Strategies for Improving Reliability in Protein/Peptide Identification Workshop National Institute of Standards and Technology Campus

On November 15, 2007, the National Cancer Institute’s (NCI) Clinical Proteomic Technologies for Cancer initiative and the National Institute of Standards and Technology (NIST) hosted the “Strategies for Improving Reliability in Protein/Peptide Identification” workshop on the NIST campus in Gaithersburg, Maryland.

While the reliability of results from proteomics experiments is of general concern and often rests on the reliability of peptide identification, this area has progressed only incrementally over the past few years. The NCI has begun looking for innovative, paradigm-shifting avenues that promise to greatly advance this area. This workshop brought together thought leaders and stakeholders in the proteomics community to assess needs, strategies, and solutions for peptide identification by mass spectrometry.

PDF File Meeting Summary (Size: 92 KB)
Agenda (Size: 31 KB)

Agenda

8:00 a.m. - 8:30 a.m.	Break

8:30 a.m. - 8:40 a.m.	Welcome Henry Rodriguez, Ph.D. National Cancer Institute, NIH Stephen Stein, Ph.D. National Institute of Standards and Technology Christopher Kinsinger, Ph.D. National Cancer Institute, NIH
Plenary Lecture
8:40 a.m. - 9:20 a.m.	Proteomics 2.0 – better, faster, cheaper Ronald Beavis, Ph.D. University of British Columbia [ View Presentation (Size: 1.5 MB) ]
Identification Methods Session (25-minute talks; 15-minute discussion)
9:20 a.m. - 10:00 a.m.	Refining Peptide Fragmentation Models for Improved Confidence in Sequence/Spectrum Matching Karl Clauser, Ph.D. Broad Institute of MIT and Harvard [ View Presentation (Size: 1.3 MB) ]

10:00 a.m. - 10:40 a.m.	Roles for Sequence Tagging in Protein Identification David Tabb, Ph.D. Vanderbilt University School of Medicine [ View Presentation (Size: 1.4 MB) ]

10:40 a.m. - 10:55 a.m.	Break

10:55 a.m. - 11:35 a.m.	Physical Models for Predicting Peptide Fragmentation Spectra Zhongqi Zhang, Ph.D. AMGEN [ View Presentation (Size: 2.6 MB) ]

11:35 a.m. - 12:15 p.m.	Spectrum Library Building and Searching Henry Lam, Ph.D. Institute for Systems Biology [ View Presentation (Size: 1.9 MB) ]

12:15 p.m. - 1:30 p.m.	Lunch

1:30 p.m. - 2:10 p.m.	Assigning Confidence to a Peptide ID Alexey Nesvizhskii, Ph.D. University of Michigan [ View Presentation (Size: 2.6 MB) ]

2:10 p.m. - 2:50 p.m.	Combining MS/MS Sequence and Spectral Library Search Algorithms Lewis Geer, Ph.D. National Center for Biotechnology Information, NIH [ View Presentation (Size: 2.0 MB) ]

2:50 p.m. – 3:05 p.m.	Break
User Community Session (20-minute talks; 10-minute discussion)
3:05 p.m. - 3:35 p.m.	Perspective and Progress in Protein and Peptide Identification Sean Seymour, Ph.D. Applied Biosystems [ View Presentation (Size: 2.1 MB) ]

3:35 p.m. - 4:05 p.m.	Getting Your Software Out There Brian Searle Proteome Software Inc. [ View Presentation (Size: 2.8 MB) ]

4:05 p.m. - 4:35 p.m.	Open-Source Software Phil Andrews, Ph.D. University of Michigan [ View Presentation (Size: 1.7 MB) ]

Panel Discussion
4:35 p.m. - 5:00 p.m.	Discussion of Next Steps and Closing Remarks

5:00 p.m.	Adjournment