Introduction | MS2spectrum and pseudospectrum classes | Extract MS^2^ spectra from *.mzXML file | Merge MS^2^ spectra that derive from the same peak/feature | Merge spectra without external peaktable | Merge spectra with external peaktable, e.g. from XCMS | Add annotations | Manual procedure | Alternative procedures | Generate distance matrices | Distance matrix for product ion spectra | Distance matrix for neutral loss patterns | Visualise distance/similarity data using multidimensional scaling (MDS) | Perform density-based clustering using the OPTICS algorithm | Perform hierarchical clustering | Create a heatmap | Create a dendrogram | Generate a correlation network | Additional functionalities | Access individual spectra from a list of spectra by various slot entries | Find spectra that contain a specific fragment or neutral loss | Match one spectrum against a set of spectra | Convert MSnbase objects to class MS2spectrum | Split polarities from polarity-switching runs | Use MS^1^ pseudospectra instead of or in addition to MS^2^ data | Extract pseudospectra | Create distance matrix for pseudospectra | Generate a correlation network for pseudospectra | Session Info

Introduction | Data import | Data preprocessing | Generation of distance matrix | Data exploration | Session Info

Introduction | Data import and preprocessing | Extraction and annotation of spectra | Generation of distance matrix | Session Info

Introduction | Data import | Data preprocessing | Generation of distance matrix | Data exploration | Session Info

Introduction | Extract MS^2^ spectra from multiple *.mzML files | Merge spectra with external peak list | Add annotations | Generate distance matrix | Explore data | Session Info