This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. A 2D ion trap has a greater ion trapping efficiency, greater ion capacity before observing space-charging effects, and a faster ion ejection rate than a traditional 3D ion trap mass spectrometer. These hardware improvements should result in a significant increase in protein identifications from complex mixtures analyzed using shotgun proteomics. In this study, we compare the quality and quantity of peptide identifications using data-dependent acquisition of tandem mass spectra of peptides between two commercially available ion trap mass spectrometers (an LTQ and an LCQ XP Max). We demonstrate that the increased trapping efficiency, increased ion capacity, and faster ion ejection rate of the LTQ results in greater than 5-fold more protein identifications, better identification of low-abundance proteins, and higher confidence protein identifications when compared with a LCQ XP Max.
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