URL: iGenomed.stanford.edu/proteomics2012/ms-sig
Date: July 14th, 2012
Start time: 8:30 a.m. - End time: 6:30 p.m.

Room Location: TBA

MS-SIG: Computational challenges in high-throughput proteomics.

Proteomics, a rapidly advancing field, attempts to understand biological functions of an organism through the large-scale study of the expressed proteins. Studying the functions and interactions of all proteins in a given organism simultaneously is a challenging task. However, advanced mass spectrometry-based approaches, which generate a large amount of meaningful information, have taken us one step closer to achieve this goal. Currently, the community has the following four specific aspects (Liebler, D. C., 2000): 1) identifying all (or many) of the proteins in a sample, 2) profiling protein expression, 3) determining how proteins interact with each other in the living systems, and 4) identifying how and where proteins are modified. Considering the complexity and enormous size of mass spectrometry data, the role of bioinformatics in this field is critical.

Mass spectrometry based proteomics has been broadly applied to biomedical research in various areas. For example, in biology, a better insight into the nature of relationship between proteins and genes can be obtained using mass spectrometry and microarray data. Quantitative profiling of protein abundances and protein posttranslational modifications allows the identification of proteins associated with specific pathways or diseases. Novel candidate biomarkers for disease diagnosis and prognosis can be discovered using this technology. The success in applications heavily depends on good experimental design as well as sound methodology development.

Noting that the importance of bioinformatics in this area, we want to discuss several challenges/issues in analyzing mass spectrometry based high throughput proteomics data. Our meeting contains three portions: oral presentation, panel discussion, and poster presentation. For oral presentation and panel discussion, we will invite experts and focus on the following specific themes:

a. Label vs. label-free protein quantification
i. Reproducibility/Quality control/Missing data
ii. Protein abundance inference from peptide abundance

b. Proteomics applications in biology and medicine
i. Experimental design
ii. Data integration (i.e. protein-gene association)

For the poster session, we invite abstract submissions on a wide range of topics about mass spectrometry data analysis (including topics listed above, but not limited to). The new challenge you share at the poster session might be the potential topic for the next year MS-SIG meeting. Please register for the MS-SIG meeting in order to attend this meeting.

Extended abstract submission deadline: 05/25/2012

Coordinator:
Soyoung Ryu
Stanford University
clairesr [at] stanford [dot] edu