High Sensitivity Collisionally‐activated Decomposition Tandem Mass Spectrometry on a Novel Quadrupole/Orthogonal‐acceleration Time‐of‐flight Mass Spectrometer

Abstract

Consideration of the special problems encountered in ultra-high sensitivity biopolymer sequencing studies has led to the development of a novel quadrupole/erthogonal-acceleration time-of-flight tandem mass spectrometer described for the first time here. The performance characteristics of this new geometry are demonstrated, including fully resolved daughter-ion spectra with mass accuracies of 0.1 dalton, which allow removal of interpretation ambiguities and easy differentiation of charge states even in weak collisionally-activated decomposition tandem mass spectra. The instrument has been applied to a variety of biopolymer research problems, including the structure determination of major histocompatibility complex peptide antigens using liquid chromatography/electrospray mass spectrometry and nanoflow-electrospray tandem mass spectrometry, and sequencing capability in the low-femtomole and attomole ranges is demonstrated.

Investigation of intact protein complexes by mass spectrometry

“…This is not only because of the virtually unlimited m/z range, but also because of the achievable high sensitivity and speed of TOF analysis. TOF measurement depends on a pulsed ion beam and, therefore, the development of orthogonal hybrid instruments that allow a proper combination of a continuous electrospray source with pulsed ion detection has been essential for protein complex mass spectrometry (Morris et al, 1996;Loboda et al, 2000). In one of its simplest forms ESI is combined with TOF analysis using a combination of quadrupole or hexapole filters orthogonally coupled to a TOF tube.…”

“…Quadrupole TOF machines combine a quadrupole mass filter with an orthogonal TOF analyzer (Morris et al, 1996;Loboda et al, 2000). These spectrometers provide supplementary structural information for ions isolated in the quadrupole, dissociated via collisional activation, and analyzed in the TOF analyzer.…”

A novel precursor ion discovery method on a hybrid quadrupole orthogonal acceleration time-of-flight (Q-TOF) mass spectrometer for studying protein phosphorylation

“…This is because the oa-TOF has a relatively high duty cycle, typically 5 to 25%, compared to that of a scanning quadrupole mass spectrometer. The tandem quadrupole orthogonal acceleration time-of-flight mass spectrometer (Q-TOF) similarly has a relatively high duty cycle [13], irrespective of whether the spectrum to be recorded is that of precursor ions from the source (MS), or fragment ions from a precursor ion selected by the quadrupole mass filter and fragmented in the collision cell (MS/MS). However, when only a single specified product ion is to be monitored, as in precursor ion scanning or in the multiple reaction monitoring (MRM) experiments, the Q-TOF type instrument is less sensitive than the equivalent triple quadrupole instrument [14].…”

A novel Interface for variable flow nanoscale LC/MS/MS for improved proteome coverage

“…All MS experiments were performed with a Q-TOF™ hybrid quadrupole/time-of-flight mass spectrometer (Micromass Ltd., Manchester, UK) equipped with a Z-spray ion source, which has been described in detail previously [6]. The instrument consists of an electrospray ionization source, a quadrupole mass filter operating as a variable bandpass device, a hexapole collision cell, and an orthogonal acceleration time-of-flight (TOF) mass analyzer.…”

“…The development of shotgun proteomics by Yates [1][2][3] couples nanoscale LC for peptide analysis [4,5], automated MS to MS/MS data acquisition software and hardware on modern tandem mass spectrometers [6], along with automated database searching software of modern search engines [7,8]. Shotgun proteomics has significantly increased the information content of protein mass spectrometry experiments, while at the same time significantly reducing the total analysis time required to analyze a complex protein mixture.…”