Proteomics, SoSe 2014 (19577)

Welcome to the Wiki of the MSc seminar Proteomics.

In this seminar we will discuss original articles that deal with the analysis of HPLC/MS based proteomics and metabolomics data.
As a participant you are expected to give a 30-40 minute presentation explaining the content of the original work. Papers will be assigned at the beginning of April.

News

Times and Places

Start: 15 April 2014, Finish: 15 July 2014

Event	Day	Time	Address	Room
Seminar	Tue	14-16	Takustr. 9	SR 053 (integr. Beamer)

Content

We will discuss original works concerning several aspects of computational proteomics. The following gives list of the different areas and possible works to be presented.

Area	Title	Seminar No
Experimental design / Quantitation	Statistical design of quantitative mass spectrometry-based proteomic experiments (Oberg, Vitek)	A
Experimental design/ Quantitation	Protein quantfication in label-free LC-MS experiments	B
Map Alignment	Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements (Lange et al)	C
Peptide ID	Antilope—A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem (Andreotti et al)	D
Peptide ID	pNovo+: De Novo Peptide Sequencing Using Complementary HCD and ETD Tandem Mass Spectra (Chi et al)	E
Protein Inference	Empirical Statistical Model To Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search (Keller et al)	F
Protein Inference	A linear programming model for protein inference problem in shotgun proteomics (Huang and He)	G
Protein Inference	Protein and gene model inference based on statistical modeling in k-partite graphs (Gerster et al.)	H
Protein Inference	Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data (Serang et al)	I

Schedule

Date	Lecture	Lecturer	Contact
15.04.2014	Knut Reinert	Overview and paper assignment
22.04.2014	Knut Reinert	Introduction to Proteomics
27.04.2014	Xiao Liang	G
03.06.2014	Block seminar
	Magdalena Wypukol	B	Knut Reinert
	Vishalini Vimalakanthan l	I	Xiao Liang
	Sven-Maurice Althoff	A	Stephan Aiche
	Timo Schüllerman	E	Sandro Andreotti

Background

• Protein inference tutorial

• slides_G.pdf: the slides of ProteinLP article G.