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PXD022448

PXD022448 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleLibrary-free BoxCarDIA solves the missing value problem in label-free quantitative proteomics
DescriptionThe last decade has seen significant advances in the application of quantitative mass spectrometry-based proteomics technologies to tackle important questions in plant biology. The current standard for quantitative proteomics in plants is the use of data-dependent acquisition (DDA) analysis with or without the use of chemical labels. However, the DDA approach preferentially measures higher abundant proteins, and often requires data imputation due to quantification inconsistency between samples. In this study we systematically benchmarked a recently developed library-free data-independent acquisition (directDIA) method against a state-of-the-art DDA label-free quantitative proteomics workflow for plants. We next developed a novel acquisition approach combining MS1-level BoxCar acquisition with MS2-level directDIA analysis that we call BoxCarDIA. DirectDIA achieves a 33% increase in protein quantification over traditional DDA, and BoxCarDIA a further 8%, without any changes in instrumentation, offline fractionation, or increases in mass-spectrometer run time. BoxCarDIA, especially, offers wholly reproducible quantification of proteins between replicate injections, thereby addressing the long-standing missing-value problem in label-free quantitative proteomics. Further, we find that the gains in dynamic range sampling by directDIA and BoxCarDIA translate to deeper quantification of key, low abundant, functional protein classes (e.g., protein kinases and transcription factors) that are underrepresented in data acquired using DDA. We applied these methods to perform a quantitative proteomic comparison of dark and light grown Arabidopsis cell cultures, providing a critical resource for future plant interactome studies. Our results establish BoxCarDIA as the new method of choice in quantitative proteomics using Orbitrap-type mass-spectrometers, particularly for proteomes with large dynamic range such as that of plants.
HostingRepositoryPRIDE
AnnounceDate2021-05-11
AnnouncementXMLSubmission_2021-05-11_10:29:44.854.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRichard Uhrig
SpeciesList scientific name: Arabidopsis thaliana (Mouse-ear cress); NCBI TaxID: 3702;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-11-10 02:00:19ID requested
12021-05-11 10:29:45announced
Publication List
Dataset with its publication pending
Keyword List
submitter keyword: label-free, BoxCar, DIA, directDIA, data acquisition, Arabidopsis
Contact List
R. Glen Uhrig
contact affiliationDepartment of Biological Sciences, University of Alberta
contact emailruhrig@ualberta.ca
lab head
Richard Uhrig
contact affiliationUniversity of Alberta
contact emailruhrig@ualberta.ca
dataset submitter
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Dataset FTP location
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