PXD002529

PXD002529 is an original dataset announced via ProteomeXchange.

Title	Milk bottom-up proteomics: method optimisation.
Description	Milk is a complex fluid whose proteome displays a diverse set of proteins of high abundance such as caseins and medium to low abundance whey proteins such as ß-lactoglobulin, lactoferrin, immunoglobulins, glycoproteins, peptide hormones and enzymes. A sample preparation method that enables high reproducibility and throughput is key in reliably identifying proteins present or proteins responding to conditions such as a diet, health or genetics. Using skim milk samples from Jersey and Holstein cows, we compared three extraction procedures which have not previously been applied to samples of cows’ milk. Method A (urea) involved a simple dilution of the milk in a urea-based buffer, method B (TCA/acetone) involved a TCA/acetone precipitation and method C (methanol/chloroform) involved a tri-phasic partition method in chloroform/methanol solution. Protein assays, SDS-PAGE profiling, and trypsin digestion followed by nanoHPLC-electrospray ionisation-tandem mass spectrometry (nLC-ESI-MS/MS) analyses were performed to assess their efficiency. Replicates were used at each analytical step (extraction, digestion, injection) to assess reproducibility. Overall 186 unique accessions, major and minor proteins, were identified with a combination of methods. Method C (methanol/chloroform) yielded the best resolved SDS-patterns and highest protein recovery rates, method A (urea) yielded the greatest number of accessions, and, of the three procedures, method B (TCA/acetone) was the least compatible of all with a wide range of downstream analytical procedures. Our results also highlighted breed differences between the proteins in milk of Jersey and Holstein cows.
HostingRepository	PRIDE
AnnounceDate	2016-01-26
AnnouncementXML	Submission_2016-01-26_06:42:44.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Delphine Vincent
SpeciesList	scientific name: Bos taurus (Bovine); NCBI TaxID: 9913;
ModificationList	iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-07-13 03:29:32	ID requested
⏵ 1	2016-01-26 06:42:46	announced

Vincent D, Ezernieks V, Elkins A, Nguyen N, Moate PJ, Cocks BG, Rochfort S, Milk Bottom-Up Proteomics: Method Optimization. Front Genet, 6():360(2015) [pubmed]

curator keyword: Technical

submitter keyword: Jersey and Holstein cow milk, nLC-ESI-MS, proteome, trypsin digestion, replicates.

Delphine Vincent
contact affiliation	AgriBio centre, Department of Economic Development, government of Victoria, Australia
contact email	delphine.vincent@ecodev.vic.gov.au
lab head
Delphine Vincent
contact affiliation	Department of Economic Development
contact email	delphine.vincent@ecodev.vic.gov.au
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002529
     1. Label: PRIDE project
     2. Name: Milk bottom-up proteomics: method optimisation.