High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis: Observations and implications

James C Williamson, Alistair V G Edwards, Thiago Verano-Braga, Veit Schwämmle, Frank Kjeldsen, Ole Nørregaard Jensen, Martin R Larsen

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Resumé

We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS-based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation that significantly impacts the choice of instrument.

OriginalsprogEngelsk
TidsskriftProteomics
Vol/bind16
Udgave nummer6
Sider (fra-til)907-914
ISSN1615-9853
DOI
StatusUdgivet - mar. 2016

Fingeraftryk

Heat-Shock Response
Mass spectrometers
Proteome
Ions
Isotope Labeling
Escherichia coli
Labels
Fusion reactions
Observation
Isotopes
Labeling
Hot Temperature

Citer dette

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abstract = "We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS-based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation that significantly impacts the choice of instrument.",
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High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis : Observations and implications. / Williamson, James C; Edwards, Alistair V G; Verano-Braga, Thiago; Schwämmle, Veit; Kjeldsen, Frank; Jensen, Ole Nørregaard; Larsen, Martin R.

I: Proteomics, Bind 16, Nr. 6, 03.2016, s. 907-914.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

TY - JOUR

T1 - High-performance hybrid Orbitrap mass spectrometers for quantitative proteome analysis

T2 - Observations and implications

AU - Williamson, James C

AU - Edwards, Alistair V G

AU - Verano-Braga, Thiago

AU - Schwämmle, Veit

AU - Kjeldsen, Frank

AU - Jensen, Ole Nørregaard

AU - Larsen, Martin R

N1 - © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

PY - 2016/3

Y1 - 2016/3

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AB - We present basic workups and quantitative comparisons for two current generation Orbitrap mass spectrometers, the Q Exactive Plus and Orbitrap Fusion Tribrid, which are widely considered two of the highest performing instruments on the market. We assessed the performance of two quantitative methods on both instruments, namely label-free quantitation and stable isotope labeling using isobaric tags, for studying the heat shock response in Escherichia coli. We investigated the recently reported MS3 method on the Fusion instrument and the potential of MS3-based reporter ion isolation Synchronous Precursor Selection (SPS) and its impact on quantitative accuracy. We confirm that the label-free approach offers a more linear response with a wider dynamic range than MS/MS-based isobaric tag quantitation and that the MS3/SPS approach alleviates but does not eliminate dynamic range compression. We observed, however, that the choice of quantitative approach had little impact on the ability to statistically evaluate the E. coli heat shock response. We conclude that in the experimental conditions tested, MS/MS-based reporter ion quantitation provides reliable biological insight despite the issue of compressed dynamic range, an observation that significantly impacts the choice of instrument.

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

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