PXD023654

PXD023654 is an original dataset announced via ProteomeXchange.

Title	Hybrid label-free quantification proteomics and QconCAT-assisted quantification of amylase-trypsin inhibitors from flours of 150 wheat varieties (3 field locations) by LC-MSE
Description	Wheat (Triticum aestivum ssp. aestivum) contributes to 20% of the human protein supply, delivers essential amino acids and is of fundamental importance for bread and pasta quality. Wheat proteins are also involved in adverse human reactions like celiac disease, wheat allergy and the non-celiac wheat sensitivity (NCWS). Using LC-MS-based LFQ proteomics of aqueous flour extracts we determined 756 proteins across 150 wheat varieties grown in three environments. However, only 303 proteins were stably expressed across all environments in at least one variety underlining the large influence of environmental conditions on the expression of many proteins. Moreover, only 89 proteins were comparably expressed by all 150 varieties, with high coefficients of variation for the other proteins. Heritability (h) ranged from 0-1 with 114 proteins having h² > 0.6. Therefore, the expression of the variable proteins should be amenable to targeted manipulation across the wheat supply chain by varietal choice and breeding. Our study provides a first approach towards a fast and high-throughput methodology for quantifying these proteins which is required to breed wheats with the desired properties. Amylase trypsin inhibitors (ATIs) appear as a potential trigger for NCWS inducing intestinal and extra-intestinal inflammation. Studies on the prevalence and genetic architecture of ATI proteins in wheat are lacking so far. Large differences in the content and composition of 8 ATIs in the different varieties were identified by QconCAT-assisted quantification. The ATI proteins had low coefficients of correlations with quality traits commonly analyzed in wheat breeding. However, heritability was quite low except for ATI 0.28 and ATI CM2. A genome wide association mapping revealed a complex genetic architecture built up on many small but few medium and two major quantitative trait loci (QTL). The latter were on chromosome 3B for ATI 0.19-like and 6B for ATI 0.28 explaining 70.6 and 68.7% of the genetic variance, respectively. Using the wheat reference genome sequence, seven potential candidate genes behind the medium and major QTL were described with only one showing polymorphism based on exome capture analysis. Consequently, wheat breeding could contribute to a reduction of ATI contents in wheat products if incidence of ATI on human health is further confirmed.
HostingRepository	PRIDE
AnnounceDate	2022-02-16
AnnouncementXML	Submission_2022-02-16_15:50:02.297.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	2021-01-18 01:18:05	ID requested
⏵ 1	2022-02-16 15:50:09	announced

Afzal M, Sielaff M, Curella V, Neerukonda M, El Hassouni K, Schuppan D, Tenzer S, Longin CFH, Characterization of 150 Wheat Cultivars by LC-MS-Based Label-Free Quantitative Proteomics Unravels Possibilities to Design Wheat Better for Baking Quality and Human Health. Plants (Basel), 10(3):(2021) [pubmed]

submitter keyword: Synapt G2-S, MSE, data-independent acquisition (DIA), label-free quantification (LFQ), QconCAT, wheat varieties, breeding, proteomics, amylase-trypsin inhibitors (ATIs), non-celiac wheat sensitivity (NCWS)

Stefan Tenzer
contact affiliation	Institute for Immunology, University Medical Center of the Johannes Gutenberg-University 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

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/2021/09/PXD023654

PRIDE project URI

• PRIDE
  1. PXD023654
     1. Label: PRIDE project
     2. Name: Hybrid label-free quantification proteomics and QconCAT-assisted quantification of amylase-trypsin inhibitors from flours of 150 wheat varieties (3 field locations) by LC-MSE