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Quantification strategy for PDX MS data

ABSTRACT: Data interpreting of PDX proteome is still a problem because with the growth of human cancerous tissue in an immunodeficient mouse, the endothelial cells and fibroblasts from the host mouse replaced human stromal components, making PDX sample a mixture of human and mouse cells. In this study, we created four human and mouse protein mixtures with different human protein percentages as the standard testing sets. We established an easy algorithm to fit the known proportions and used this strategy on a pair of PDX samples. Our data suggested that our new algorithm is feasible and may help to offer more information on PDX proteome data analysis.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human) Mus Musculus (mouse)

TISSUE(S): Cell Culture

SUBMITTER: Lili Qian

LAB HEAD: Minjia Tan

PROVIDER: PXD008611 | Pride | 2022-05-19

REPOSITORIES: Pride

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			Action	DRS
	20160105_QLL_PDX0080_Fr1.raw	Raw
	20160105_QLL_PDX0080_Fr2.raw	Raw
	20160106_QLL_PDX0080_Fr10.raw	Raw
	20160106_QLL_PDX0080_Fr3.raw	Raw
	20160106_QLL_PDX0080_Fr4.raw	Raw

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Publications

SPA: A Quantitation Strategy for MS Data in Patient-derived Xenograft Models.

Cheng Xi X Qian Lili L Wang Bo B Tan Minjia M Li Jing J

Genomics, proteomics & bioinformatics 20210223 4

With the development of mass spectrometry (MS)-based proteomics technologies, patient-derived xenograft (PDX), which is generated from the primary tumor of a patient, is widely used for the proteome-wide analysis of cancer mechanism and biomarker identification of a drug. However, the proteomics data interpretation is still challenging due to complex data deconvolution from the PDX sample that is a cross-species mixture of human cancerous tissues and immunodeficient mouse tissues. In this study, ...[more]

PMID: 33631430

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