Introduction | Load the packages | Load the data | Plot samples summaries | Plot extracted ion chromatograms | The same plot with base R graphics | Quality control of peak detection | Plot grouped peaks across samples (features) | Plot peak density alongside chromatograms | Plot spectra | Select the closest scan to a specified retention time | Select the scan closest to a detected peak apex | Select multiple scans across a detected peak | Plot standalone spectra | Session information

Introduction | Preprocessing of LC-MS data | Data import | Initial data inspection | Inspecting chromatographic data | Inspecting chromatographic data, legacy framework | Chromatographic peak detection | Chromatographic peak quality | Refining peak detection | Alignment | Subset-based alignment | Correspondence | Gap filling | Final result | Further data processing and analysis | Quality-based filtering of features | Alignment to an external reference dataset | Additional details and notes | Subsetting and filtering | Parallel processing | Main differences to the MSnbase-based xcms version 3 | Additional documentation resources | Session information | References

Introduction | Peak detection | Calibration | Correspondence | Further analysis | Session information

Introduction | Compounding of LC-MS data | Grouping of features by similar retention time | Grouping of features by abundance correlation across samples | Grouping of features by similarity of their EICs | Grouping of subsets of features | Session information | References

Introduction | Analysis of DDA data | DIA (SWATH) data analysis | Chromatographic peak detection in MS1 and MS2 data | Reconstruction of MS2 spectra | Outlook | Session information | References

Introduction | Mass spectrometry raw data | Spectral data access | Chromatogram access | Identification result access | Metadata access | Example | mzXML/mzML files | mzIdentML files | Future plans | Session information

Introduction | Decomposing isotope patterns | Chemical background | Identification schema | Working with molecules and isotope peaklists | Functions decomposeMass and decomposeIsotopes | Interaction with other BioConductor packages | Acknowledgments | References

Introduction | Usage

Introduction | Short Background | Processing with CAMERA | Wrapper functions and combination with diffreport | Function Overview | Create rule table

Introduction | Usage