Mining the human placenta proteome ≥ 2000 proteins deep using CID/ETD on the amaZon ion trap

Poster

Expression Proteomics

Ion Trap

2009

"Simone Lemeer1, Hannes Hahne1, Andrea Schneider2, Markus Lubeck2, Bernhard Kuster1,3 "

Abstract

The amazon ion trap mass spectrometer delivers 2,500- 5,000 resolution at 8,100 amu/sec scan speed, 0.2 amu mass accuracy and attomol level sensitivity for protein identification from very complex protein mixtures

>2,000 proteins were identified from human placenta using a 5-tier approach consisting of 1D PAGE protein separation, nanoLC peptide separation, gas phase ion separation and
complementary CID and ETD fragmentation. This is the largest set of proteins identified from human placenta to date.

The achieved depth of proteome coverage enabled the detection of singaling molecules and phosphorylation sites involved in embryonal development. However, analytical depth is limited by the presence of significant amounts of blood proteins in the placenta sample.

CID identifies more proteins than ETD and ETD adds a modest 20% extra proteins compared to
CID alone. Currently it is unclear if this 20% difference is due to ETD as a alternative technique or a result of experimental variation associated with LC-MS analysis of complex samples.

Gas phase fractionation increases protein ID by a very modest ~10% protein compared to ordinary full scan analysis. However, it does improves sequence coverage for many proteins.

The combination of CID, ETD and gas phase fractionation doubles the number of identified phosphorylation sites.

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