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MS-EmpiReS

The study of alternative splicing on the protein level is challenging due to the comparably low sequence coverage of current mass spectrometry-based proteomics. This often prevents alternatively spliced isoforms from being resolved in the data. Consequently, studies on fundamental aspects of splicing, such as the regulation of splicing (differential alternative splicing) are still at an early stage and often not feasible on a proteome wide scale. The computational tool MS-EmpiReS detects differential alternative splicing by not only relying on sequence information, but also on quantitative information which allows to also resolve splice events which would otherwise not be accessible and allows proteome-wide screening for differential alternative splicing.
Quick Start

MS-EmpiReS requires quantified peptides measured over different conditions
(e.g. healthy, disease, etc.) and a label map, mapping individual samples to their
respecitive conditions in the format specified below. We currently support human and
mouse data.

"Quantified peptides table" format example:

input table

"Label map" format example:

labelmap table

Example call from the commandline to test human data for differential alternative splicing:

java -jar MS-EmpiReS10.jar -peptides_tsv < quant_peptides_file > -labelmap_tsv < labelmap_file >
An output table with tested differential alternative splicing events and corresponding significance scores is written in the folder where the peptides input file is located.

For further details, for example on plotting options, see the README in the MS-EmpiReS distribution.
Download
Version 1.0 MS-EmpiReS-1.0.zip README

Requirements

JAVA >= 1.8 http://www.oracle.com Required
R (>=3.0) https://www.r-project.org/ Optional
R package 'gplots' https://cran.r-project.org/web/packages/gplots/index.html Optional
R package 'Cairo' https://cran.r-project.org/web/packages/Cairo/index.html Optional
Contact

In case of problems/questions concerning MS-EmpiReS, please do not hesitate to contact Constantin Ammar

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