PXD044157-1

PXD044157 is an original dataset announced via ProteomeXchange.

Title	ProteoMixture: A Cell Deconvolution Tool for Bulk Tissue Proteomics Data
Description	Numerous multi-omic investigations of cancer tissue have documented varying and poor pairwise transcript:protein quantitative correlations and most deconvolution tools aiming to predict cell type proportions (cell admixture) have been developed and credentialed using transcript-level data alone. To estimate cell admixture using protein abundance data, we analyzed proteome (and transcriptome data) generated from contrived admixtures of tumor, stroma, and immune cell models or those selectively harvested from the tissue microenvironment by laser microdissection from high grade serous ovarian cancer (HGSOC) tumors. Co-quantified transcripts and proteins performed similarly to estimate stroma and immune cell admixture in two commonly used deconvolution algorithms ESTIMATE and ConsensusTME (r ≥ 0.63). Here we have developed and optimized protein-based signatures to estimate cell admixture proportions and benchmarked these using bulk tumor proteomics data from over 150 HGSOC patients. The optimized protein signatures supporting cell type proportion estimates from bulk tissue proteomic data are available at https://lmdomics.org/ProteoMixture/.
HostingRepository	PRIDE
AnnounceDate	2024-01-12
AnnouncementXML	Submission_2024-01-12_08:34:55.748.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Thomas Conrads
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2023-07-27 15:39:42	ID requested
⏵ 1	2024-01-12 08:34:56	announced

Dataset with its publication pending

submitter keyword: laser microdissection,High grade serous ovarian cancer, proteomics, stroma signature, immune signature, cellular admixture, tumor signature

Thomas P. Conrads
contact affiliation	Women’s Service Line Ionva Health System
contact email	conrads@whirc.org
lab head
Thomas Conrads
contact affiliation	Inova Health System
contact email	conrads@whirc.org
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD044157
     1. Label: PRIDE project
     2. Name: ProteoMixture: A Cell Deconvolution Tool for Bulk Tissue Proteomics Data