantages:

Time-saver software

Error-free and reproducible experiments

Already applied in real studies

Future work:

Currently working on version 1.2
Acknowledgements

H. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia.

J. E. Araújo is supported by a pre-doctoral grant from Portuguese Foundation for Science and Technology
(SFRH/BD/109201/2015).

Funding

"Platform of integration of intelligent techniques for analysis of biomedical information” project (TIN201347153-C3-3-R) from Spanish Ministry of Economy and Competitiveness.

“Discovery of biomarkers for bladder carcinoma diagnosis” project from Nova Medical School.

Unidade de Ciências Biomoleculares Aplicadas (UCIBIO), which is financed by national funds from
FCT/MEC/Portugal (UID/Multi/04378/2013)

Consellería de Cultura, Educación e Ordenación Universitaria (Xunta de Galicia) and FEDER (European
Union).

ProteoMass Scientific Society.
Questions?
Thank
you!
11th International Conference on
Practical Applications of Computational Biology & Bioinformatics
This work is licensed under a Creative Commons AttributionShareAlike 4.0 International License.