PXD005573-1

PXD005573 is an original dataset announced via ProteomeXchange.

Title	Heralds of parallel MS: Data-independent acquisition surpassing sequential identification of data dependent acquisition in proteomics
Description	Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present a parallel mass spectrometry method based on data-independent acquisition that surpasses the serial limitation of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we quantified over 7,500 proteins of human cell lines and 9,000 proteins of mouse tissues, with fewer than 2.5% missing proteins and median coefficients of variation of 5% among replicates. In very complex mixtures, we could quantify more than 15,000 proteins, outperforming data-dependent acquisition methods by more than four-fold. Using this method, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in murine barrel cortex. This work shows that parallel mass spectrometry enables proteome profiling with high coverage, reproducibility, precision and scalability to hundreds of samples.
HostingRepository	PRIDE
AnnounceDate	2017-04-24
AnnouncementXML	Submission_2017-04-24_04:56:00.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roland Bruderer
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Caenorhabditis elegans; NCBI TaxID: 6239; scientific name: Candida albicans (Yeast); NCBI TaxID: 5476; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; acetylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2016-12-15 06:37:06	ID requested
⏵ 1	2017-04-24 04:56:01	announced
2	2017-10-27 00:14:10	announced	Updated project metadata.
3	2017-11-01 08:51:38	announced	Updated publication reference for PubMed record(s): 29070702.
4	2017-11-06 05:24:10	announced	Updated project metadata.
5	2024-10-22 04:41:18	announced	2024-10-22: Updated project metadata.

Bruderer R, Bernhardt OM, Gandhi T, Xuan Y, Sondermann J, Schmidt M, Gomez-Varela D, Reiter L, WITHDRAWN: Heralds of parallel MS: Data-independent acquisition surpassing sequential identification of data dependent acquisition in proteomics. Mol Cell Proteomics, ():(2017) [pubmed]

curator keyword: Technical

submitter keyword: DIA, mouse brain development, Spectronaut

Lukas Reiter
contact affiliation	Biognosys AG
contact email	lukas.reiter@biognosys.com
lab head
Roland Bruderer
contact affiliation	Biognosys AG
contact email	roland.bruderer@biognosys.ch
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/2017/04/PXD005573

PRIDE project URI

• PRIDE
  1. PXD005573
     1. Label: PRIDE project
     2. Name: Heralds of parallel MS: Data-independent acquisition surpassing sequential identification of data dependent acquisition in proteomics