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

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 full MS scan remains extremely inefficient. Here we report a data novel acquisition method, termed BoxCar, in which filling multiple narrow mass-to-charge segments increases the mean ion injection time more than ten-fold compared to a standard full scan. In 1 hour analyses, the method provided MS1 evidence for more than 90% of the proteome of a human cancer cell line that had previously been identified in 24 fractions, and quantified more than 6,200 proteins in ten of ten replicates. In mouse brain tissue, we achieved broad proteome coveragedetected more than 10,000 proteins in only 100 min and sensitivity extended into the low attomol range.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Matthias Mann

PROVIDER: MSV000084418 | MassIVE | Fri Oct 04 10:44:00 BST 2019

SECONDARY ACCESSION(S): PXD006109

REPOSITORIES: MassIVE

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

Meier Florian F Geyer Philipp E PE Virreira Winter Sebastian S Cox Juergen J Mann Matthias M

Nature methods 20180507 6

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. ...[more]

PMID: 29735998

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