[BBC] [Gtpb] QPB16 - Quantitative Proteomics using Bioinformatics

[Pedro L. Fernandes]

The Gulbenkian Training Programme in Bioinformatics

Applications for the bioinformatics training course
QPB16 - Quantitative Proteomics using Bioinformatics
with Mikhail Savitski, Roman Zubarev and Bo Zhang

Please refer to the course website
http://gtpb.igc.gulbenkian.pt/bicourses/QPB16
for details.

    IMPORTANT DATES for this Course
    Deadline for applications: Sep 24th 2016
    Course dates: Oct 17th - Oct 19th 2016

Course Description
Recent years have seen rapid development in biological mass  
spectrometry and proteomics. In particular, the quantitative  
performance has taken a huge leap forward, both as a label-free (LF)  
approach and as multiplexed quantitative mass spectrometry. This  
development has enabled new technologies for unbiased characterization  
of drug molecules with protein targets, which is one of the major  
challenges in drug development. Here we will explain the basic  
principle of protein quantification by mass spectrometry. A pragmatic  
description of strengths and weaknesses of both label-free as well as  
the multiplexed methodology will be presented. A novel technology,  
thermal proteome profiling (TPP), will be explained that detects  
protein drug interactions in living cells. A practical session will  
take the students through the analysis and interpretation of  
quantitative mass spectrometry data stemming from the TPP experiment  
using an R package. In the LF part of the course, we will explain the  
basics of the identification software DeMix that performs  
deconvolution of the naturally multiplexed tandem mass spectra, thus  
significantly improving the identification aspects. An extension to  
quantification, DeMix Q, introduces the false discovery rate (FDR) for  
peptide identity transfer between the LC-MS runs, and greatly improves  
the quantification performance. Both DeMix and DeMix Q are realized  
based on Open MS package. The participants will learn how to use these  
programs and process their data.
Target audience
This course is intended for all scientists interested in mass  
spectrometry, proteomics and drug development.
Pre-requisites
Basic biological knowledge, especially with regard to proteins.  
Interest in biotechnology. General computer literacy, (e.g. editing  
plain text data files, familiarity with Excel, navigating using the  
command line) will be assumed.




Best regards
Pedro Fernandes

-- 
Pedro Fernandes
GTPB Coordinator
Instituto Gulbenkian de Ciência
Apartado 14
2781-901 OEIRAS
PORTUGAL
Tel +351 21 4407912
http://gtpb.igc.gulbenkian.pt


Upcoming courses:
PM16 - Precision Medicine, Sep 27
3DAROC16 - 3C-based data analysis and
    3D reconstruction of chromatin folding, Oct 10
QPB16 - Quantitative Proteomics using Bioinformatics, Oct 17
AAIRR16 - Analysis of Adaptive Immune Receptor Repertoires, Nov 2
AET16 - Applied Evolutionary Theory, Nov 7
IBSTAT16 - Introductory Biostatistics for Biologists, Nov 14
IB16S - Introductory Bioinformatics, Dec 12

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