PXD021381

PXD021381 is an original dataset announced via ProteomeXchange.

Title	Hybrid QconCAT-based Targeted Absolute and Data-independent Acquisition-based Label-free Quantification Enables In-depth Proteomic Characterization of Wheat ATI Extracts
Description	In this study, we present a novel hybrid data-independent acquisition LC-MS approach, combining QconCAT technology with short microflow LC gradients and DIA and apply the method towards the quantitative proteome analysis of ATI extracts from wheat flour. The novel method is fast, robust and reproducible and provides accurate QconCAT-based absolute quantification of major ATI proteins while simultaneously quantifying the non-targeted proteome by DIA-based label-free quantification. Using a set of 120 samples of full kernel flour derived from 60 varieties of common wheat grown in replication, we assess the repeatability and accuracy of the workflow for the quantification of ATI at the peptide and protein level. Applying the method to analyze different wheat species (i.e. common wheat, spelt, durum wheat, emmer and einkorn) and comparing the results to published data, we validate inter-laboratory and cross-methodology reproducibility of ATI quantification, which are essential in the context of large-scale breeding projects. Additionally, we apply our workflow to assess environmental effects on ATI expression, analyzing ATI content and proteome of wheat species grown at different locations. Finally, we explore the potential of combining QconCAT-based absolute quantification with DIA-based untargeted proteome analysis and LFQ for the generation of new hypotheses or assay development.
HostingRepository	PRIDE
AnnounceDate	2021-04-22
AnnouncementXML	Submission_2021-04-21_23:40:59.120.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Malte Sielaff
SpeciesList	scientific name: Triticum aestivum (Wheat); NCBI TaxID: 4565;
ModificationList	iodoacetamide derivatized residue
Instrument	Synapt MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-09-09 22:20:05	ID requested
⏵ 1	2021-04-21 23:40:59	announced

Sielaff M, Curella V, Neerukonda M, Afzal M, El Hassouni K, Distler U, Schuppan D, Longin CFH, Tenzer S, Hybrid QconCAT-Based Targeted Absolute and Data-Independent Acquisition-Based Label-Free Quantification Enables In-Depth Proteomic Characterization of Wheat Amylase/Trypsin Inhibitor Extracts. J Proteome Res, 20(3):1544-1557(2021) [pubmed]

submitter keyword: Amylase-Trypsin Inhibitor, ATI, Wheat, Triticum, Data-independent Acquisition, DIA, QconCAT, Absolute Quantification, Microflow LC-MS

Stefan Tenzer
contact affiliation	Institute for Immunology University Medical Center Mainz Langenbeckstr. 1 55131 Mainz, Germany
contact email	tenzer@uni-mainz.de
lab head
Malte Sielaff
contact affiliation	University Medical Center Mainz
contact email	malte.sielaff@uni-mainz.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD021381
     1. Label: PRIDE project
     2. Name: Hybrid QconCAT-based Targeted Absolute and Data-independent Acquisition-based Label-free Quantification Enables In-depth Proteomic Characterization of Wheat ATI Extracts