Preliminary Program

Friday, April 6, 2012
CSE Auditorium, 1202 Computer Science and Engineering Building, UCSD

9:00a - 10:30a Tutorial: Jeremy Carver and Mingxun Wang, University of California, San Diego
ProteoSAFe: A Scalable, Accessible, and Flexible Software Environment for Proteomics Analysis

10:30a - 10:50a Break

10:50a - 12:20p Tutorial: Sangtae Kim, University of California, San Diego
A tour of MS-GF+: A Universal and Sensitive MS/MS Database Search Engine

12:20p - 2:00p Lunch Break

2:00-3:30p Tutorial: Phillip Wilmarth, Oregon Health & Science University
Optimizing Proteomic Data Analyses

3:30-3:50p Break

3:50-5:20p Tutorial: Veavi Chang, Purdue University
Statistical methods and tools for quantitative proteomics

Saturday, April 7, 2012
Calit2 Auditorium, First Floor Atkinson Hall, UCSD

8:00a - 9:00a Registration, Continental Breakfast and Poster Setup for Session A

9:00a - 9:15a Introductory Remarks

Morning Session Chair: Nuno Bandeira, UCSD

9:15a - 9:50a Invited speaker: Ruedi Aebersold
Fragment ion spectra of chemically crosslinked peptides: Their analysis and significance

9:50a - 10:10a Jin Wook Kim, Sunho Lee, Kunsoo Park, Seungjin Na, Eunok Paek, Hyung Seo Park, Heejin Park, Kong-Joo Lee, Jaeho Jeong and Hwa-Young Kim
- Monoisotopic Mass Determination Algorithm for Selenocysteine-containing Polypeptides from Mass Spectrometric Data based on Theoretical Modeling of Isotopic Peak Intensity Ratios

10:10a - 10:40a Invited speaker: Michael MacCoss
Topograph: a Software Platform for Precursor Enrichment Corrected Global Protein Turnover Measurements

10:45a - 11:15a Break / Networking Opportunities

11:15a - 11:35a Marina Spivak and William Stafford Noble
- Learning score function parameters for improved spectrum identification in tandem mass spectrometry experiments

11:35a - 11:55a Hyungwon Choi, Sinae Kim, Damian Fermin, Chih-Chiang Tsou and Alexey Nesvizhskii
- QPROT: model-based differential expression analysis for continuously measured label-free quantitative proteomics data

11:55a - 12:30p Invited speaker: Richard Higgs
High resolution label free quantification: capabilities, limitations, and industrial applications

12:30p - 2:00p Lunch / Networking Opportunities

Afternoon Session Chair: Pavel Pevzner, UCSD

2:00p - 2:35p Invited speaker: Mark Chance
Computational approaches in structural mass spectrometry

2:35p - 3:35p Panel Discussion

3:35p - 4:00p Break / Networking Opportunities

4:00p - 4:20p Yakov Sirotkin, Xiaowen Liu, Maxim Gladkikh, Pavel Pevzner and Kira Vyatkina
- Peptide Sequence Tags for Top-Down Spectra

4:20p - 5:25p "Poster Flash" Presentations

1. Stefka Tyanova, Jürgen Cox, Tamar Geiger, Dmitrij Frishman and Matthias Mann
   Efficient Feature Selection from Large-scale Clinical Proteomics Data Sets
2. Laurent Gerfault, Pascal Szacherski, Jean-François Giovannelli, Jean-Philippe Charrier, Pierre Mahé and Pierre Grangeat
   A hierarchical SRM acquisition chain model for improved protein quantification in serum samples
3. Kevin Crowell, Samuel Payne, Erin Baker, Yehia Ibrahim, Gordon Anderson and Richard Smith
   Annotating Multiplexed IMS-CID-MS Peptide Spectra
4. Kyle Bemis, Livia Eberlin, Christina Ferreira, R. Graham Cooks and Olga Vitek
   Signal Processing and Spatial Segmentation of DESI Imaging Mass Spectrometry Data with Regularized and Spatially-Aware Clustering
5. Markus Muller, Oliver Horlacher, Christina Ludwig, Ruedi Aebersold and Frédérique Lisacek
   Comparing Phosphorylation Positions Reported by Different MS/MS Search Tools
6. Nathan J. Edwards
   Protein Inference by Generalized Protein Parsimony reduces False Positive Proteins in Bottom-Up Workflows

5:25p - 7:00p Poster Session A / Reception

7:00p - 8:00p Poster Take Down

Sunday, April 8, 2012
Calit2 Auditorium, First Floor Atkinson Hall, UCSD

8:00a - 9:15a Continental Breakfast and Poster Setup for Session B

Morning Session Chair: Olga Vitek, Purdue University

9:15a - 9:50a Invited speaker: Vineet Bafna
Segmentation algorithms for imaging mass spectrometry

9:50a - 10:10a Jian Cui, Xuepo Ma and Jianqiu Zhang
- Accurate LC Peak Detection and Blind Corresponding Feature Identification for 16O/18O Labeled LC-MS Replicates

10:10a - 10:45a Invited speaker: Pieter Dorrestein
Creating Microbial Rosetta Stones With Mass Spectrometry

10:45a - 11:15a Break / Networking Opportunities

11:15a - 11:50a Invited speaker: David Tabb
Measuring quality of proteomics instruments and data sets

11:50a - 12:10a Sudipto Saha, Jean-Eudes Dazard and Rob Ewing
- A framework for global analysis of large-scale human interaction proteomics data reveals novel interactions and refines protein network models

12:10p - 2:40p Lunch / Poster Session B

Afternoon Session Chair: Vineet Bafna, UCSD

2:40p - 3:15p Invited speaker: Vicki Wysocki
Pairing Surface-Induced Dissociation with Ion Mobility for Characterization of Protein Complexes

3:15p - 3:35p Dongbo Bu, Shiwei Sun, Yaojun Wang and Bin Ma
- MS-Simulator: Predicting y ion intensities for peptides with two charges based on the intensity ratio of neighboring ions

3:35p - 4:10p Invited speaker: Anne-Claude Gingras
Tracking and analyzing interactome data to navigate signaling networks

4:10p Conference Close

4:10p - 4:40p Poster Take Down