envibee developes and maintains the below software packages. Most 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. Other Software, such as enviMass, is available as part of a Software- and Support-Package for commercial usage but available free of charge upon request for academic users.

envibee can be contracted for data analysis tasks, also in conjunction with the usage of its software packages. Some of these projects are listed in the below portfolio as well.

Software and workflow development


enviMass v4.2

Data-mining routine for (large) liquid or gas chromatography (LC/GC) mass spectrometry (MS) measurement sequences. The cross-platform workflow comprises an extensive and flexible set of tools for mass spec analysis, such as:
  • (batch) file and compound uploads,
  • self-parametrized chromatogram extraction and peak picking,
  • mass recalibration, intensity normalization, RT alignment and LOD-estimation,
  • replicate and blank annotations,
  • cross-file profiling,
  • trend detection and customizable queries,
  • quantification,
  • compound screening and nontargeted componentization,
  • homologue series detection and filtering,
  • MS2 processing,
  • ...
Packages up to version 2.2 were commenced at Eawag Dübendorf; and are now, among other contributors and users, further developed for the Rhine monitoring station Basel (CH, Kantonales Umweltlabor Basel Stadt / Amt für Umwelt und Energie).

Further workflow information

Availability and installation

Software maintenance

enviPat v2.4

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


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

Current projects

Customized LC-MS data analysis, support and extensions assigned by the Department of Environmental Chemistry at Eawag Dübendorf.


Automated LC/LC- and GC/GC-MS noise removal and signal detection (peak picking). Extension of the above enviPick R package for an additional dimension and for larger raw data sets.

→ Looking for contributors / project partners

Completed projects

Assistance with the data analysis for an international interlaboratory trial of monitoring stations along the Rhine River. Commissioned by the IKSR/SANA.


Suspect screening plus prioritization of industrial emissions. Spatial and process-based data clustering of selected sewage treatment plant effluents. Commissioned by the cantonal department for waste, water, energy and air (Amt für Abfall, Wasser, Energie und Luft, AWEL, Zürich, CH).


Sample data processing and prioritization of known and unknown trace organic compound time series. Summer monitoring campaign at the River Thur catchment, canton St Gallen. Commissioned by the cantonal department for water and energy (Amt für Wasser und Energie, AWE, St Gallen, CH), and in collaboration with the cantonal laboratory for the protection of water and soil (AWA/GBL, Bern, CH).

Industrial partner for a project on outlier detection as part of a bachelor-thesis, in collaboration with the Institute of Data Analysis and Process Design at the ZHAW School of Engineering, Winterthur, CH.