Data analysis for single sample | Data structure of GC/LC-MS full scan mode | Data structure of GC-MS SIM mode | Data input | Visualization of mass spectrum data | Data analysis for influence from GC-MS | Data analysis for molecular isotope ratio | Quantitative analysis for short-chain chlorinated paraffins(SCCPs) | Data analysis for multiple samples | Importing peaks list data | Data imputation and filtering | Visualization of peaks list data | Summary

Introduction | Installation | Experimental Desgin | Feature extraction | Feature alignment | Save feature list | Using the Results | Downstream Analysis | Interoperability and Visualization | Normalization and Transformation | Advanced Usage | Conclusion

Introduction of Paired Mass Distance analysis | PMD from the same compound | PMD from different compounds | Data format | GlobalStd algorithm | STEP1: Retention time hierarchical clustering | STEP2: Relationship among adducts, neutral loss, isotopologues and common fragments ions | STEP3: Screen the independent peaks | Extra filter with correlation coefficient cutoff | Validation by principal components analysis(PCA) | Comparison with other pseudo spectra extraction method | Benchmark different datasets by Normalized Spectral Entropy (Sample Consistency Metric) | Structure/Reaction directed analysis | Structure/reaction directed analysis for peaks/compounds only data | Wrap function for GlobalStd algorithm | Use independent peaks for MS/MS validation (PMDDA) | Shiny application | Conclusion

PMD network analysis | Shiny application | Tracing specific reaction paths and homologous series | Source appointment | Biomarker reaction | Reactomics analysis for MS only data | PMD Reaction Database

Peaks profile | Density distribution | Relative Log Abundance (RLA) plots | Relative Log Abundance Ridge (RLAR) plots | Density Weighted Total Usable Signal | Run order effect analysis