PXD005573

PXD005573 is an original dataset announced via ProteomeXchange.

Title	Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
Description	Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the limitation of serial MS2 acquisition of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we identified and quantified 6,383 proteins in human cell lines using 2-or-more peptides/protein and over 7,100 proteins when including the 717 proteins that were identified on the basis of a single peptide sequence. 7,739 proteins were identified in mouse tissues using 2-or-more peptides/protein and 8,121 when including the 382 proteins that were identified on the basis of a single peptide sequence. Missing values for proteins were within 0.3 to 2.1% and median coefficients of variation of 4.7 to 6.2% among technical triplicates. In very complex mixtures, we could quantify 10,780 proteins and 12,192 proteins when including the 1,412 proteins that were identified on the basis of a single peptide sequence. Using this optimized DIA, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1 barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:41:17.455.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roland Bruderer
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; deamidated 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.

10.1074/mcp.ra117.000314;

Bruderer R, Bernhardt OM, Gandhi T, Xuan Y, Sondermann J, Schmidt M, Gomez-Varela D, Reiter L, Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results. Mol Cell Proteomics, 16(12):2296-2309(2017) [pubmed]

ProteomeXchange project tag: deep learning, retention time, benchmarking, machine learning

curator keyword: Technical

submitter keyword: human DIA proteomics

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.com
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/2017/10/PXD005573

PRIDE project URI

• PRIDE
  1. PXD005573
     1. Label: PRIDE project
     2. Name: Optimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results