PXD006109

PXD006109 is an original dataset announced via ProteomeXchange.

Title	BoxCar acquisition method enables single shot proteomics at a depth of 10,000 proteins in 100 minutes
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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:04:45.247.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Mario Oroshi
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2017-03-17 05:19:31	ID requested
1	2018-05-02 01:12:36	announced
2	2018-05-09 09:24:09	announced	Updated publication reference for PubMed record(s): 29735998.
⏵ 3	2024-10-22 04:04:53	announced	2024-10-22: Updated project metadata.

10.1038/s41592-018-0003-5;

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, 15(6):440-448(2018) [pubmed]

ProteomeXchange project tag: deep learning, benchmarking, machine learning

curator keyword: Technical

submitter keyword: cerebellum, Q Exactive, plasma, cell lines, mouse,human

Matthias Mann
contact affiliation	Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry
contact email	mmann@biochem.mpg.de
lab head
Mario Oroshi
contact affiliation	Proteomics
contact email	oroshi@biochem.mpg.de
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD006109

PRIDE project URI

• PRIDE
  1. PXD006109
     1. Label: PRIDE project
     2. Name: BoxCar acquisition method enables single shot proteomics at a depth of 10,000 proteins in 100 minutes