Phase Correction for Collision Model Analysis and Enhanced Resolving Power of Fourier Transform Ion Cyclotron Resonance Mass Spectra

Vining, Bryan A.; Bossio, Robert E.; Marshall, Alan G.

doi:10.1021/ac9808019

Cited by 31 publications

(43 citation statements)

References 38 publications

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“…Both eFT and conventional FT make use of complex numbers, which can be represented by magnitude and phase, or by real and imaginary components. As the initial phase of the ion package appears to be dependent on initial parameters of the ions in a very complex way (25), FT spectra have to be presented in the so-called magnitude mode, which amounts to disregarding the phase information. However, in Orbitrap mass spectrometers the built-in excitation-by-injection mechanism (26) provides an initial phase of ion oscillations that is almost m/z independent.…”

Section: Methodsmentioning

confidence: 99%

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

Michalski

Damoc

Hauschild

et al. 2011

Molecular & Cellular Proteomics

733

645

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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.

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Section: Methodsmentioning

confidence: 99%

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

Michalski

Damoc

Hauschild

et al. 2011

Molecular & Cellular Proteomics

733

645

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“…In addition, mass resolution of FTMS analysis decays exponentially as function of m/z [25], which can also complicate lipid identification and bias quantification depending on the m/z of monitored lipid species. Notably, the Orbitrap Fusion is equipped with a new ultra-high-field Orbitrap mass analyzer and utilizes a dedicated apodization algorithm (eFT) that allows acquisition of FTMS spectra with a mass resolution up to 450,000 (FWHM at m/z 200) [25,37,38]. To evaluate the efficacy of the higher resolving power of FTMS analysis on the Orbitrap Fusion, we analyzed a sample containing three pairs of synthetic lipid species differing by one double bond [i.e., Cer 42:1;2 and Cer 42:2;2, PC 34:1 and PC 34:2, TAG 54:1 and TAG 54:2 ( Figure 1)].…”

Section: Evaluation Of High Resolution Ftms Analysis and Isotope Fidementioning

confidence: 99%

Comprehensive Lipidome Analysis by Shotgun Lipidomics on a Hybrid Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer

Almeida

Pauling

Sokol

et al. 2014

J. Am. Soc. Mass Spectrom.

125

174

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Abstract. Here we report on the application of a novel shotgun lipidomics platform featuring an Orbitrap Fusion mass spectrometer equipped with an automated nanoelectrospray ion source. To assess the performance of the platform for indepth lipidome analysis, we evaluated various instrument parameters, including its high resolution power unsurpassed by any other contemporary Orbitrap instrumentation, its dynamic quantification range and its efficacy for in-depth structural characterization of molecular lipid species by quadrupole-based higher-energy collisional dissociation (HCD), and ion trap-based resonant-excitation collision-induced dissociation (CID). This evaluation demonstrated that FTMS analysis with a resolution setting of 450,000 allows distinguishing isotopes from different lipid species and features a linear dynamic quantification range of at least four orders of magnitude. Evaluation of fragmentation analysis demonstrated that combined use of HCD and CID yields complementary fragment ions of molecular lipid species. To support global lipidome analysis, we designed a method, termed MS ALL , featuring high resolution FTMS analysis for lipid quantification, and FTMS 2 analysis using both HCD and CID and ITMS 3 analysis utilizing dual CID for in-depth structural characterization of molecular glycerophospholipid species. The performance of the MS ALL method was benchmarked in a comparative analysis of mouse cerebellum and hippocampus. This analysis demonstrated extensive lipidome quantification covering 311 lipid species encompassing 20 lipid classes, and identification of 202 distinct molecular glycerophospholipid species when applying a novel high confidence filtering strategy. The work presented here validates the performance of the Orbitrap Fusion mass spectrometer for in-depth lipidome analysis.

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“…Here we describe an Orbitrap analyzer that achieves higher resolving power through reduced trap dimensions. Resolution is further increased by making use of the phase information during Fourier Transformation (8–11). This ultra high resolution Orbitrap analyzer was combined with other instrumental improvements to construct a novel linear ion trap Orbitrap hybrid mass spectrometer termed the Orbitrap Elite.…”

mentioning

confidence: 99%

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

Michalski

Damoc

Lange

et al. 2012

Molecular & Cellular Proteomics

330

290

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Although only a few years old, the combination of a linear ion trap with an Orbitrap analyzer has become one of the standard mass spectrometers to characterize proteins and proteomes. Here we describe a novel version of this instrument family, the Orbitrap Elite, which is improved in three main areas. The ion transfer optics has an ion path that blocks the line of sight to achieve more robust operation. The tandem MS acquisition speed of the dual cell linear ion trap now exceeds 12 Hz. Most importantly, the resolving power of the Orbitrap analyzer has been increased twofold for the same transient length by employing a compact, high-field Orbitrap analyzer that almost doubles the observed frequencies. An enhanced Fourier Transform algorithm—incorporating phase information—further doubles the resolving power to 240,000 at m/z 400 for a 768 ms transient. For top-down experiments, we combine a survey scan with a selected ion monitoring scan of the charge state of the protein to be fragmented and with several HCD microscans. Despite the 120,000 resolving power for SIM and HCD scans, the total cycle time is within several seconds and therefore suitable for liquid chromatography tandem MS. For bottom-up proteomics, we combined survey scans at 240,000 resolving power with data-dependent collision-induced dissociation of the 20 most abundant precursors in a total cycle time of 2.5 s—increasing protein identifications in complex mixtures by about 30%. The speed of the Orbitrap Elite furthermore allows scan modes in which complementary dissociation mechanisms are routinely obtained of all fragmented peptides.

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Phase Correction for Collision Model Analysis and Enhanced Resolving Power of Fourier Transform Ion Cyclotron Resonance Mass Spectra

Cited by 31 publications

References 38 publications

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

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

Comprehensive Lipidome Analysis by Shotgun Lipidomics on a Hybrid Quadrupole-Orbitrap-Linear Ion Trap Mass Spectrometer

Ultra High Resolution Linear Ion Trap Orbitrap Mass Spectrometer (Orbitrap Elite) Facilitates Top Down LC MS/MS and Versatile Peptide Fragmentation Modes

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