Mining the Human Placenta Proteome > 2000 Proteins deep using CID/ETD on an Ion Trap

Poster

Expression Proteomics

PWA 113

Ion Trap

2009

Simone Lemeer1, Hannes Hahne1, Andrea Schneider2, Markus Lubeck2, Arnd Ingendoh2Bernhard Kuster1,3

Poster IMSC 2009

Abstract

• The amazon ion trap delivers up to 5,000 resolution at 8,100 amu/sec scan speed, 0.2 amu mass accuracy and attomol sensitivity for protein ID from complex proteomes.
• ~2,200 proteins were identified using a 5-tier approach, the largest set of protein ID from human placenta to date.
• CID identifies more proteins than ETD which adds 20% extra proteins compared to CID alone.
• Gas phase fractionation increases protein ID by a very modest ~10% compared to full scan analysis, but it mostly improves sequence coverage.
• The combination of CID, ETD and gas phase fractionation doubles the number of identified phosphorylation sites.

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IMSC 2009

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