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PXD005573

PXD005573 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimization of Experimental Parameters in Data-Independent Mass Spectrometry Significantly Increases Depth and Reproducibility of Results
DescriptionComprehensive, 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.
HostingRepositoryPRIDE
AnnounceDate2017-11-06
AnnouncementXMLSubmission_2017-11-06_05:24:09.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRoland Bruderer
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListphosphorylated residue; monohydroxylated residue; acetylated residue; deamidated residue
InstrumentQ Exactive HF
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-12-15 06:37:06ID requested
12017-04-24 04:56:01announced
22017-10-27 00:14:10announcedUpdated project metadata.
32017-11-01 08:51:38announcedUpdated publication reference for PubMed record(s): 29070702.
42017-11-06 05:24:10announcedUpdated project metadata.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: human DIA proteomics
Contact List
Lukas Reiter
contact affiliationBiognosys AG
contact emaillukas.reiter@biognosys.com
lab head
Roland Bruderer
contact affiliationBiognosys AG
contact emailroland.bruderer@biognosys.com
dataset submitter
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