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文章题目	检索作者	期刊	时间	组学	检索单位	样本	研究方向	DOI
快速血液样本前处理+质谱数据深度学习+血清标志物panel筛查策略
Rapid Sample Preparation Workflow for Serum Sample Analysis with Different Mass Spectrometry Acquisition Strategies	Xiaohui Liu	Anal Chem	2021 Jan	蛋白组	复旦	胰腺癌血清	血清快速样本前处理开发和应用	10.1021/acs.analchem.0c03985
Rapid sample preparation workflow based on enzymatic nanoreactors for potential serum biomarker discovery in pancreatic cancer	Xiaohui Liu	Talanta	2022 Feb	蛋白组	复旦	胰腺癌血清	血清高通量样本前处理开发和应用	10.1016/j.talanta.2021.123018
In silico spectral libraries by deep learning facilitate data-independent acquisition proteomics	Liang Qiao	Nat Commun	2020 Jan	DIA蛋白组算法	复旦	胰腺癌血清	DeepDIA基于深度学习生成谱图库	10.1038/s41467******
Circulating proteomic panels for risk stratification of intracranial aneurysm and its rupture.	Xiaohui Liu	EMBO Mol Med	2022 Feb	蛋白组、PRM	复旦	颅内动脉瘤血清	颅内动脉瘤血清标志物panel筛查	10.15252/emmm.202114713
Comprehensive mass spectrometry for development of proteomic biomarkers of intracranial aneurysms	Xiaohui Liu	Talanta	2022 Apr	蛋白组	复旦	颅内动脉瘤血清	颅内动脉瘤血清标志物panel筛查	10.1016/j.talanta.2021.123159
The characterization of serum proteomics and metabolomics across the cancer trajectory in chronic hepatitis B-related liver diseases	Xiaohui Liu	VIEW	2024	蛋白组、代谢组	复旦	肝癌血清	肝癌血清标志物panel筛查	10.1002/VIW.20240031
微量-单细胞-空间样本前处理+赛鹰微流控单细胞操控仪
Ultrasensitive Trace Sample Proteomics Unraveled the Protein Remodeling during Mesenchymal-Amoeboid Transition	Xiaohui Liu	Anal Chem	2022 Jan	微量蛋白组	复旦	迁移细胞	微量样本前处理开发和应用空间限制条件下细胞的蛋白质组分析	10.1021/acs.analchem.1c03212
In-depth and high-throughput spatial proteomics for whole-tissue slice profiling by deep learning-facilitated sparse sampling strategy	贺福初	Cell Discovery	2025	极微量蛋白质组	国家蛋白质科学中心（北京）	鼠脑切片激光显微切割条带	空间蛋白组新技术突破	10.1038/s41421******
Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell	Qun Fang	Nat Commun	2024 Feb	单细胞（所见即所得分选）	浙大	迁移细胞	单细胞微流控液体处理机器人	10.1038/s41467******/td>
Single Cell-Pair Proteomics for Decoding lmmune-CancerCell interactions	Qun Fang	Advanced Science	2025	单细胞（所见即所得分选）	浙大	免疫-癌细胞对	微流控单细胞操控仪	10.1002/advs.202414769
微量磷酸化样本前处理+全蛋白多组学联合
An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells	Shisheng Wang, Yansheng Liu	Nat Commun	2023	磷酸组		内皮细胞	光遗传学和磷酸组揭示内皮细胞中Akt1信号传导的动态特征	10.1038/s41467******/td>
DeepFLR facilitates false localization rate control in phosphoproteomics	Liang Qiao	Nat Commun	2023 Apr	磷酸组	复旦、OMICSOLUTION	HeLa细胞	磷酸化位点定位错误率估计算法 DeepFLR	10.1038/s41467******/td>
Rapid and High-Sensitive Phosphoproteomics Elucidated the Spatial Dynamics of the Mouse Brain.	Xiaohui Liu	Anal Chem	2023 Jul	微量磷酸组+全蛋白	复旦	小鼠冠状脑切片	微量磷酸化样本前处理开发空间蛋白组及磷酸组的联合分析	10.1021/acs.analchem.3c01486
