envibee

enviMass v4.5

UI- and command-line based 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,
• combined DDA and DIA MS2 processing,
• statistical toolset,
• a multitude of other features ...

The workflow has a growing number of users and contributors, and is used in both commercial and non-commercial applications.

→ Workflow overview

→ Installation and availability

elastiMass v1.9

elastiMass aligns and synchronizes larger sets of enviMass projects (e.g., from a multi-user setting on a common server) into a single database, in realtime (as a background process), and fully autonomously. From this database, peaks, profiles and any annotated target and nontarget screening information can be queried and compared across projects with an additional visualization interface.

In addition, the elastiMass interface can be used to merge and re-distribute new target und watchlist entries made in a single project into all other stored projects, and to notify users of any required project management tasks.

→ More information

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

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

Contracted implementation of an international cross-laboratory data management system to track target and non-target micropollutant trends in the River Rhine catchment, and as part of the project Non-target screening in the Rhine basin.

Commissioned by the IKSR/SANA, including long-termed user support and software maintenance.

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 K2IXplore project on using artificial and collective intelligence for tracking organic trace contaminants in surface waters for sustainable drinking water production.

Software optimization and adapations for the LC-HRMS routine monitoring 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.

Adaptions in the enviMass workflow for the processing of DDA and DIA MS2 measurements in profiled LC-HRMS data sets. Includes UI data management and data visualization changes, and the automatized and customizable combination of both MS2 modes from larger sets of profiled measurements. Commissioned by the Ministerie van Infrastructuur en Waterstaat / DG Rijkswaterstaat.

R-package NTS4UBA for combining json-based NTS data exports, compound lists with toxicity data and, optionally, enviMass projects into a common database. Includes a shiny UI for the synchronization and data query. Commissioned by the Umweltbundesamt Berlin.

Providing a command-line interface of the enviMass workflow for Docker-based server integration for the first and completed stage of the K2I project.

Processing of LC-HRMS measurements, multivariate statistical data analysis and comprehensive reporting for two sampling campaings at two river locations in Germany and Switzerland (ERMES project).

Commissioned by AUE Basel and LUBW Karlsruhe.

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

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.