简介：

Comprehensive, accurate identification of proteins in complex sample mixtures is an important fundamental apability for any proteomics research laboratory. Technology dvancements in both hardware and software continue to xpand and refine our view of any proteomic system in erms of protein identities and their post-translational odifications (PTMs). It has been suggested that the very ecent ability to routinely obtain accurate mass measurements(< 5 ppm RMS) on precursor and MS/MS fragment ions n proteomic experiments should lead to unprecedented ccuracy in the ability to identify and characterize proteins. This paper compares alternative approaches to this challenging application using two high performance platforms for proteomics: a QqTOF instrument (QSTAR® Elite from Applied Biosystems) and a hybrid linear ion traporbitrap instrument (Thermo Scientific LTQ Orbitrap XL).

仪器：

LTQ Orbitrap XL with nanospray ion source

总结：

Protein identification and PTM assignment remain critically important experiments in support of biological, drug research, biomarker, and clinical applications of proteomics.

In this study, it has been shown that in identical experiments:

1. The Orbitrap is able to identify more than 2.5 times as many proteins as the QqTOF in a complex E. coli lysate. In a 500 ng sample, the Orbitrap confidently (Mascotp < 0.001, FPR << 1%) identified over 300 proteins, compared to just 125 by the QqTOF. In a 100 ng sample, the Orbitrap confidently identified 150 proteins compared to 60 by the QqTOF. The Orbitrap data provided enhanced primary sequence coverage for almost all of the 125 proteins on the QqTOF list.

2. The Orbitrap is more sensitive than the QqTOF. The Orbitrap analysis of a 100 ng sample yielded more protein identifications than analysis of a 500 ng sample by the QqTOF – more proteins were identified with five times less sample.

3. Protein database search results from Mascot, SEQUEST and ProteinPilot search engines appear to be highly

similar at FPR << 1%.

4. Parallel acquisition – ability to perform Data Dependent™ MS/MS analyses in the ion trap while accurate mass

precursor measurements are performed in the Orbitrap –provides ideal data for proteomics experiments. The combination of accurate precursor mass and robust peptide fragment ion information allow highly sensitive and confident peptide identification and PTM assignment.