Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition

Weng, Shuang; Wang, Mingchao; Zhao, Yingyi; Ying, Wantao; Qian, Xiaohong

doi:10.1016/j.jprot.2021.104152

Cited by 7 publications

(6 citation statements)

References 38 publications

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“…For all strategies, PBMCs were lysed and subjected to the optimized DIA analysis on a Q-Exactive HF mass spectrometer (Figure 1). 16 Optimization of Proteomic Workflows for Microscale PBMCs. The enriched cells were analyzed by FACS to observe the components and purity.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells

Weng

Qian

et al. 2022

Anal. Chem.

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Peripheral blood mononuclear cells (PBMCs) play vital roles in physiological and pathological processes and represent a rich source for disease monitoring. Typical molecular profiling on PBMCs involves the sorting of cell subsets and thus requires a large volume of peripheral blood (PB), which impedes the clinical practicability of omics tools in PBMC measurements. It would be clinically invaluable to develop a convenient approach for preparing PBMCs from small volumes of PB and for deep proteome profiling of PBMCs. To this end, here, we designed an apparatus (PBMC-mCap) for microscale enrichment and proteome analysis of PBMCs, which pushed the needed PB volume from the normal 2 mL or higher to 100 μL or lower, comparable to the volume of a drop of finger blood. A PBMC-specific mass spectra library containing 8869 proteins and 121,956 peptides was further built, which, in combination with the optimized data-independent acquisition strategy, helped to identify 6000 and 6500 proteins from PBMCs with 100 μL and 1 mL of PB as initial materials, respectively. Further application of the strategy for PBMC proteomes revealed a steady difference between gender (male vs female) and upon stimulus (COVID-19 vaccination). For the latter, we observed differentially expressed genes and pathways involving the activation of immune cells, including the NF-κB pathway, inflammation response, and antiviral response. Our strategy for the proteome analysis of microscale PBMCs may provide a convenient clinical toolkit for disease diagnosis and healthy state monitoring.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells

Weng

Qian

et al. 2022

Anal. Chem.

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“…Liquid chromatography-coupled tandem mass spectrometry (LC−MS/MS) is a powerful technique for proteomic studies, allowing accurate quantification of proteins from complex biological samples for further analysis. 48 An acquisition strategy plays a very important role in the analysis of LC-MS. 49 Currently, the commonly used acquisition strategy is DDA, which selects ions for analysis according to the abundance of parent ion fragments. 50 Therefore, this acquisition strategy has a certain bias, and the obtained proteomic results usually need to be further validated.…”

Section: ■ Discussionmentioning

confidence: 99%

Proteomic Profiling and Tumor Microenvironment Characterization Reveal Molecular and Immunological Hallmarks of Left-Sided and Right-Sided Colon Cancer Tumorigenesis

Hong,

Wang,

Wang

et al. 2023

J. Proteome Res.

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Left-sided and right-sided colon cancer (LSCC and RSCC) display different biological and clinical characteristics. However, the differences in their tumorigenesis and tumor microenvironment remain unclear. In this study, we profiled the proteomic landscapes of LSCC and RSCC with data-independent acquisition mass spectrometry (DIA-MS) using fresh tumor and adjacent normal tissues from 24 patients. A total of 7403 proteingroups were primarily identified with DIA-MS. After quality control, 7212 proteingroups were used for further analysis. Through comparing the difference in proteomic profiles between LSCC and RSCC samples, 2556 commonly and 1982 region-type-specific regulated proteingroups were characterized. During the development of LSCC and RSCC, metabolic, growth, cell division, cell adhesion, and migration pathways were found to be significantly dysregulated (P < 0.05), which was further confirmed by transcriptome data from TCGA. Compared to RSCC, most parts of the immune-related signatures, immune cell infiltration scores, and overall immune scores of LSCC were higher. The systematic elucidation of proteomic and transcriptomic profiles in this work improves our understanding of tumorigenesis and immune microenvironment characteristics of LSCC and RSCC.

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“…The liquid chromatography-tandem mass spectrometry (LC—MS/MS) detection system consisted of a nanoflow high-performance liquid chromatography (HPLC) instrument (Easy nLC1200, Thermo Fisher) coupled to an Orbitrap Q-Exactive HF mass spectrometer (Thermo Fisher). For acquisition of mass spectra, the optimal data-independent acquisition (DIA) parameters described in the article by Shuang Weng et al [18] were used. In brief, 2 µg of the peptide mixture resolved with buffer A was loaded on a 30-cm self-packing column (150-μm inner diameter, ReproSil-Pur C18-AQ, 1.9 µm; Dr. Maisch) with a 120-min LC gradient time ( Table S2 ) at a flow rate of 600 nl/min.…”

Section: Methodsmentioning

confidence: 99%

Autophagy and biotransformation affect sorafenib resistance in hepatocellular carcinoma

Zheng

Weng

et al. 2023

Computational and Structural Biotechnology Journal

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Optimised data-independent acquisition strategy recaptures the classification of early-stage hepatocellular carcinoma based on data-dependent acquisition

Cited by 7 publications

References 38 publications

Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells

Strategy for Microscale Extraction and Proteome Profiling of Peripheral Blood Mononuclear Cells

Proteomic Profiling and Tumor Microenvironment Characterization Reveal Molecular and Immunological Hallmarks of Left-Sided and Right-Sided Colon Cancer Tumorigenesis

Autophagy and biotransformation affect sorafenib resistance in hepatocellular carcinoma

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