Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

Florian Meier; Andreas-David Brunner; Scarlet Koch; Heiner Koch; Markus Lubeck; Michael Krause; Niels Goedecke; Jens Decker; Thomas Kosinski; Melvin A Park; Nicolai Bache; Ole Hoerning; Jürgen Cox; Oliver Räther; Matthias Mann

doi:10.1074/mcp.TIR118.000900

Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

Florian Meier, Andreas-David Brunner, Scarlet Koch, Heiner Koch, Markus Lubeck, Michael Krause, Niels Goedecke, Jens Decker, Thomas Kosinski, Melvin A Park, Nicolai Bache, Ole Hoerning, Jürgen Cox, Oliver Räther, Matthias Mann

120 Citations (Scopus)

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Abstract

In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.

Original language	English
Journal	Molecular and Cellular Proteomics
Volume	17
Issue number	12
Pages (from-to)	2534-2545
ISSN	1535-9476
DOIs	https://doi.org/10.1074/mcp.TIR118.000900
Publication status	Published - Dec 2018

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Online Parallel Accumulation–SerialFragmentation (PASEF) with a Novel TrappedIon Mobility Mass SpectrometerFinal published version, 3.25 MBLicence: CC BY

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Meier, F., Brunner, A-D., Koch, S., Koch, H., Lubeck, M., Krause, M., Goedecke, N., Decker, J., Kosinski, T., Park, M. A., Bache, N., Hoerning, O., Cox, J., Räther, O., & Mann, M. (2018). Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer. Molecular and Cellular Proteomics, 17(12), 2534-2545. https://doi.org/10.1074/mcp.TIR118.000900

Meier, F, Brunner, A-D, Koch, S, Koch, H, Lubeck, M, Krause, M, Goedecke, N, Decker, J, Kosinski, T, Park, MA, Bache, N, Hoerning, O, Cox, J, Räther, O & Mann, M 2018, 'Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer', Molecular and Cellular Proteomics, vol. 17, no. 12, pp. 2534-2545. https://doi.org/10.1074/mcp.TIR118.000900

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title = "Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer",

abstract = "In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.",

author = "Florian Meier and Andreas-David Brunner and Scarlet Koch and Heiner Koch and Markus Lubeck and Michael Krause and Niels Goedecke and Jens Decker and Thomas Kosinski and Park, {Melvin A} and Nicolai Bache and Ole Hoerning and J{\"u}rgen Cox and Oliver R{\"a}ther and Matthias Mann",

note = "Published under license by The American Society for Biochemistry and Molecular Biology, Inc.",

year = "2018",

month = dec,

doi = "10.1074/mcp.TIR118.000900",

language = "English",

volume = "17",

pages = "2534--2545",

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T1 - Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

AU - Meier, Florian

AU - Brunner, Andreas-David

AU - Koch, Scarlet

AU - Koch, Heiner

AU - Lubeck, Markus

AU - Krause, Michael

AU - Goedecke, Niels

AU - Decker, Jens

AU - Kosinski, Thomas

AU - Park, Melvin A

AU - Bache, Nicolai

AU - Hoerning, Ole

AU - Cox, Jürgen

AU - Räther, Oliver

AU - Mann, Matthias

N1 - Published under license by The American Society for Biochemistry and Molecular Biology, Inc.

PY - 2018/12

Y1 - 2018/12

N2 - In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.

AB - In bottom-up proteomics, peptides are separated by liquid chromatography with elution peak widths in the range of seconds, whereas mass spectra are acquired in about 100 microseconds with time-of-flight (TOF) instruments. This allows adding ion mobility as a third dimension of separation. Among several formats, trapped ion mobility spectrometry (TIMS) is attractive because of its small size, low voltage requirements and high efficiency of ion utilization. We have recently demonstrated a scan mode termed parallel accumulation - serial fragmentation (PASEF), which multiplies the sequencing speed without any loss in sensitivity (Meier et al., PMID: 26538118). Here we introduce the timsTOF Pro instrument, which optimally implements online PASEF. It features an orthogonal ion path into the ion mobility device, limiting the amount of debris entering the instrument and making it very robust in daily operation. We investigate different precursor selection schemes for shotgun proteomics to optimally allocate in excess of 100 fragmentation events per second. More than 600,000 fragmentation spectra in standard 120 min LC runs are achievable, which can be used for near exhaustive precursor selection in complex mixtures or accumulating the signal of weak precursors. In 120 min single runs of HeLa digest, MaxQuant identified more than 6,000 proteins without matching to a library and with high quantitative reproducibility (R > 0.97). Online PASEF achieves a remarkable sensitivity with more than 2,500 proteins identified in 30 min runs of only 10 ng HeLa digest. We also show that highly reproducible collisional cross sections can be acquired on a large scale (R > 0.99). PASEF on the timsTOF Pro is a valuable addition to the technological toolbox in proteomics, with a number of unique operating modes that are only beginning to be explored.

U2 - 10.1074/mcp.TIR118.000900

DO - 10.1074/mcp.TIR118.000900

M3 - Journal article

C2 - 30385480

SN - 1535-9476

VL - 17

SP - 2534

EP - 2545

JO - Molecular and Cellular Proteomics

JF - Molecular and Cellular Proteomics

IS - 12

ER -

Online parallel accumulation - serial fragmentation (PASEF) with a novel trapped ion mobility mass spectrometer

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