MassIVE MSV000084418

Imported Reanalysis Dataset Public PXD006109

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

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Description

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. [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: human ; cell lines ; plasma ; mouse ; cerebellum ; Q Exactive

Contact

Principal Investigators:
(in alphabetical order) 		Matthias Mann, Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry, N/A
Submitting User: ccms

Publications

Meier F, Geyer PE, Virreira Winter S, Cox J, Mann M.
BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes.
Nat. Methods. 2018 Jun;15(6):440-448. Epub 2018 May 7.

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Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

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Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.