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Exploring the Proteome II
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Poster Number:

30

Presenter:
Shiaw-Lin Wu
Institute: Lab or Branch
ThermoFinnigan, San Jose, CA  
Title:
A General Approach to the Analysis of Post-Translational Modifications Combining Ion Trap Technology, Accurate Mass Detection, and Data Mining Software
Authors:
S-L. Wu, A. Huhmer, K. Miller
Abstract:
Protein analysis by peptide mass maps has become an important technique for proteomic studies. A protein from a gel spot or a separated subcellular fraction is proteolytically digested and analyzed by LC-MS/MS. Proteins are identified by comparison of measured peptide fragment ions with those predicted by in silico digestion of a protein database. This technique can account for some modifications to the protein primary sequence, i.e. post-translational modifications (PTMs), but the protein must be present in the database and the modification must be known a priori.

Locations and structures of unexpected PTMs can be determined by further fragmentation of the modified peptide (e.g. MS to 3 in an ion trap). They can also be identified by analysis of existing data using enhanced software tools for spectral interpretation, de novo sequencing, and spectral pattern analysis. The confidence of all of these techniques is enhanced with access to data sets with very high mass accuracy, e.g. <2ppm.

In this report, we will demonstrate use of an ion trap mass spectrometer (LTQ FT), coupled with protein identification (TurboSEQUEST®), de novo sequencing (DenovoXTM), and pattern analysis (SALSA) software to study phosphorylation, glycosylation, and methylation in a complex biological sample mixture.

 
 

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