PXD011599

PXD011599 is an original dataset announced via ProteomeXchange.

Title	Discovery and quantification of non-human proteins in human milk
Description	The question whether and which non-human peptides or proteins are present in human milk was raised many decades ago. However, due to cross-reactivity or nonspecific antibody recognition, the accuracy of detection by immunochemical methods has been a concern. Additionally, the relative low-abundance of non-human peptides/proteins in the complex milk sample makes them a challenging target to detect. Here, by deep proteome profiling we detected several non-human peptides, which could be grouped as non-human proteins. We next estimated their concentration in human milk by combining data-dependent shotgun proteomics and parallel reaction monitoring. First, we fractionated human milk at the protein level by using sodium dodecyl sulfate polyacrylamide gel electrophoresis followed by reduction, alkylation and in-gel digestion. The resulted peptide mixtures were subjected to proteomics analysis. We were able to detect 1577 human proteins in human milk. Additionally, we identified 109 non-human peptides, of which 71 were grouped in to 36 non-human proteins. In the next step, we targeted 37 non-human peptides and 9 of them could be repeatedly quantified in human milk samples. Peptides/proteins originating from bovine milk products were the dominant non-human proteins observed, notably bovine caseins (α-S1-, α-S2-, β-, κ-caseins) and β-lactoglobulin.
HostingRepository	PRIDE
AnnounceDate	2018-12-04
AnnouncementXML	Submission_2018-12-05_05:59:34.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD011599
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Jing Zhu
SpeciesList	scientific name: Canis lupus familiaris; NCBI TaxID: 9615; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Oryza sativa (Rice); NCBI TaxID: 4530; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796; scientific name: Felis catus; NCBI TaxID: 9685;
ModificationList	Oxidation; Carbamidomethyl
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-11-07 05:19:03	ID requested
1	2018-12-04 02:10:03	announced
⏵ 2	2018-12-05 05:59:35	announced	Updated publication reference for PubMed record(s): 30489082.

Zhu J, Garrigues L, Van den Toorn H, Stahl B, Heck AJR, Discovery and Quantification of Nonhuman Proteins in Human Milk. J Proteome Res, 18(1):225-238(2019) [pubmed]

submitter keyword: non-human peptides, non-human proteins, shotgun proteomics, parallel reaction monitoring, mass spectrometry, human milk

Albert J.R. Heck
contact affiliation	Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Science4Life, University of Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
contact email	a.j.r.heck@uu.nl
lab head
Jing Zhu
contact affiliation	Utrecht University
contact email	j.zhu@uu.nl
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/2018/12/PXD011599

PRIDE project URI

• PRIDE
  1. PXD011599
     1. Label: PRIDE project
     2. Name: Discovery and quantification of non-human proteins in human milk