EasyDIA a comprehensive and robust pipeline for DIA proteomics research and its application in multi-organ mouse proteomics atlas generation

Supplementary data of the article " EasyDIA: a comprehensive and robust pipeline for DIA proteomics research, and its application in multi-organ mouse proteomics atlas generation". Mass spectrometry-based proteomics measurement has emerged as a routine tool for detecting protein constitution and expression level change in most organisms. But till now, long-term stability, reproducibility, throughput, identification depth, multi-center consistency, robustness cannot be satisfied simultaneously by traditional proteomics method. We introduced EasyDIA pipeline with widely used commercial products, state-of-art direct DIA-PASEF method and EasyDIA software platform for data quality evaluation and bioinformatics analysis. With EasyDIA pipeline, even entry level researchers can conduct a complete proteomics experiment in less than one day. We further generated a multi-organ mouse proteomics atlas dataset in less than four days. Up to 8000 protein groups can be quantified in a single organism with only 60 minutes LC gradient. This pipeline provides a promising solution for both small-scale proteomics experiment and large-cohort clinical research.