双压线性离子阱质谱为蛋白质组学实验提供突破性优越表现

简介：

Comprehensive definition of a proteome is a necessary foundation for subsequent investigations of proteome dynamics. Proteome characterization should be as efficient, reliable, and exhaustive as possible. Tandem mass spectrometry,particularly using linear ion traps and trap-based hybrid mass spectrometers, has become the technology of choice for peptide and protein identification. The preference for this instrumentation is attributable to robustness, ease of use, superior MS and especially MS/MS performance.

Undiscovered components within a proteome frequently include dynamically modified forms which exist at abundance levels undetectable by most instrumentation. Therefore, the development of more sophisticated instrumentation is essential for a more exhaustive characterization of complex proteomes.

This application note addresses the challenging analysis of a complex, multi-organ peptide digest of Caenorhabditis elegans (C. elegans) to assess the performance of an innovative new dual-pressure linear ion trap mass spectrometer. Performance of the new instrument is benchmarked against the previous state-ofthe- art linear ion trap and also against a well-known quadrupole time-of-flight (Q-TOF) mass spectrometer.

仪器：

Thermo Scientific LTQ Velos ion trap mass spectrometer

总结：

The sensitive detection and identification of components within a complex proteomic sample is crucial for the

characterization and understanding of proteome dynamics. The technological advancements of the LTQ Velos dual-pressure linear ion trap mass spectrometer, including increased speed of acquisition and sensitivity, have resulted in significant improvement in the identification of peptides and proteins, including an increase in identification of lower intensity precursors, when compared to existing state-of-the-art technologies.

• The LTQ Velos ion trap identified ~240% more proteins and ~130% more unique peptides from a highly complex sample than did a Q-TOF , where >90% of the proteins identified by the Q-TOF were also identified by the LTQ Velos.

• The LTQ Velos dual-pressure ion trap demonstrated higher sensitivity for samples at lower levels, with more than a 150% increase in the number of identified unique peptides for a low load of 20 ng, versus the LTQ XL ion trap.

• With the increase in the number of identified proteins, the LTQ Velos offered greater access to low-abundance proteins as shown by a 133% increase in the number of identified signal transduction proteins.

• The LTQ Velos dual-pressure ion trap offered an increase in experimental throughput, identifying more proteins and peptides than the LTQ XL ion trap in 1/3 the separation time for a complex sample.

• The better quality of the MS/MS scans in the linear ion traps produced higher Mascot scores for equivalent peptides compared to those of the Q-TOF instrument. Higher mass accuracy of analytical scans acquired with the Q-TOF was beneficial but not sufficient to produce superior peptide identification.

• Increasing the scan rate on the Q-TOF resulted in a decrease in signal and spectral quality for MS and MS/MS scans and a corresponding decrease in the number of identified peptides.