enviMass

Mass spectrometric data analysis and trend detection with a new interface

MASS SPEC

enviMass is a versatile data-mining workflow for the automatized detection of patterns and compounds in

hyphenated (LC or GC) or
direct-injection (DIMS)
mass spectrometry (MS, MS/MS)

measurement sequences.

DATA ANALYSIS

The workflow can handle large data sets and provides a user-friendly interface for routine analysis.

All provided with the necessary support to get you introduced to the workflow and to keep you going.

enviMass can be used to monitor environmental media such as air, surface- and groundwater as well as drinking water resources for the occurrence of organic pollutants.

TOOLS

enviMass can be used for a multitude of mass spec data analysis tasks, adaptable to various fields of application.

The workflow includes a growing bundle of data mining functionalities such as targeted screening, nontargeted peak grouping, homologue series detection, quantification and statistical analysis.

A full listing of all features can be found further below.

Feel free to → contact us if you want to find out how enviMass can improve your analysis or if you would like to view a live workflow tour .

enviMass in action at a Swiss cantonal lab, → aka youtube user insights ('Unterwegs mit dem Umweltchemiker', german language video).

Now available: → integrated target & nontarget analysis approach for PFAS compounds.

enviMass applications

Long-term monitoring

The anthropogenic release of a large variety of micropollutants such as pesticides, pharmaceuticals and their transformation products is a hot topic.

Monitoring of affected aquatic systems, STP effluents, drinking water resources as well as treatment steps has therefore become crucial.

enviMass provides the tools to quickly mine your big mass spec data sets for pollutant trends and patterns of concern, at various temporal and spatial scales, and under varying monitoring constraints.

Profiling

Tracing intensity variations of masses over sets of measurements is often the first steps in mass spec analysis.

enviMass provides all necessary tools for such a profiling - including peak picking, RT alignment, mass recalibration, normalization, blind annotation and a replicate intersection step.

Furthermore, adaptive algorithms combine multiple mass and peak shape criteria for profiling - and thereby remain reliable when other workflows fail.

A dynamic filtering UI finally provides you with a comprehensive overview of your profiling results.

Prioritization

Rank your mass spec profiling results and view intensity distributions across time, space or treatments for prioritized masses.

Moreover, use the build-in editor with a simplified syntax to easily define your own queries for searching any intensity patterns of interest.

Such queries may comprise fold changes, specific trends, correlation with discharge, presence/absence analysis or statistical tests - and even combinations thereof.

Statistics

Use your mass spec profiling results with embedded statistical toolsets and their interactive and comprehensive result views.

Whether fold-changes and volcanoe plots, PCA or heatmap analysis - all can be intersected with target and nontarget screening results or customized profile queries.

Routine usage

enviMass has been built for non-programmers and for user-friendly analysis. Hence, it comes with a full-fledged user interface to automatically keep track of inputs and workflow interactions, organising all data into individual projects. All settings are checked for consistency.

The workflow has been tested at various labs and for different research questions, and is now being applied by a growing number of routine users.

Target and suspect screening

Screen for lengthy lists of target, suspect and isotopically labelled compounds.

Screening accounts for a resolution-specific simulation of isotopologue patterns, and for user-defined ESI adducts. Matches with fragment masses in tandem MS spectra are reported as well.

Nontarget analysis

Keep track of yet unidentified compound masses. Group all available information on their exact mass, atom counts, isotopologues, ESI adducts, in-source and tandem MS fragments as well as their occurrence patterns for later identification.

Refine this information by cross-file filtering algorithms.

With enviMass, you can also store such nontarget information on observation lists and use these for screening - prior to any identification steps.

Cross-platform processing

You are using mass spec data from different vendor instruments, with different resolutions and with different MS2 experiment settings?

enviMass has been specifically designed for such cross-platform applications. For example, a build-in parameter estimation aids at adapting peak picking parameters to different acquisition setups and changing matrixes automatically.

Homologue serie detection

An unsupervised detection of peak series with repeating mass units can indicate the presence of homologuous compounds and may quickly point at specific compound classes such as surfactants, polymers or certain congeners (e.g., perfluorinated compounds).

This unique detection tool works even for non-linear RT changes and different mass units across series.

Subsequent filtering steps and an interactive visualization then aid in prioritizing the detected series, even in complicated matrices.

Large scale clustering

enviMass can detect cluster of mass profiles with similar intensity patterns, even in very large data sets and across ionization modes.

Clustering highlights related temporal or spatial release patterns, associated compounds or such with similar (environmental) behavior. It thereby reveals any structuring your data may otherwise hide.