Multidimensional Proteomic Landscape Reveals Distinct Activated Pathways Between Human Brain Tumors	Xiaohui Liu	Adv Sci (Weinh)	2025 Feb	微量磷酸组+全蛋白、N-糖肽	交大 OMICSOLUTION	原发性和继发性脑癌和癌旁组织	人脑肿瘤多维度蛋白组学图谱构建	10.1002/advs.202410142
微生物菌群蛋白序列库构建策略+定量方法优化+各领域应用
Metaproteomics characterizes human gut microbiome function in colorectal cancer	Liang Qiao	npj Biofilms and Microbiomes	2020	宏蛋白质组	复旦	14结直肠癌粪便vs14对照	肠菌蛋白功能变化与结直肠癌发病关联	10.1038/s41522******/td>
Quantitative metaproteomics reveals composition and metabolism characteristics of microbial communities in Chinese liquor fermentation starters	Liang Qiao	Front. Microbiol	2023	宏蛋白质组	复旦	90例茅台酒曲	酒曲蛋白功能变化与发酵风味和香气关联	10.3389/fmicb.2022.1098268
Metaproteomics profiling of the microbial communities in fermentation starters (Daqu) during multi-round production of Chinese liquor	Liang Qiao	Frontiers in Nutrition	2023	宏蛋白质组、PRM	复旦	42例茅台酒曲	酒曲蛋白功能变化与发酵风味和香气关联	10.3389/fnut.2023.1139836
Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota	Liang Qiao	npj Biofilms and Microbiomes	2023	宏蛋白质组（DIA vs TMT vs LFQ-DDA）	复旦	轻度认知障碍粪便（MCI）、胰腺癌粪便（PC）	质谱采集模式方法比较脑肠轴研究，肠菌蛋白功能变化与发病关联	10.1038/s41522******/td>
High-Abundance Protein-Guided Hybrid Spectral Library for Data Independent Acquisition Metaproteomics	Liang Qiao	Anal Chem	2023	宏蛋白质组HAP建库	复旦	粪便	人肠道内容物公共库构建	10.1021/acs.analchem.3c03255
Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics	Liang Qiao	Microbiome	2024	宏蛋白质组ConDiGA建库	复旦	粪便	宏基因组注释优化建库	10.1186/s40168******/td>
完整糖肽样本前处理+定性定量工具+生信分析云平台
Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Modified Saccharide Units with pGlyco3	Weiqian Cao	Nature Methods	2021	糖肽组	复旦、 OMICSOLUTION	酵母	完整糖肽定性解析工具pGlyco3	10.1038/s41592******/td>
pGlycoQuant with a deep residual network for quantitative glycoproteomics at intact glycopeptide level	Weiqian Cao	Nature Communications	2022	糖肽组	复旦、 OMICSOLUTION	肝癌细胞系	完整糖肽定量分析工具pGlycoQuant	10.1038/s41467******
GlycAP, a glycoproteomic analysis platform for site-specific N-glycosylation research	Weiqian Cao	Int J Mass Spectrom	2022	糖肽组	复旦、 OMICSOLUTION	多物种	完整糖肽在线分析平台GlycAP	10.1016/j.ijms.2022.116947
Uncovering missing glycans and unexpected fragments with pGlycoNovo for site-specific glycosylation analysis across species	Weiqian Cao, Chao Liu	Nature Communications	2024	糖肽组	复旦、 OMICSOLUTION	多物种	稀有糖型、缺乏糖库物种糖肽分析再进一步	10.1038/s41467******/td>
In-depth mapping of the mouse brain N-glycoproteome reveals widespread N-glycosylation of diverse brain proteins	Weiqian Cao	Oncotarget	2016	糖肽组	复旦、 OMICSOLUTION	小鼠脑组织	完整糖肽ZIC-HILIC富集策略	10.18632/oncotarget.9737
蛋白代谢多组学联合--标志物筛选文章经验
Proteomic and metabolomic features in patients with HCC responding to lenvatinib and anti-PD1 therapy	Feng Liu	Cell Rep	2024 Mar	蛋白组、代谢组等	复旦、 OMICSOLUTION	肝癌血浆	肝癌治疗敏感分层	10.1016/j.celrep.2024.113877
