In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples
文献类型：期刊论文
| 作者 | Zou, Xun4; Wang, Lulu1,3; Chen, Yulu3,4; Fu, Hang3; Gao, Yuan1,3; Liu, Bin4; Tan, Minjia1,2,4; Zhai, Linhui2 |
| 刊名 | CLINICAL PROTEOMICS
 |
| 出版日期 | 2025-12-11 |
| 卷号 | 23期号:1页码:18 |
| 关键词 | DDA DIA Mass spectrometry quantification Proteomics Reproducibility Interferon pathway |
| ISSN号 | 1542-6416 |
| DOI | 10.1186/s12014-025-09572-2 |
| 英文摘要 | Data-Dependent Acquisition (DDA) and Data-Independent Acquisition (DIA) are widely used in MS-based proteomics. However, a comprehensive evaluation of their data characteristics-including protein and peptide identification, differential expression analysis, and the performance in revealing biological insights-remains lacking. In this study, we conducted a systematic comparison of DDA and DIA across three model sample types: one disease model, two drug-treated models, and their respective controls. Our analysis extended beyond conventional metrics such as total protein and peptide counts, precision, and accuracy, to include data completeness, detection of positive control markers, reproducibility, functional annotation reliability, and sources of methodological variation. The results demonstrated that DIA outperformed DDA in terms of protein identification (disease group: 7,735 vs. 5,067; drug-treated group 1: 7,987 vs. 4,605), quantitative coverage (average quantifiable protein ratio: DIA 98-99% vs. DDA 95-96%), and reproducibility (intragroup correlation coefficients: DIA > 0.98 vs. DDA 0.93-0.98). We also found DIA exhibited lower variability (intragroup CV < 10% vs. > 15% for DDA) and improved accuracy for low-abundance and housekeeping proteins. Additionally, the functional enrichment analyses further revealed DIA's superior capability in detecting pathway activation. Finally, discrepancies between DIA and DDA were primarily attributed to proteins identified with <= 5 peptides, the exclusion of single-peptide proteins enhanced overall data quality. Overall, this study systematically assess the overall capabilities of DDA and DIA approaches in uncovering biologically relevant findings and driving mechanistic insights within authentic pharmacological and disease models, thereby offering practical guidance for methodological choices in future research. |
| 资助项目 | National Natural Science Foundation of China[22225702] ; National Natural Science Foundation of China[32171434] |
| WOS研究方向 | Biochemistry & Molecular Biology |
| 语种 | 英语 |
| WOS记录号 | WOS:001663028900001 |
| 出版者 | BMC |
| 源URL | [http://119.78.100.183/handle/2S10ELR8/322622]  |
| 专题 | 国家级研究中心_原创新药研究全国重点实验室 |
| 通讯作者 | Zhai, Linhui |
| 作者单位 | 1.Nanjing Univ Chinese Med, Sch Chinese Mat Med, Sch Pharm, Nanjing, Jiangsu, Peoples R China 2.Tongji Univ, Shanghai Peoples Hosp 4, Translat Res Inst Brain & Brain Like Intelligence, Sch Med, Shanghai 200434, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Mat Med, State Key Lab Drug Res, Shanghai 201203, Peoples R China 4.Jiangsu Ocean Univ, Coll Pharm, Lianyungang 222000, Jiangsu, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zou, Xun,Wang, Lulu,Chen, Yulu,et al. In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples[J]. CLINICAL PROTEOMICS,2025,23(1):18. |
| APA | Zou, Xun.,Wang, Lulu.,Chen, Yulu.,Fu, Hang.,Gao, Yuan.,...&Zhai, Linhui.(2025).In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples.CLINICAL PROTEOMICS,23(1),18. |
| MLA | Zou, Xun,et al."In-depth analysis of data characteristics and comparative evaluation of dda and dia accuracy in label-free quantitative proteomics of biological samples".CLINICAL PROTEOMICS 23.1(2025):18. |
入库方式： OAI收割
来源：上海药物研究所
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