Use the interactive visualization tool to browse through your clustering results and to find profile aggregations of target or suspect compound groups or those containing your most intense or frequent mass spec signals.

Quantification

Use the enviMass calibration tab to define linear and nonlinear calibration models with/without internal standards and for different sets of calibration files in one single project.

Copy calibration models between such sets and handle different calibration models for the same target compound.

Estimate concentrations across large sample batches and quantify their recoveries using spiked measurements.

Quality control

Check the consistency of your measurements and ensure that no outliers obscure your results. Several statistical quality checks assist you in this task, and are set as default output during workflow usage.

Know how

enviMass is not a black-box tool.

Either features are documented or registered users are welcome to ask how they function and what they do.

Smaller stand-alone parts of enviMass are even freely available as open-source R packages, i.e., enviPick, enviPat and nontarget.

Free data access & analysis

Apart from custom analysis with its build-in editor, all raw data and enviMass workflow results can be optionally exported into the freely available R statistical environment with ready-to-go enviMass R functions.

With thousands of R open-access packages available, this offers countless possibilities for virtually any type of data analysis and visualization. Customized R scripts form part of our service package.

enviMass features

User-friendly and interactive interface + project structuring to handle your mass spectrometry data with a large and growing set of analysis tools.

Data

Cross-platform processing of SCIEX, Thermo, Agilent and Waters file formats via .mzXML. Batch file upload and annotation. Direct upload of Thermo .raw files.

Speed

Multi-core processing and adapative workflow structure: changes in parameters, compounds, files or workflow choices are traced and calculations adapted accordingly to minimize computational costs. Fast access to all raw and processed data.

Signals

Auto-parametrized noise removal, chomatogram extraction (EICs, XICs), peak picking and interactive data visualization. Exportable peak tables.

Blank

Flexible blind and blank file annotation and subtraction steps.

Preprocessing

Intensity normalization; based on median intensities or internal standards.
Mass recalibration.
Retention time alignment.

Replicates

Replicate intersection filter.

Quality control steps, outlier detection in cross-file peak intensity and count distributions.

Targets

Upload of suspect, target and internal standard compound lists and resolution-specific calculation of their (ESI adduct) isotopic patterns.
Compound screening; includes a combinatorial algorithm to find the most plausible matches of compound isotopic patterns.
MS2 fragment screening.
Filewise interpolation of limits of detection (LODs).

Quantification

Calibration, quantification and recovery with/without internal standards. Handling of different calibration sets in one project. Copying of calibration models between such sets.

Nontargets

EIC correlation, e.g., to hint at in-source fragments, dimer formation or other unusual ESI adducts.
Resolution-specific isotopologue and adduct grouping.
Filewise and cross-file componentization and annotation; adaptive component filtering.
Estimation of atom counts for nontarget components.
Nontargeted black-/observation-listing.

Series

Unsupervised homologue series detection and visualization. Merging of gapped series and extensive series filtering.

Profiling

Extraction of cross-file mass profiles to yield intensity patterns across time, space, processes, treatments, etc.
Improved profiled mass estimation.

MS2

Processing of DDA, DIA, SWATH MS/MS spectra. Filtering of tandem mass spectra for nontargeted profiling.

Trends

Profile trend detection; works for hundreds of uploaded files and several thousand profiles.

Statistics

Fold-change and volcanoe plots, PCA, dendrogram heatmaps. Various normalization and visualization methods.
Editor for sample-subsetting and defining user-specific comparisons to trace different intensity changes across processes and sampling locations or to run statistical test.

Blacklist

Screening of nontargets (known unknowns) via assembling their mass spec informations as observation list entries.

Clustering

Interactive clustering to extract and highlight profile sets with similar patterns - even across very large data sets. Profile similarity search.

Modes

Workflow handles positive and negative ionization modes in one project.

Export

Workflow data availability in the R statistical environment - countless possibilities for custom-tailored analysis such as large-scale clustering, PCA or simple Venn-diagrams. Access functions to all data. R functions to filter and merge profile data to matrix outputs. Export of UI peak, EIC, screening, concentration and profiling tables to .csv and Excel.

Users

A normal user mode helps to avoid some common application mistakes and makes the workflow easier to use. Can be switched to an expert mode for advanced capabilities.

Reporting

Possibility for custom-made .pdf and Excel outputs on overall or selected profiling results to match the reporting and the summaries you need.

Support

Service with extensive online and human-based user help and possible workflow adaptions. Workflow trainings. On-demand data processing services. Cooperations.

