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Proteomics informed deconvolution of 3 cell lines

ABSTRACT: The project aimed to investigate the possibility to use proteomics data to deconvolute cell line proportions in mixed samples. Samples containing either HEK 293, Caco-2, or A549 cells and mixtures of the three cell lines was analysed using the total protein approach. This was then used for proteomics informed deconvolution. The results show that proteome deconvolution provides an effective tool for investigating cellular composition in mixed samples. This was later applied also to in silico mixtures of primary human liver cells and liver tissue. However, those data are presented elsewhere.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Niklas Handin

LAB HEAD: Per Artursson

PROVIDER: PXD027282 | Pride | 2023-10-24

REPOSITORIES: Pride

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Proteome deconvolution of liver biopsies reveals hepatic cell composition as an important marker of fibrosis.

Handin Niklas N Yuan Di D Ölander Magnus M Wegler Christine C Karlsson Cecilia C Jansson-Löfmark Rasmus R Hjelmesæth Jøran J Åsberg Anders A Lauschke Volker M VM Artursson Per P

Computational and structural biotechnology journal 20230904

Human liver tissue is composed of heterogeneous mixtures of different cell types and their cellular stoichiometry can provide information on hepatic physiology and disease progression. Deconvolution algorithms for the identification of cell types and their proportions have recently been developed for transcriptomic data. However, no method for the deconvolution of bulk proteomics data has been presented to date. Here, we show that proteomes, which usually contain less data than transcriptomes, c ...[more]

PMID: 37711184

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