Mass spectrometric data analysis and trend detection with a new interface

enviMass is a data-mining workflow for the automatized detection of intensity patterns in hyphenated (LC/GC) or direct-injection (DIMS) mass spectrometry (MS, MS/MS) measurement sequences, including a growing bundle of additional functionalities such as targeted screening, nontargeted peak grouping, homologue series detection, quantification and statistical analysis.

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 a common task and applies to different fields of mass spec analysis, such as metabolomics, lipidomics or environmental analysis.

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

The dynamic filtering UI provides you with a comprehensive overview of your profiling results.
Prioritization and statistics
Rank 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 multiple queries for searching any intensity patterns of interest for your customized data analysis.

Queries may comprise fold changes, specific trends, presence/absence analysis or statistical tests - and even combinations thereof.
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

UI
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.
EICs
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.
QC
Quality control steps, outlier detection in cross-file peak intensity and count distributions.
RT
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.
table
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
Editor for defining user-specific comparisons to trace different intensity changes across processes or statistical test on intensity changes, e.g., certain fold changes or specific profile intensity patterns across treatments.
MSMS
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 or Excel.
Service
Extensive online and human-based user help and possible workflow adaptions. Workflow trainings. On-demand data processing services. Cooperations.
cluster

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

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.

Software contributors