Key Dates
* First Call for Papers:
September 28, 2009
* Paper submissions begin:
November 15, 2009
* Paper submissions deadline: December 15, 2009
* Paper decisions announced:
February 1, 2010
* Conference dates:
March 26-28, 2010
Program Committee Chairs
Nuno Bandeira, University of California, San Diego, USA
Oliver Kohlbacher, University of Tuebingen, Germany
Martin McIntosh, Fred Hutchinson Cancer Research Center, USA
Program
March 26, 2010
9:00a - 10:30a Tutorial: Assigning statistical significance to peptide/protein identifications
Sangtae Kim, Dept of Computer Science and Engineering, University of California, San Diego
10:30a - 10:50a Break
10:50a – 12:20p Tutorial: Proteogenomics: using mass spectrometry for genome and proteome annotation
Natalie Castellana , Dept of Computer Science and Engineering, University of California, San Diego
12:20p - 2:00p Lunch break
2:00-3:30p Tutorial: Statistical design and analysis of quantitative mass spectrometry-based proteomic experiments
Olga Vitek, Depts of Statistics and Computer Science, Purdue University
3:30-3:50p Break
3:50-5:20p Tutorial: Dereplication and Sequencing of Cyclic Non-Ribosomal Peptides Using Mass Spectrometry
Julio Ng, Bioinformatics Program, University of California, San Diego
March 27, 2010
8:00a - 9:00a Registration & Continental Breakfast & Poster Setup for Session A
9:00a - 9:15a Introductory remarks
Morning Session Chair: Nuno Bandeira
9:15a - 9:50a Invited speaker: Ole Jensen
Interpreting the protein language: Quantitative proteomics approaches for characterization of post-translational modifications.
9:50a - 10:10a Xi Chen, Marshall Bern
Identification of Tandem Mass Spectra of Mixtures of Isomeric Peptides
10:10a - 10:45a Invited speaker: Karl Clauser
Scoring Identification and Localization of Phosphorylation Sites in Peptide MS/MS Spectra
10:45a - 11:15a Break / Networking opportunities
11:15a - 11:35a Andreas Bertsch, Stephan Jung, Alexandra Zerck, Nico Pfeifer, Sven Nahnsen, Carsten Henneges, Alfred Nordheim, Oliver Kohlbacher
-Optimal Selection and Scheduling of MRM Transitions for Rapid Quantitation Assay Development
11:35a - 11:55a Chao Yang, Can Yang, Weichuan Yu
A Regularized Regression Method for Peptide Quantification
11:55a - 12:30p Invited speaker: Martin McIntosh
Computational tools and crowd sourcing to improve quantitative proteomics experiments.
Afternoon Session Chair: Vineet Bafna
12:30p - 2:00p Lunch / Networking opportunities
2:00p - 2:35p Invited speaker: Roman Zubarev
Bioinformatics in mass spectrometry based proteomics: the importance of respecting chemistry and biology
2:35p - 3:35p Panel: Current and future challenges in Computational Proteomics
Moderator: Pavel Pevzner.
Panelists: Ole Jensen, Dick Smith, Karl Clauser, Roman Zubarev, Michael MacCoss, Oliver Kohlbacher, Nuno Bandeira, Martin McIntosh.
3:35p - 4:00p Break / Networking opportunities
4:00p - 4:20p Qi Zhu, Dirk Valkenborg, Tomasz Burzykowski
-A Markov-chain-based heteroscedastic regression model for the analysis of high-resolution enzymatically 18O-labeled mass spectra
4:20p - 5:25p "Poster flash" presentations
(A 03) Comparative Proteogenomics / J Eli Venter, Samuel Payne.
(A 14) Ms/Ms Sequencing of Cyclic Peptides: Revolution or Era? / Michelle L. Colgrave, Aaron G. Poth, Quentin Kaas, David J. Craik.
(A 15) Charge-State and Sequence-Dependent Scoring Dramatically Improves Matching of Peptide Etd Spectra / Robert J. Chalkley, Peter R. Baker, Katalin F. Medzihradszky, A. L. Burlingame.
