LC-MS trend detection with the new enviMass workflow interface

enviMass is a data-mining workflow for the automatized trend detection in liquid chromatography (LC) mass spectrometry (MS) measurement sequences, including a bundle of additional functionalities such as targeted screening, nontargeted grouping, homologue series detection or quantification. Please note that enviMass is mainly developed for 64bit Windows for the time being.

enviMass is freely available for private usage, universities and contributors. In-depth support and customized adaptions are provided as part of an enviMass Software- & Support-Package only; please → contact us.

Isotopologue tree The enviMass workflow features:

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

  • Cross-platform processing of SCIEX, Thermo, Agilent and Waters LC-MS formats. File upload (.mzXML format; direct conversion and upload of Thermo .raw files via ProteoWizard supported); batch file upload from folder.

  • 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.

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

  • Upload of suspect, target and internal standard compounds and resolution-specific calculation of their isotopic patterns.

  • Mass recalibration.

  • Intensity normalization; based on median intensities or labelled internal standards.

  • Replicate intersection filter.

  • Compound screening; includes filewise interpolation of limits of detection (LODs) and a combinatorial algorithm to find the most plausible matches of compound isotopic patterns.

  • Blind and blank file annotation and subtraction steps.

  • Quality control steps.

  • Isotopologue (Sciex TOF and Thermo Orbitrap instruments) and adduct grouping, filewise and cross-file componentization.

  • EIC correlation.

  • Homologue series detection and visualization.

  • Estimation of atom counts for nontarget components.

  • Extraction of time-intensity profiles.

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

  • Calibration, quantification and recovery with internal standards.

  • Workflow data availability in the R statistical environment - countless possibilities for custom-tailored analysis such as large-scale clustering, PCA or simple Venn-diagrams.

  • Handles positive and negative ionization modes in one project.

Major contributors

AUE logo Eawag logo Sciex logo IRSA logo