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PXD019539 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProcess and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis
DescriptionWe investigated the effect of homogenization strategy and protein precipitation on downstream protein quantitation using multiple reaction monitoring mass spectrometry (MRM-MS). Our objective was to develop a workflow capable of processing disparate tissue types with high throughput, minimal variability, and maximum purity. Similar abundances of endogenous proteins were measured in nine different mouse tissues regardless of homogenization method, however protein precipitation had strong positive effects on several targets. Best throughput was achieved by lyophilizing tissues to dryness followed by homogenization via bead-beating without sample buffer. Finally, the effect of tissue perfusion prior to dissection and collection was explored in 20 mouse tissues. MRM-MS showed decreased abundances of blood-related proteins in perfused tissues, however complete removal was not achieved. Concentrations of non-blood proteins were largely unchanged, although significantly higher variances were observed for proteins from perfused lung indicating perfusion may not be suitable for this organ. We present a simple yet effective tissue processing workflow consisting of harvest of fresh non-perfused tissue, novel lyophilization and homogenization by bead-beating, and protein precipitation. This workflow can be applied to a range of mouse tissues with the advantages of simplicity, minimal manual manipulation of samples, use of commonly available equipment, and high sample quality.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterSarah Michaud
SpeciesList scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationListLabel:13C(6)15N(2); Label:13C(6)15N(4)
Instrument6495B Triple Quadrupole LC/MS
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-06-03 06:35:25ID requested
12020-11-05 11:26:09announced
22021-01-24 19:48:09announced: Added PubMed ID
Publication List
Michaud SA, Pětrošová H, Jackson AM, McGuire JC, Sinclair NJ, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Schibli D, Smith D, Borchers CH, Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis. J Proteome Res, 20(1):305-316(2021) [pubmed]
Keyword List
submitter keyword: Tissue proteomics, mass spectrometry, sample preparation, homogenization, acetone precipitation, tissue lyophilization
Contact List
Christoph Borchers
contact affiliationMcGill University / University of Victoria
contact emailchristoph.borchers@mcgill.ca
lab head
Sarah Michaud
contact affiliationU Victoria - Genome BC Proteomics Centre
contact emailsarah@proteincentre.com
dataset submitter
Full Dataset Link List
Panorama Public dataset URI