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.


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)


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


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


Topic attachments
I Attachment Action Size Date Who Comment
slides_G.pdfpdf slides_G.pdf manage 912 K 29 Apr 2014 - 13:38 XiaoLiang the slides of ProteinLP article G.
Topic revision: r9 - 06 May 2014, KnutReinert
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