Rapid sample preparation workflow based on enzymatic nanoreactors for potential serum biomarker discovery in pancreatic cancer

Chenxin Zhu; Shuang Yang; Hengchao Li; Yuning Wang; Yueting Xiong; Fenglin Shen; Lei Zhang; Pengyuan Yang; Xiaohui Liu

doi:10.1016/j.talanta.2021.123018

Rapid sample preparation workflow based on enzymatic nanoreactors for potential serum biomarker discovery in pancreatic cancer

Talanta. 2022 Feb 1;238(Pt 2):123018. doi: 10.1016/j.talanta.2021.123018. Epub 2021 Nov 5.

Authors

Chenxin Zhu¹, Shuang Yang¹, Hengchao Li², Yuning Wang³, Yueting Xiong¹, Fenglin Shen¹, Lei Zhang¹, Pengyuan Yang¹, Xiaohui Liu⁴

Affiliations

¹ The Fifth People Hospital, Fudan University, And the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institute of Biomedical Science, Fudan University, Shanghai, 200433, China.
² Department of Pancreatic Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
³ Department of Chemistry, Fudan University, Shanghai, 200433, China.
⁴ The Fifth People Hospital, Fudan University, And the Shanghai Key Laboratory of Medical Epigenetics, The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institute of Biomedical Science, Fudan University, Shanghai, 200433, China. Electronic address: liuxiaohui@fudan.edu.cn.

PMID: 34808569
DOI: 10.1016/j.talanta.2021.123018

Abstract

Mass spectrometry (MS)-based proteomics have been extensively applied in clinical practice to discover potential protein and peptide biomarkers. However, the traditional sample pretreatment workflow remains labor-intensive and time-consuming, which limits the application of MS-based proteomic biomarker discovery studies in a high throughput manner. In the current work, we improved the previously reported procedure of the simple and rapid sample preparation methods (RSP) by introducing macroporous ordered siliceous foams (MOSF), namely RSP-MOSF. With the aid of MOSF, we further reduced the digestion time to 10 min, facilitating the whole sample handling process within 30 min. Combining with 30 min direct data independent acquisition (DIA) of LC-MS/MS, we accomplished a serum sample analysis in 1 h. Comparing with the RSP method, the performance of protein and peptide identification, quantitation, as well as the reproducibility of RSP-MOSF is comparable or even outperformed the RSP method. We further applied this workflow to analyze serum samples for potential candidate biomarker discovery of pancreatic cancer. Overall, 576 serum proteins were detected with 41 proteins significantly changed, which could serve as potential biomarkers for pancreatic cancer. Additionally, we evaluated the performance of RSP-MOSF method in a 96-well plate format which demonstrated an excellent reproducibility of the analysis. These results indicated that RSP-MOSF method had the potential to be applied on an automatic platform for further scaled analysis.

Keywords: Macroporous ordered siliceous foams; Pancreatic cancer; Proteomic analysis; Serum pretreatment.

MeSH terms

Biomarkers
Chromatography, Liquid
Humans
Nanotechnology
Pancreatic Neoplasms* / diagnosis
Proteomics*
Reproducibility of Results
Specimen Handling
Tandem Mass Spectrometry
Workflow

Substances

Biomarkers