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

Meier, F., Geyer, P. E., Winter, S. V., Cox, J., & Mann, M. (2018). BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes. Nature methods, 15(6), 440-448. doi:10.1038/s41592-018-0003-5.

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 Creators:
Meier, Florian1, Author              
Geyer, Philipp E.1, Author              
Winter, Sebastian Virreira1, Author              
Cox, Jürgen2, Author              
Mann, Matthias1, Author              
Affiliations:
1Mann, Matthias / Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Max Planck Society, ou_1565159              
2Cox, Jürgen / Computational Systems Biochemistry, Max Planck Institute of Biochemistry, Max Planck Society, ou_2063284              

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Free keywords: DATA-INDEPENDENT ACQUISITION; ORBITRAP MASS-SPECTROMETRY; TARGETED PROTEOMICS; DNA-REPLICATION; COPY-NUMBER; QUANTIFICATION; STRATEGY; ACCURATE; REPRODUCIBILITY; PERFORMANCEBiochemistry & Molecular Biology;
 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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Language(s): eng - English
 Dates: 2018
 Publication Status: Published in print
 Pages: 11
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: ISI: 000434487400024
DOI: 10.1038/s41592-018-0003-5
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Project name : MSmed project (F.M., P.E.G., S.V.W., J.C., M.M.)
Grant ID : 686547
Funding program : Horizon 2020 (H2020)
Funding organization : European Commission (EC)

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Title: Nature methods
  Other : Nature methods
Source Genre: Journal
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Publ. Info: New York, NY : Nature Pub. Group
Pages: - Volume / Issue: 15 (6) Sequence Number: - Start / End Page: 440 - 448 Identifier: ISSN: 1548-7091
CoNE: https://pure.mpg.de/cone/journals/resource/111088195279556