Software contributors

Availability

enviMass is freely available for all contributors, and as part of the enviMass Software- & Support-Package otherwise. This Software- & Support-Package includes download access, provides in-depth user support, a possibility for customized software adaptions and applies to any commercial usage of the software. Special package conditions apply to educational workflow usage at universities.

Feel free to → contact us for more information.

enviMass: selected literature

Unveiling industrial emissions in a large European river: Insights from data mining of high-frequency measurements, T. Chonova, S. Ruppe, I. Langlois, D. Griesshaber, M. Loos, M. Honti, K. Fenner, H. Singer, Water Research Volume 268, Part B, 1 January 2025, 122745

Organische Spurenstoffe – Emerging Pollutants. Untersuchung von Deponiesickerwasser, AWEL – Amt für Abfall, Wasser, Energie und Luft, Kanton Zürich, 2023

Retrospective non-target analysis to support regulatory water monitoring: from masses of interest to recommendations via in silico workflows, A. Lai, R. Singh, L. Kovalova, O. Jaeggi, T. Kondic, E. Schymanski, Environmental Sciences Europe, 2021, 33, Article number 43.

Characterization of water-soluble synthetic polymeric substances in wastewater using LC-HRMS/MS, T. Mairinger, M. Loos, J. Hollender, Water Research 190, 2021.

Assessing emissions from pharmaceutical manufacturing based on temporal high-resolution mass spectrometry data, S. Anliker, M. Loos, R. Comte, M. Ruff, K. Fenner, H. Singer, Environ. Sci. Technol., 2020, 54, 7, 4110–4120.

Application of immobilized TiO2 on PVDF dual layer hollow fibre membrane to improve the photocatalytic removal of pharmaceuticals in different water matrices, L. Paredes, S. Murgolo, H. Dzinun, M. Othmanc, A. Ismail, M. Carballa, G. Mascolo, Applied Catalysis B: Environmental 240, 2019, 9–18.

Biotransformation of antibiotics: Exploring the activity of extracellular and intracellular enzymes derived from wastewater microbial communities, M. Zumstein, D. Helbling, Water Research 155, 2019, 115-123.

Fall creek monitoring station: highly resolved temporal sampling to prioritize the identification of nontarget micropollutants in a small stream, C. Carpenter, L. Wong, C. Johnson, D. Helbling, Environ. Sci. Technol. 2019, 53, 77−87.

Photocatalytic degradation of diclofenac by hydroxyapatite–TiO2 composite material: identification of transformation products and assessment of toxicity, S. Murgolo, I. Moreira, C. Piccirillo, P. Castro, G. Ventrella, C. Cocozza, G. Mascolo, Materials 2018, 11, 1779.

Surface water and groundwater analysis using aryl hydrocarbon and endocrine receptor biological assays and liquid chromatography-high resolution mass spectrometry in Susquehanna County, PA, M. Bamberger, M. Nell, A. Ahmed, R. Santoro, A. Ingraffea, R. Kennedy, S. Nagel, D. Helbling, R. Oswald Environ Sci Process Impacts. 2019 May 16.

Comparison of different types of landfill leachate treatments by employment of nontarget screening to identify residual refractory organics and principal component analysis, C. Pastore, E. Barca, G. Del Moro, C. Di Iaconi, M. Loos, H. Singer, G. Mascolo, Science of the Total Environment 635, 2018, 984–994.

Comprehensive micropollutant screening using LC-HRMS/MS at three riverbank filtration sites to assess natural attenuation and potential implications for human health, J. Hollender, J. Rothardt, D. Radny, M. Loos, J. Epting, P. Huggenberger, P. Borer, H. Singer, Water Research X 1, 2018, 100007.

Detective work on the Rhine River in Basel – finding pollutants and polluters, S. Ruppe, D. Griesshaber, I. Langlois, H. Singer, J. Mazacek CHIMIA 2018, 72, No. 7/8.

Nitrate determines growth and protease inhibitor content of the cyanobacterium Microcystis aeruginosa, C. Burberg, M. Ilić, T. Petzoldt, E. Elert, Journal of Applied Phycology, 2018, https://doi.org/10.1007/s10811-018-1674-0.

Non-target screening to trace ozonation transformation products in a wastewater treatment train including different post-treatments, J. Schollee, M. Bourgin, U. Gunten, C. McArdell, J. Hollender, Water Research 142, 2018, 267-278.

Exploring micropollutant biotransformation in three freshwater phytoplankton species, M. Stravs, F. Pomati, J. Hollender, Environ. Sci.: Processes Impacts, 2017, 19, 822–832.

Keeping afloat in modern water analysis, A. Sage, The Analytical Scientist, 2017, 22 - 23.

