peakPantheR

Peak Picking and ANnoTation of High resolution Experiments in R

peakPantheR is designed to detect and integrate multiple compounds in multiple files in parallel and store results in a single object.

To extract compounds intensity from data files, the following information is required:

Path(s) to netCDF / mzML MS file(s)
An expected region of interest (RT / m/z window) for each compound

The following steps take place during parallel compound annotation:

Data Import: Load a list of regions of interest and files to process.
Detection and integration: Detect features in each region of interest, integrate and calculate peak statistics
Diagnostic: Plot the resulting fits and update regions of interest, and return the corresponding statistics
View results: Explore the fitting results across samples or features
Export: Save the integration values and fit statistics, plot the extracted ion chromatograms

Abbreviations:

EIC: extration ion chromatogram
RT: retention time
m/z: mass over charge ratio
ROI: region of interest, region to search for a targeted compound
uROI: updated region of interest, refined search region
FIR: Fallback integration region, region to integrate if not valid peak can be found

1 - Import Data

Inputs:

Path(s) to netCDF / mzML MS file(s)
An expected region of interest (RT / m/z window) for each compound

The output object will be initialised with the targeted ROI and file paths.

2 - Run annotation: detection and integration

Once the object is initialised, the data can be processed.

For each file, features in each region of interest are detected, the highest intensity feature is integrated and peak statistics determined.

Results and EICs for each ROI are stored in the output object.

3 - Diagnostic: plot & update

Visually inspect the quality of fit for each features across all samples.

Based on the results obtained, updated regions of interest (uROI) and fallback integration regions (FIR) an be determined. (if no feature is detected the median RT / m/z start and end of the found features is set)

4 - View results

Summarise all integration results across all samples and all features.

Integration properties (e.g. peak found, peak area, peak apex RT / m/z) can be assessed individually.

5 - Export results

Export an annotation object or parameter files to reload the annotation at a later stage.

Save integration values (row: file, col: compound), fit statistics, and EIC plots.

Copyright

The present software is licensed under GPLv3.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
See the GNU General Public License for more details. http://www.gnu.org/licenses/