Dataset Information

In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics

ABSTRACT: We assessed two physical disruption methods to homogenize cells —sonication and BeatBox—alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based, and SDC (Sodium deoxycholate)-based in-solution digestion, and two are commercially available kits: the EasyPep kit from Thermo Fisher Scientific and S-Trap from Protifi. Each method's efficacy was evaluated based on protein recovery, peptide yield, and number of unique proteins identified through LC-MS analysis.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Travis Uslan

LAB HEAD: Tsui-fen Chou

PROVIDER: PXD056409 | Pride | 2026-01-07

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	GO_Panther_text_files.zip	Other
	TU_20240518_QE_Aur2hr_SDC_BeatBox_C18_N1_01.pepXML	Pepxml
	TU_20240518_QE_Aur2hr_SDC_BeatBox_C18_N1_01.pin	Other
	TU_20240518_QE_Aur2hr_SDC_BeatBox_C18_N1_01.raw	Raw
	TU_20240518_QE_Aur2hr_SDC_BeatBox_C18_N1_01_c.pepXML	Pepxml

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Publications

In-Depth Comparison of Reagent-Based Digestion Methods and Two Commercially Available Kits for Bottom-Up Proteomics.

Uslan Travis T Quan Baiyi B Wang Ting-Yu TY Pang Marion M Qiu Yanping Y Chou Tsui-Fen TF

ACS omega 20250306 10

Proteomic analysis plays an essential role in biology with several methodologies available for sample preparation and analysis. This study evaluates and compares various cell lysis and protein digestion protocols for bottom-up proteomics using HeLa S3 cells. We assessed two physical disruption methods to homogenize cells-sonication and BeatBox-alongside four digestion protocols. Two of them are lab-reagent strategies: urea-based and sodium deoxycholate (SDC)-based in-solution digestion, and two ...[more]

PMID: 40124045

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