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Workshop Computational Proteomics and Metabolomics

Galloping technological advances in mass spectrometry (MS) continue to advance existing analytical capabilities towards a unified understanding of the dynamic complement of the cell.

As was recognized by the 2002 Nobel prize in Chemistry, mass spectrometry is nowadays the major technique for the analysis of proteins, metabolites, carbohydrates, and lipids. More than 14,000 articles from the life sciences that are related to MS have been published in the year 2011. MS is also an indispensable tool for studies in chemistry, biochemistry, pharmacy, or medicine.

Computers and computer programs have supported MS experts in the interpretation of mass spectra since at least the 1960′s. With a more formal treatment of problems and methods, computational mass spectrometry became a mainstream technique in the mid–1990s and has since become an indispensable tool for the automated analysis of MS data. Questions of interest include the identification of peptides, proteins, metabolites, and glycans, as well as quantitative proteomics and metabolomics. As mass spectrometry is rapidly evolving, questions and paradigms for the computational analysis perpetually change.

We invite researchers to present new original research spanning the whole field of computational mass spectrometry, for application in proteomics, metabolomics, glycomics, or lipidomics. Potential topics include, but are not limited to:

• Raw data analysis and peak picking
• Advanced methods for searching spectral libraries
• Computational analysis of quantitative data
• De novo sequencing of peptides and proteins
• Identifying and localizing posttranslational modifications
• Proteogenomics
• Interpreting metabolite MS data
• Characterizing novel metabolites
• Glycan de novo sequencing
• Interpreting glycan MS data

We invite submissions of the following types: Either a current paper plus an extended abstract (300 words), or a two pages long extended abstract describing your “work in progress”.

Deadline for submission is 9th August 2012. Notification of acceptance will be sent on 16th August 2012.

Submissions should be sent via e-mail to

Preliminary Program

The workshops take place on 19 September 2012 on Jena’s Beutenberg Campus.

11:00 René Rex
Predicting concentration, enzyme capacity and flux distribution changes from integrated systems biology data using Boolean algebra
11:30 Max von Haugwitz
High Quality MRM Data Analysis for LC/MS‐based Metabolomics: Using Wavelet‐ and Pattern Recognition Techniques for 13C‐Labeling Data Evaluation
12:00 Markus Heinonen
Metabolite identification and molecular fingerprint prediction via machine learning
12:30 Lunch break
13:30 Bernhard Y. Renard
Overcoming species boundaries in protein identification with a Bayesian Information Criterion-driven Error-tolerant Peptide Search (BICEPS)
14:00 Christoph Dieterich
The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein- Coding Transcripts
14:30 Heiko Giese
Cluster methods for complexome profiling
15:00 Coffee break
Imaging MS
15:30 Aleš Svatoš
MS Imaging of biological 3D-surfaces: problems and solutions
16:00 Theodore Alexandrov
Exploring 3D MALDI imaging mass spectrometry data: 3D spatial segmentation of mouse kidney
16:30 Final Discussion