Mass spectrometric trend detection with the new enviMass workflow interface

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

enviMass is freely available for NON-COMMERCIAL usage and for all contributors. For COMMERCIAL usage, certain steps in the workflow can only be operated as part of an enviMass Software- & Support-Package. This Software- & Support-Package also provides in-depth support and customized adaptions. Please → contact us for more information.

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, outlier detection in intensity distributions.

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

  • EIC correlation, e.g., to hint at in-source fragments, dimer formation or other unusual ESI adducts.

  • 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.

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

  • Editor for defining user-specific comparisons to trace different intensity changes across processes or statistical test on intensity changes.

  • Calibration, quantification and recovery with/without 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