Mass Spectrometry-based Proteomics Using Q Exactive, a High-performance Benchtop Quadrupole Orbitrap Mass Spectrometer

By Annette Michalski, Eugen Damoc, J. Hauschild, Oliver Lange, A. Wieghaus, A. Makarov, Nagarjuna Nagaraj, Jüergen Cox, Matthias Mann, S. Horning. Molecular & Cellular Proteomics, 2011

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Mass spectrometry-based proteomics has greatly benefitted from enormous advances in high resolution instrumentation in recent years. In particular, the combination of a linear ion trap with the Orbitrap analyzer has proven to be a popular instrument configuration. Complementing this hybrid trap-trap instrument, as well as the standalone Orbitrap analyzer termed Exactive, we here present coupling of a quadrupole mass filter to an Orbitrap analyzer. This “Q Exactive” instrument features high ion currents because of an S-lens, and fast high-energy collision-induced dissociation peptide fragmentation because of parallel filling and detection modes. The image current from the detector is processed by an “enhanced Fourier Transformation” algorithm, doubling mass spectrometric resolution. Together with almost instantaneous isolation and fragmentation, the instrument achieves overall cycle times of 1 s for a top10 higher energy collisional dissociation method. More than 2500 proteins can be identified in standard 90-min gradients of tryptic digests of mammalian cell lysate— a significant improvement over previous Orbitrap mass spectrometers. Furthermore, the quadrupole Orbitrap analyzer combination enables multiplexed operation at the MS and tandem MS levels. This is demonstrated in a multiplexed single ion monitoring mode, in which the quadrupole rapidly switches among different narrow mass ranges that are analyzed in a single composite MS spectrum. Similarly, the quadrupole allows fragmentation of different precursor masses in rapid succession, followed by joint analysis of the higher energy collisional dissociation fragment ions in the Orbitrap analyzer. High performance in a robust benchtop format together with the ability to perform complex multiplexed scan modes make the Q Exactive an exciting new instrument for the proteomics and general analytical communities.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/790eadc2727b31514350c244991646f7b3cbd733

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Citations in the corpus

Parallel Reaction Monitoring for High Resolution and High Mass Accuracy Quantitative, Targeted Proteomics* (2012, neutral): “bench-top quadrupole-Orbitrap MS (QqOrbi) (47), which,”
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation (2017, background): “MS instruments have expanding but limited capacity for parallel ion processing and analysis [12, 36, 37].”
Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. (2014, methodology): “The instrument parameters on the quadrupole Orbitrap instrument used (Q Exactive [Michalski et al., 2011]) were optimized for phosphopeptide identification (Figure S1).”
Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ (2014, background): “Recent advances in mass spectrometer hardware (76, 77) have provided a boost in the depth of standard analyses and enabled near-complete model proteome quantification in minimal measuring time (6).”