envibee

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 and availability

→ Installation

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 Journal of Cheminformatics

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

Implementation of an international cross-laboratory data management system to track target and non-target micropollutant trends in the River Rhine catchment. Commissioned by the IKSR/SANA, including long-termed user support and software maintenance.

Software optimization and adapations for target quantification at AUE Basel.

Self-parameterized algorithms for high-precision and high-throughput profiling of hyphenated mass spec data sets.

Aligns, groups and smoothes chromatograms of re-occuring analytes, while separating isobaric ones. Testing for high levels of noise and different instrument types and applications (groundwater, surface water monitoring, different STP effluents). Replacement or supplement for existing greedy approaches in enviMass.

R-packaged reimplemenation of the Swiss micropollutant and nutrient routing model for the Swiss Association of Experts on Wastewater and Water Protection.

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

Providing a command-line interface of the enviMass workflow for Docker-based server integration, along with assistance in parametrising enviMass for different labs. Part of the K2I project on using artificial and collective intelligence for tracking organic trace contaminants in surface waters for sustainable drinking water production.

Multivariate data analysis on emerging NTS pollutants for different landfill sites in the Canton Zürich (CH). Commissioned by the department for waste, water, energy and air (Amt für Abfall, Wasser, Energie und Luft, AWEL, Zürich, CH).

NTS data analysis for the interlaboratory trial of cantonal laboratories, Switzerland. Commissioned by the Federal Office for the Environment FOEN (BAFU).

NTS data analysis for the interlaboratory trial of drinking water producers, Germany. Commissioned by the state water supply Langenau (Zweckverband Landeswasserversorgung).

Data analysis for a spatiotemporal monitoring campaign in the Furtbach catchment (CH, Canton Zürich). Extraction of main and clustered intensity variations for mass spec target and nontarget profiles. Elucidation of patterns with discharge characteristics in the catchment. Commissioned by the cantonal department for waste, water, energy and air (Amt für Abfall, Wasser, Energie und Luft, AWEL, Zürich, CH).

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.

Detection of characteristic ESI in-source fragments for perfluorinated compounds, based on customized enviMass scripts. Commissioned for HS Fresenius / IFAR .

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.