Nontargeted homologue series extraction from hyphenated high resolution mass spectrometry data, M. Loos, H. Singer, J Cheminform 2017, 9:12.

Open-source workflow for smart biotransformation product elucidation using LC-HRMS data, M. Stravs, J. Hollender, CEST 2017, 01416.

Unravelling contaminants in the anthropocene using statistical analysis of liquid chromatography−high-resolution mass spectrometry nontarget screening data recorded in lake sediments, A. Chiaia-Hernandez, B. Guenthardt, M. Frey, J. Hollender, Environ. Sci. Technol. 2017, 51, 12547-12556.

Effect-directed analysis supporting monitoring of aquatic environments — an in-depth overview, W. Brack et al., Science of the Total Environment 544, 2016, 1073–1118.

Rapid screening for exposure to “non-target” pharmaceuticals from wastewater effluents by combining HRMS-based suspect screening and exposure modeling, H. Singer, A. Wössner, C. McArdell, K. Fenner, Environ. Sci. Technol. 2016, 50, 6698−6707.

Vom Unfall zur praeventiven Ueberwachung, J. Mazacek, S. Ruppe, D. Griesshaber, I. Langlois, R. Dolf, H. Singer, J. Leve, A. Hofacker, Aqua & Gas 11, 2016, 66-75.

Prioritizing unknown transformation products from biologically treated wastewater using high-resolution mass spectrometry, multivariate statistics, and metabolic logic, J. Schollee, E. Schymanski, S. Avak, M. Loos, J. Hollender, Anal. Chem. 2015, 87, 12121−12129.

Target screening of chemicals of concern in recycled water, F. Busetti, M. Ruff, K. Linge, Environ. Sci.: Water Res. Technol., 2015, 1, 659.

Targeted and non-targeted liquid chromatography-mass spectrometric workflows for identification of transformation products of emerging pollutants in the aquatic environment, A. Bletsou, J. Jeon, J. Hollender, E. Archontaki, N. Thomaidis, Trends in Analytical Chemistry 66 2015, 32–44.

20 Jahre Rheinueberwachung - Erfolge und analytische Neuausrichtung in Weil am Rhein, M. Ruff, H. Singer, S. Ruppe, J. Mazacek, R. Dolf, C. Leu., Aqua & Gas No 5, 2013, 16 - 25.

Advances in liquid chromatography–high-resolution mass spectrometry for quantitative and qualitative environmental analysis, J. Aceña, S. Stampachiacchiere, S. Pérez, D. Barceló, Anal Bioanal Chem, 2015, 407:6289–6299.

Exploring the behaviour of emerging contaminants in the water cycle using the capabilities of high resolution mass spectrometry, J. Hollender, M. Bourgina, K. Fenner, P. Longrée, C. McArdella, C. Moschet, M. Ruff, E. Schymanskia, H. Singer, Chimia 68, 2014, 793–798.

Investigation of pharmaceuticals and illicit drugs in waters by liquid chromatography-high-resolution mass spectrometry, F. Hernández, M. Ibáñez, R. Bade, L. Bijlsma, J.V. Sancho, Trends in Analytical Chemistry 63, 2014, 140–157.

Iodinated contrast media electro-degradation: Process performance and degradation pathways, G. Moro, C. Pastore, C. Iaconi, G. Mascolo, Science of the Total Environment 506–507, 2015, 631–643.

Plasma lipidomic profiling method based on ultrasound extraction and liquid chromatography mass spectrometry, C. Pizarro, I. Arenzana-Ramila, N. Perez-del-Notario, P. Perez-Matute, J. Gonzalez-Saiz, Anal. Chem. 2013, 85, 12085−12092.

Strategies to characterize polar organic contamination in wastewater: exploring the capability of high resolution mass spectrometry, E. Schymanski, H. Singer, P. Longree, M. Loos, M. Ruff, M. Stravs, C. Vidal, J. Hollender, Environ. Sci. Technol. 2014, 48, 1811−1818.

Screening for pharmaceutical transformation products formed in river sediment by combining ultrahigh performance liquid chromatography/high resolution mass spectrometry with a rapid data-processing method, Z. Li, M. Maier, M. Radke, Analytica Chimica Acta 810 2014, 61–70.

State-of-the-art of screening methods for the rapid identification of chemicals in drinking water, M. Llorca, S. Rodríguez-Mozaz, Report EUR 26155 EN, European Comission 2013.

Suspect and nontarget screening approaches to identify organic contaminant records in lake sediments, A. Chiaia-Hernandez, E. Schymanski, P. Kumar, H. Singer, J. Hollender, Anal Bioanal Chem, 2014, 406:7323–7335.