Dataset Information

Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues

ABSTRACT: Tissue lysis using urea buffer was adopted in our previously published CPTAC protocol for mass spectrometry (MS)-based quantitative global proteomic and phosphoproteomic analysis. Herein, we reported an update to this initial protocol by implementing a sonication step into urea-based tissue lysis. Similar to the initial CPTAC protocol, we identified >12,000 proteins and >25,000 phosphopeptides in a TMT set containing both non-sonicated and sonicated tumor tissues from patient-derived xenograft mouse models. However, an improvement in the detection of membrane-bound and DNA-binding proteins was observed by including the sonication. We also offered recommendations for optimal sonication conditions such as buffer composition, timing, and instrumentation settings, and a troubleshooting section for potential users. Additionally, the protocol is equally applicable to other biological specimens.

INSTRUMENT(S):

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

TISSUE(S): Breast

DISEASE(S): Breast Cancer

SUBMITTER: Yingwei HU

LAB HEAD: Tung-Shing Mamie Lih

PROVIDER: PXD050336 | Pride | 2025-07-28

REPOSITORIES: Pride

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			Action	DRS
	03_CPTAC_TMT_HARMONIZATION_JHUZ_20170529_LUMOS_01.raw	Raw
	03_CPTAC_TMT_HARMONIZATION_JHUZ_20170529_LUMOS_02.raw	Raw
	03_CPTAC_TMT_HARMONIZATION_JHUZ_20170529_LUMOS_03.raw	Raw
	03_CPTAC_TMT_HARMONIZATION_JHUZ_20170529_LUMOS_04.raw	Raw
	03_CPTAC_TMT_HARMONIZATION_JHUZ_20170529_LUMOS_05.raw	Raw

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Sonication-assisted protein extraction improves proteomic detection of membrane-bound and DNA-binding proteins from tumor tissues.

Li Qing Kay QK Lih T Mamie TM Clark David J DJ Chen Lijun L Schnaubelt Michael M Zhang Hui H

Nature protocols 20250217 8

Deep-scale, mass spectrometry-based proteomic studies by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) program involves tissue lysis using urea buffer before data acquisition via mass spectrometry for quantitative global proteomic and phosphoproteomic analysis. This is described in a 2018 protocol<sup>1</sup>. Here we report an update to this initial protocol by implementing a sonication step into urea-based tissue lysis. Similar to the initial CPTAC protocol, we identified >12,000 pr ...[more]

PMID: 39962197

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