PXD007688

PXD007688 is an original dataset announced via ProteomeXchange.

Title	Allergen detection in commercial foods
Description	The frequent use of precautionary food allergen labeling statements such as “may contain” poses challenges to allergic individuals relying on such labeling to determine whether a food is safe to consume. To survey the frequency at which these precautionary statements indicate allergen contamination in commercial foods we developed a multiplexed liquid chromatography-mass spectrometry assay targeting 14 common allergens. For each allergen, we selected two or more tryptic peptides belonging to two or more clinically-recognized allergenic proteins by following one of two approaches. For certain allergenic proteins, a wealth of existing mass spectrometry literature suggests ideal tryptic peptide targets. In these cases, such for milk proteins Bos d 5 and Bos d 9, as well as peanut protein Ara h 3, we chose peptides using the Allergen Peptide Browser (APB), a freely available online database we developed. To choose peptides for the remaining allergenic proteins, as well as validate our choices, we applied shotgun proteomics to pure allergen protein extracts of the aforementioned allergens.
HostingRepository	PRIDE
AnnounceDate	2019-07-17
AnnouncementXML	Submission_2019-08-19_04:32:24.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD007688
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Derek Croote
SpeciesList	scientific name: Arachis hypogaea (Peanut); NCBI TaxID: 3818; scientific name: Anacardium occidentale; NCBI TaxID: 171929; scientific name: Sesamum indicum; NCBI TaxID: 4182; scientific name: Corylus avellana; NCBI TaxID: 13451; scientific name: Avena sativa; NCBI TaxID: 4498; scientific name: Carya illinoinensis; NCBI TaxID: 32201; scientific name: Lupinus angustifolius; NCBI TaxID: 3871; scientific name: Prunus dulcis; NCBI TaxID: 3755; scientific name: Juglans; NCBI TaxID: 16718; scientific name: Triticum aestivum (Wheat); NCBI TaxID: 4565; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Sinapis alba; NCBI TaxID: 3728; scientific name: Secale cereale; NCBI TaxID: 4550; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Apium graveolens; NCBI TaxID: 4045; scientific name: Pistacia vera; NCBI TaxID: 55513; scientific name: Glycine max (Soybean) (Glycine hispida); NCBI TaxID: 3847; scientific name: Fagopyrum esculentum; NCBI TaxID: 3617; scientific name: Bertholletia excelsa; NCBI TaxID: 3645; scientific name: Hordeum vulgare (Barley); NCBI TaxID: 4513;
ModificationList	Dethiomethyl; Glu->pyro-Glu; Deamidated; Oxidation; Acetyl; Carbamidomethyl; Dicarbamidomethyl; Gln->pyro-Glu
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2017-09-07 02:55:47	ID requested
1	2019-07-17 00:08:45	announced
⏵ 2	2019-08-19 04:32:25	announced	Updated publication reference for PubMed record(s): 31339301.

Croote D, Braslavsky I, Quake SR, Addressing Complex Matrix Interference Improves Multiplex Food Allergen Detection by Targeted LC-MS/MS. Anal Chem, 91(15):9760-9769(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Food, allergen, allergy, IgE,

Stephen Quake
contact affiliation	Department of Bioengineering, Stanford University, Stanford, CA 94305, USA Department of Applied Physics, Stanford University, Stanford, CA 94305, USA Chan Zuckerberg Biohub, San Francisco, CA 94518, USA
contact email	quake@stanford.edu
lab head
Derek Croote
contact affiliation	Stanford University
contact email	dcroote@stanford.edu
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/2019/07/PXD007688

PRIDE project URI

• PRIDE
  1. PXD007688
     1. Label: PRIDE project
     2. Name: Allergen detection in commercial foods