Proteomic and metabolomic analysis of plasma for pain at different labor stages	Kun Qian	Talanta	2025 Jan	蛋白组、代谢组	交大	纵向队列： 32名顺产妇女的185份血浆样本	分娩过程中疼痛和应激变化的分子变化	10.1016/j.talanta.2024.126905
The characterization of serum proteomics and metabolomics across the cancer trajectory in chronic hepatitis B-related liver diseases	Xiaohui Liu	VIEW	2024	蛋白组、代谢组	复旦	肝癌血清	肝癌血清标志物panel筛查	10.1002/VIW.20240031
LC-MS/MS and SWATH based serum metabolomics enables biomarker discovery in pancreatic cancer	Xiaohui Liu	Clin Chim Acta	2020 Jul	蛋白组、代谢组	复旦	胰腺癌血清	肿瘤标志物	10.1016/j.cca.2020.03.043
Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer	Liang Qiao	Front Oncol	2022 Apr	蛋白组、代谢组	复旦、 OMICSOLUTION	子宫内膜组织（蛋白+代谢）、尿液和宫腔内刷检样本（代谢）	通路相关早诊标志物	10.3389/fonc.2022.861142
其他分析工具或客户文章经验
High-resolution spatially resolved proteomics of complex tissues based on microfluidics and transfer learning	Guibing Wang	cell	2025	蛋白组	国家蛋白质科学中心（北京）	小鼠脑组织激光显微切割条带	空间蛋白组新技术突破	10.1016/j.cell.2024.12.023
High spatial-resolved heat manipulating membrane heterogeneity alters cellular migration and signaling	Di Li	PNAS	2023	蛋白组	华东师范 OMICSOLUTION	细胞	细胞应对热扰动	10.1073/pnas.2312603120
Proteomic landscape of primary and metastatic brain tumors for heterogeneity discovery	Xiaohui Liu	Proteomics Clin Appl	2024 Mar	蛋白组	复旦	原发性和转移性脑肿瘤组织	脑癌类型异质性研究	10.1002/prca.202300010
Comprehensive Evaluation and Optimization of the Data-Dependent LC-MS/MS Workflow for Deep Proteome Profiling	Chao Liu, Chengpin Shen	Anal Chem	2023 May	DDA	北航、OMICSOLUTION		开发MSRefine，47种深度指标评估和优化蛋白组工作流程性能	10.1021/acs.analchem.3c00338
Deep Learning Powers Protein Identification from Precursor MS Information	Liang Qiao	J. Proteome Res	2024	DDA	复旦	大肠杆菌、血清、单细胞	基于深度学习提高DDA MS1鉴定能力	10.1021/acs.jproteome.4c00118
In-depth mass spectrometry analysis of rhGH administration altered energy metabolism and steroidogenesis	Liang Qiao	Talanta	2024	代谢组	复旦	健康男性血清、尿液	重组人生长激素（rhGH）注射前后代谢变化	10.1016/j.talanta.2023.125069
WD repeat-containing protein 1 maintains β-Catenin activity to promote pancreatic cancer aggressiveness	Xiaohui Liu	Br J Cancer	2020 Sep	标记蛋白组	复旦	不同分期胰管腺癌组织	疾病进程相关蛋白	10.1038/s41416******/td>
Identification of transaldolase as a novel serum biomarker for hepatocellular carcinoma metastasis using xenografted mouse model and clinic samples.	Xiaohui Liu	Acta Pharmacol Sin	2018 Sep	标记蛋白组	复旦	仓鼠肝脏	天然产物潜在新靶蛋白	10.1016/j.canlet.2011.08.031
Quantitative proteomic analysis identifies CPNE3 as a novel metastasis-promoting gene in NSCLC	Xiaohui Liu	J Proteome Res	2013 Jul	标记蛋白组	复旦	高与低转移潜能肺腺癌细胞	寻找癌细胞内与转移相关蛋白质	10.1021/pr400273z
iTRAQ quantitative proteomic analysis reveals the pathways for methanation of propionate facilitated by magnetite	Jingjing Wan	Water Res（11.5，Q1）	2017 Jan	标记蛋白组	复旦