PXD008758-1

PXD008758 is an original dataset announced via ProteomeXchange.

Title	A technique to identify context-based protein biomarkers: Application to a mouse liver cancer model
Description	To date, most proteomic analyses towards cancer biomarker discovery have been based on protein quantification. However, proteins function in association with other proteins to form modules that are localized in specific subcellular compartments. Cellular mislocalization of proteins has in fact been detected as a key feature in a variety of cancer cells1,2. Here, we describe a strategy for biomarker detection based on a mitochrondrial enrichment score (mtES), which is sensitive to protein abundance as well as protein translocation between mitochondria and cytosol. The mtES score integrates protein expression data from total cellular lysates and enriched mitochondrial fractions and provides important information for the classification of cancer samples, which is not apparent from conventional quantitative protein measurements. We apply the new strategy to a panel of wild-type and mutant mice that are either healthy or present liver cancer. We show that proteome changes based on mtES scores outperform protein abundance measurements in discriminating liver cancer from healthy liver tissue and that they are uniquely robust against strong genetic perturbation. Overall, our method provides a more sensitive approach to cancer biomarker discovery that takes into account contextual information of tested proteins.
HostingRepository	PRIDE
AnnounceDate	2019-05-09
AnnouncementXML	Submission_2019-05-09_07:06:29.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tatjana Sajic
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-26 00:31:10	ID requested
⏵ 1	2019-05-09 07:06:46	announced

Sajic T, Ciuffa R, Lemos V, Xu P, Leone V, Li C, Williams EG, Makris G, Banaei-Esfahani A, Heikenwalder M, Schoonjans K, Aebersold R, A new class of protein biomarkers based on subcellular distribution: application to a mouse liver cancer model. Sci Rep, 9(1):6913(2019) [pubmed]

curator keyword: Biomedical

submitter keyword: Mouse Liver, Cancer, SWATH-MS

Prof. Dr. Ruedi Aebersold
contact affiliation	Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Tatjana Sajic
contact affiliation	IMSB, ETH Zurich
contact email	sajic@imsb.biol.ethz.ch
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD008758
     1. Label: PRIDE project
     2. Name: A technique to identify context-based protein biomarkers: Application to a mouse liver cancer model