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PXD017209 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleA mouse SWATH-MS reference spectral library enables deconvolution of species-specific proteomic alterations in human tumour xenografts
DescriptionSWATH-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.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLukas Krasny
SpeciesList scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListiodoacetamide derivatized residue; deamidated residue
InstrumentTripleTOF 5600
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-01-20 08:19:56ID requested
12020-06-22 22:03:21announced
Publication List
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]
Keyword List
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
xenograft model
Contact List
Paul Huang
contact affiliationDivision of Molecular Pathology Molecular and Systems Oncology Team The Institute of Cancer Research 237 Fulham Road, SW3 6JB London United Kingdom
contact emailPaul.Huang@icr.ac.uk
lab head
Lukas Krasny
contact affiliationThe Institute of Cancer Research
contact emailLukas.Krasny@icr.ac.uk
dataset submitter
Full Dataset Link List
Dataset FTP location
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