PXD019539-2

PXD019539 is an original dataset announced via ProteomeXchange.

Title	Process and Workflow for Preparation of Disparate Mouse Tissues for Proteomic Analysis
Description	We 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.
HostingRepository	PanoramaPublic
AnnounceDate	2021-01-24
AnnouncementXML	Submission_2021-01-24_19:48:09.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Sarah Michaud
SpeciesList	scientific name: Mus musculus; NCBI TaxID: 10090;
ModificationList	Label:13C(6)15N(2); Label:13C(6)15N(4)
Instrument	6495B Triple Quadrupole LC/MS

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-03 06:35:25	ID requested
1	2020-11-05 11:26:09	announced
⏵ 2	2021-01-24 19:48:09	announced	: Added PubMed ID

Michaud SA, P, ě, tro, š, ov, á 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]

submitter keyword: Tissue proteomics, mass spectrometry, sample preparation, homogenization, acetone precipitation, tissue lyophilization

Christoph Borchers
contact affiliation	McGill University / University of Victoria
contact email	christoph.borchers@mcgill.ca
lab head
Sarah Michaud
contact affiliation	U Victoria - Genome BC Proteomics Centre
contact email	sarah@proteincentre.com
dataset submitter

Panorama Public dataset URI