HotTopics: Peptide and protein quantification using Mass Spectrometry


March 5, 2012, SURF Utrecht

To date in addition to protein identification, quantification of abundances of proteins and peptides is common practice. In general there are stable isotope labeling, label-free and MSn approaches to obtain abundance levels of proteins using mass spectrometry. Each technique has its pro’s and con’s with differences in applicability and computational approaches. In the HotTopics Proteomics meeting an overview of these techniques will be shown, followed by the detailed presentation of the current state of the art of these three approaches. Finally the HotTopics Proteomics meeting will conclude by addressing the need for follow-up analysis using pathway or network discovery methods.

Keywords: proteomics, peptides, quantification, statistics, mass spectrometry

Programme March 5th

12:30 – 12:35 Welcome – Marc van Driel
12:35 – 13:05 Lunch
13:05 – 13:20 Introduction: Overview of quantitative approaches
Bas van Breukelen, Utrecht University
13:20 – 14:10 Label-free proteomics for biomarker discovery and validation
Connie Jimenez, VUmc
14:10 – 15:00 Current challenges of label-free quantitative proteomics
Peter Horvatovich, University of Groningen
15:00 – 15:10 Tea break
15:10 – 16:00 Quantitative Proteomics analysis in multiple dimensions:
Challenges in data processing and results visualisation
Twan America, Wageningen University & Research Centre
16:00 – 16:50 Methods for Statistical and Bioinformatics Analysis of
Quantified Mass Spectrometry Data
Elizabeth McClellan, Erasmus Medical Centre
16:50 – 17:20 General discussion
17:20 – 17:30 Closing


Universiteit Utrecht, HR Kruyt Building, De Uithof, Padualaan 8, 3584 CH Utrecht,  6th floor, room O622 (lunch: Z612). Route description:

About HotTopics

NBIC HotTopics are a new series of NBIC meetings committed to bringing scientists together to discuss the concepts and methods on a hot topic in their research field. It should provide a platform to keep in touch with peers in the field and foster sharing of new insights, applications and collaborations. Therefore, the aim of the meeting is not to present the latest results of your own work, but rather to identify new trends and breakthroughs in the field in general.

Four scientists will give a 20 minute lecture followed by 40 minutes of discussion on the important computational concepts:

  • What does a method try to accomplish?
  • What assumptions were made?
  • How does this method compare to similar ones?
  • What are the strengths, weaknesses and pitfalls?
  • Can we apply it in other areas?
  • What are the limitations and challenges for new applications and developments?

Flip over, beamer and laptop are available.

Organising committee