(B 06) Improved quantitative analysis of mass spectrometry using quadratic equations / Joo Young Yoon, Kyung Young Lim, Sunho Lee, Kunsoo Park, Eunok Paek, Un-Beom Kang, Jeonghun Yeom, Cheolju Lee.
(B 22) An R Package for Protein Quantification in Label-Free Lc-Ms Experiments / Timothy Clough, Ching-Yun Chang, Susanne Ragg, Olga Vitek.
(A 33) Automatic querying and identification of molecules by spatial localization in MALDI Mass Spectrometry Imaging / Jocelyne Bruand, Srinivas Sistla, Pieter Dorrestein, Majid Ghassemian, Céline Mériaux, Maxence Wisztorski, Isabelle Fournier, Michel Salzet, Terry Gaasterland,Eduardo Macagno, Vineet Bafna.
5:25p - 7:00p Poster session A / Reception
7:00p-8:00p Poster Take Down
March 28, 2010
8:00a - 9:15a Continental Breakfast & Poster Setup for Session B
Morning Session Chair: Pieter Dorrestein
9:15a - 9:50a Invited speaker: Neil Kelleher
On the use of highly accurate MS/MS information in contemporary proteomics
9:50a - 10:10a Chris Bielow, Silke Ruzek, Christian G. Huber, Knut Reinert
-Optimal Decharging and Clustering of Charge Ladders Generated in ESI-MS
10:10a - 10:45a Invited speaker: Ron Beavis
Using literature annotations to improve peptide PTM assignments
10:45a - 11:15a Break / Networking opportunities
11:15a - 11:35a Sean McIlwain, Paul Draghicescu, Pragya Singh, David R. Goodlett, William Stafford Noble
-Detecting cross-linked peptides by searching against a database of cross-linked peptide pairs
11:35a - 11:55a Hao Chi, Rui-Xiang Sun, Bing Yang, Chun-Qing Song, Le-Heng Wang, Chao Liu, Yan Fu, Zuo-Fei Yuan, Hai-Peng Wang, Si-Min He, Meng-Qiu Dong
-pNovo: de novo Peptide Sequencing and Identification Using HCD Spectra
11:55a - 12:30p Invited speaker: Al Burlingame
Factors essential for optimization of automated electron transfer dissociation (ETD)-based mass spectral peptide identification: Implementation of Charge-State and Sequence-Dependent Scoring.
12:30p - 2:30p Lunch / Poster session B
Afternoon Session Chair: Oliver Kohlbacher
2:30p - 3:05p Invited speaker: Michael MacCoss
Targeted Analysis of Complex Protein Mixtures: A computational workflow from discovery to validation
3:05p - 3:25p Manfred Claassen, Lukas Reiter, Michael O. Hengartner, Joachim M. Buhmann, Ruedi Aebersold
-Generic Comparison of Protein Inference Engine Families
3:25p - 4:00p Invited speaker: Donal Hunt
Instrument and methods development for characterization of protein and peptide post-translational modifications by mass spectrometry
4:00p - 4:30p Break / Networking opportunities
4:30p - 5:05p Invited speaker: Richard Smith
LC-IMS-TOF MS Platform for Proteomics; Challenges for Data Processing and Analysis
5:05p - 5:25p Todd M Greco, Steven H Seeholzer, Adrian Mak, Lynn Spruce, and Harry Ischiropoulos
-Quantitative Mass Spectrometry-based Proteomics Reveals the Dynamic Range of Primary Mouse Astrocyte Protein Secretion
5:25p - 5:45p Rency S. Varghese, Amrita K. Cheema, Prabhdeep Cheema, Marc Bourbeau, Leepika Tuli, Mira Jung, Anatoly Dritschilo, Habtom W. Ressom
-Analysis of LC-MS Data for Characterizing the Metabolic Changes in Response to Radiation
5:45p Conference close
5:45p - 6:30p Poster Take Down