PXD017209

PXD017209 is an original dataset announced via ProteomeXchange.

Title	A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts
Description	SWATH-MS enables accurate and reproducible label-free quantification of proteomes including in extensively studied model organisms such as the mouse. Here we present a comprehensive mouse reference spectral library (MouseRefSWATH) that allows quantification of up to 10,597 proteins (62.2% of mouse proteome) by SWATH-MS. We exploit MouseRefSWATH to develop an analytical pipeline for species-specific deconvolution of proteomic alterations in human tumour xenografts (XenoSWATH). This method overcomes the challenge of high protein sequence similarity between the mouse and human, facilitating the study of host microenvironment-tumour interactions from ‘bulk tumour’ measurements. We apply XenoSWATH to characterise a xenograft model of breast ductal carcinoma in-situ and uncover complex regulation of cell migration pathways that is not restricted to the tumour cells but also operates in the mouse stromal upon progression to invasive disease. MouseRefSWATH and XenoSWATH opens new possibilities for in-depth proteomic assessment to address wide-ranging biological questions involving this important model organism.
HostingRepository	PRIDE
AnnounceDate	2020-06-23
AnnouncementXML	Submission_2020-06-22_22:03:20.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lukas Krasny
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue; deamidated residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-20 08:19:56	ID requested
⏵ 1	2020-06-22 22:03:21	announced

Krasny L, Bland P, Burns J, Lima NC, Harrison PT, Pacini L, Elms ML, Ning J, Martinez VG, Yu YR, Acton SE, Ho PC, Calvo F, Swain A, Howard BA, Natrajan RC, Huang PH, A mouse SWATH-mass spectrometry reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts. Dis Model Mech, 13(7):(2020) [pubmed]

ProteomeXchange project tag: Cancer (B/D-HPP), Biology/Disease-Driven Human Proteome Project (B/D-HPP), Human Proteome Project

submitter keyword: SWATH-MS

breast cancer

DCIS

mouse

human

xenograft model

Paul Huang
contact affiliation	Division of Molecular Pathology Molecular and Systems Oncology Team The Institute of Cancer Research 237 Fulham Road, SW3 6JB London United Kingdom
contact email	Paul.Huang@icr.ac.uk
lab head
Lukas Krasny
contact affiliation	The Institute of Cancer Research
contact email	Lukas.Krasny@icr.ac.uk
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/2020/06/PXD017209

PRIDE project URI

• PRIDE
  1. PXD017209
     1. Label: PRIDE project
     2. Name: A mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts