looscomputing developes and maintains the below software packages. All packages can be run directly from the freely available R statistical computing environment, either after download from R CRAN repositories or following an installation from their GitHub repositories.

Software and workflows under development

webMass

enviMass v3.2

Data-mining workflow for liquid chromatography (LC) mass spectrometry (MS) measurement sequences; comprises file and compound uploads, chromatogram extraction, peak picking, mass recalibration, intensity normalization, profiling, trend detection, compound screening, blind subtraction and replicate intersections. Packages up to version 2.2 were commenced at Eawag Dübendorf; now further developed for the Rhine monitoring station Basel (CH, Kantonales Umweltlabor Basel Stadt / Amt für Umwelt und Energie).

Installation

Find the latest package release on GitHub

enviQuant

enviQuant is being developed for the Rhine monitoring station Basel (CH) to support the quantification of aquatic micropollutants. As such, enviQuant will integrate into the workflow of enviMass projects, providing interactive calibration and recovery calculations and the required data management for mass spectrometric calibration measurements.

Software maintenance

enviPat v2.1

Fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing. Package originally commenced at Eawag Dübendorf.

Find the latest package version on GitHub

Get the last CRAN release

Run enviPat online

Read the publication in Analytical Chemistry

Isotopologue tree

nontarget v1.9

Screening a liquid chromatrography (LC) - high resolution mass spectrometry (HRMS) data set for peaks related by (1) isotope patterns, (2) different adducts of the same molecule and/or (3) homologue series. The resulting isotopic pattern and adduct groups can then be combined to so-called components, with homologue series information attached. Also allows plotting and filtering HRMS data for mass defects, frequent m/z distances and components vs. non-components. Package originally commenced at Eawag Dübendorf.

Find the latest package version on GitHub

Get the last CRAN release

Detect homologue series online

Read the publication in Journal of Cheminformatics

nontargetData

Exemplary data set for resolution-specific isotope pattern grouping of LC-HRMS peaks with the above package nontarget and its function pattern.search2(). Based on a large set of unique PubChem molecular formulas, quantized (a) m/z, (b) m/z differences, (c) intensity ratios and (d) marker centroids of simulated centroid pairs are listed for one instrument resolution function. Package version 1.1 was contributed 2014 to the CRAN repository while working at Eawag Dübendorf; further instrument-specific data sets are available on demand.

Find the latest package version on GitHub

Get the last CRAN release

enviPick v1.4

Sequential partitioning, clustering and peak detection of centroided LC-MS mass spectrometry data (.mzXML). Interactive result and raw data plot. Package up to version 1.3 commenced at Eawag Dübendorf.

Find the latest package version on GitHub

Get the last CRAN release