This implements raw targeted feature extraction from DIA/diaPASEF mzML files using a spectral library (tsv/pqp) and optionally supplemented with search results (diann tsv/osw). The extracted results can then be visualized in 1D, 2D and 3D.
Note: I do not include any test files in this branch, I will include tests later in a separate branch.
Inputs:
Spectral library - can be either TSV or PQP
Mass Spec Files - can be either DIA or diaPASEF data strictly in mzML format
Search results (Optional) - can be either a DIA-NN report file or a OSW sqlite file
Plotting:
1D plotting - spectrum, chromatogram and mobilogram (diaPASEF) plots
2D plotting - heatmaps of any combination of two dimensions. Option to aggregate all precursors and fragments into a single heatmap, default is to split them into individual heatmaps.
3D plotting - vertical line spectrum-chromatogram plots for DIA and diaPASEF data. Aggregated 3D scatter heatmap plots of precursors and fragments, and contour plots for any two dimensions for diaPASEF data.
Loaders:
reportLoader - TSV based search results loader (based off DIA-NNs report). TODO: need to generalize to other TSV based reports like OSW or Spectronaught
DiaNNLoader - Loads a DIA-NN report file
OSWLoader - Loaders OSW sqlite-based report file
mzMLLoader - Loads an mzML file into an onDiscExperiment
TargetedDIADataAccess - Main class that does the actual targeted extraction
TargetDIALoader - Combines everything together to load the mzML data and perform the extraction and exports the data to a DF or TransitionGroup per precursor and per file.
Preprocess:
transformations - moved min-max scaling to this file from the chromatogram_data_handling.py file
Server:
RawTargetedExtractionAnalysisServer - Main script to perform targeted extraction analysis
OneDimensionPlotterServer (Two and Three) - scripts to prepare and generate the interactive plots calling the individual interactive plotter methods from plotting
UI:
RawTargetedExtractionAnalysisFormUI - front end user input forum for input files
FileInputRawDataUISettings - file input settings for displaying files in the sidebar and extracting list of files if a path if given for raw data.
RawTargetedExtractionAnalysisUI - front end for displaying components in the siderbar, i.e. search results information, extraction parameters, and for displaying plots and dataframes.
This is a fairly large PR.
This implements raw targeted feature extraction from DIA/diaPASEF mzML files using a spectral library (tsv/pqp) and optionally supplemented with search results (diann tsv/osw). The extracted results can then be visualized in 1D, 2D and 3D.
Note: I do not include any test files in this branch, I will include tests later in a separate branch.
Inputs:
Plotting:
Loaders:
Preprocess:
Server:
UI:
Examples
DIA (two runs)
diaPASEF (one run)