Dataset Information

Automated sample preparation with SP3 for low-input clinical proteomics

ABSTRACT: High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples originating from a variety of sources, including frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format, performing unbiased protein purification and digestion delivering peptides that can be directly analyzed by LCMS. AutoSP3 eliminates hands-on time and minimizes the risk of error, and we show it reduces the protein quantification variability, and improves longitudinal performance and reproducibility. We demonstrate the distinguishing ability of autoSP3 to process low-input samples, reproducibly quantifying 500-1000 proteins from 100-1000 cells (<100 ng protein). Furthermore we applied it to process a cohort of clinical FFPE pulmonary adenocarcinoma (ADC) samples, and recapitulate their separation into known histological growth patterns based on proteome profiles. Collectively, autoSP3 provides a generic, scalable, and cost-effective pipeline for routine and standardized proteomic sample processing that should enable reproducible proteomics in broad range of clinical and non-clinical applications.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Lung, Epithelial Cell, Hela Cell

DISEASE(S): Non-small Cell Lung Carcinoma

SUBMITTER: Torsten Mueller

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD014556 | Pride | 2020-01-10

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20180223_QE1_TM_MSP3_4H_DTT_T1.raw	Raw
	20180223_QE1_TM_MSP3_4H_DTT_T2.raw	Raw
	20180223_QE1_TM_MSP3_4H_DTT_TL1.raw	Raw
	20180223_QE1_TM_MSP3_4H_DTT_TL2.raw	Raw
	20180223_QE1_TM_MSP3_4H_TCEP_T1.raw	Raw

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Automated sample preparation with SP3 for low-input clinical proteomics.

Müller Torsten T Kalxdorf Mathias M Longuespée Rémi R Kazdal Daniel N DN Stenzinger Albrecht A Krijgsveld Jeroen J

Molecular systems biology 20200101 1

High-throughput and streamlined workflows are essential in clinical proteomics for standardized processing of samples from a variety of sources, including fresh-frozen tissue, FFPE tissue, or blood. To reach this goal, we have implemented single-pot solid-phase-enhanced sample preparation (SP3) on a liquid handling robot for automated processing (autoSP3) of tissue lysates in a 96-well format. AutoSP3 performs unbiased protein purification and digestion, and delivers peptides that can be directl ...[more]

PMID: 32129943

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