BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

Florian Meier; Philipp E. Geyer; Sebastian Virreira Winter; Juergen Cox; Matthias Mann

doi:10.1038/s41592-018-0003-5

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

Florian Meier, Philipp E. Geyer, Sebastian Virreira Winter, Juergen Cox, Matthias Mann

138 Citations (Scopus)

Abstract

Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we detected more than 10,000 proteins in only 100 min, and sensitivity extended into the low-attomolar range.

Original language	English
Journal	Nature Methods
Volume	15
Issue number	6
Pages (from-to)	440-448
Number of pages	9
ISSN	1548-7091
DOIs	https://doi.org/10.1038/s41592-018-0003-5
Publication status	Published - 2018

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abstract = "Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we detected more than 10,000 proteins in only 100 min, and sensitivity extended into the low-attomolar range.",

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T1 - BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

AU - Meier, Florian

AU - Geyer, Philipp E.

AU - Virreira Winter, Sebastian

AU - Cox, Juergen

AU - Mann, Matthias

PY - 2018

Y1 - 2018

N2 - Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we detected more than 10,000 proteins in only 100 min, and sensitivity extended into the low-attomolar range.

AB - Great advances have been made in sensitivity and acquisition speed on the Orbitrap mass analyzer, enabling increasingly deep proteome coverage. However, these advances have been mainly limited to the MS2 level, whereas ion beam sampling for the MS1 scans remains extremely inefficient. Here we report a data-acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than tenfold as compared to that of a standard full scan. In 1-h analyses, the method provided MS1-level evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and it quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we detected more than 10,000 proteins in only 100 min, and sensitivity extended into the low-attomolar range.

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DO - 10.1038/s41592-018-0003-5

M3 - Journal article

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EP - 448

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JF - Nature Methods

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BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

Abstract

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