Proteomics and data analysis
3D-DIA
REGRESSION
We used the 3D-DIA Proteomics Assays to measure the relative abundance of proteins based on their spectral counts. We excluded proteins that were undetectable in more than 40 samples from the analysis. We normalized the spectral counts by the total number of spectra in each sample and then log-transformed them to obtain the protein expression values.We performed linear mixed model (LMM) regression analysis using the lme4 R packageFor the specific markers for responses to FOLFOX4-ATRA treatment, a protein was considered to be significantly differentially expressed across the different response evaluations if the raw For the potential targets of FOLFOX4-ATRA treatment, a protein was considered to be significantly differentially expressed between pre- and post-treatment within one type of response evaluation and treatment arm if the raw 