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Software tools for MS data processing & analysis

Boosting Information, Boosting Knowledge

Spectroswiss software solutions provide a step-change in mass spectrometry data quality and processing sophistication, helping you to take on the most complex and challenging applications. Our computationally-efficient tools are capable of processing large datasets, whether these are unreduced data (time-domain data or transients and full profile mass spectra) OR reduced data (reduced profile and centroided mass spectra). Our application-specific workflows enable step-by-step data processing and data analysis giving you the tools to powerfully investigate your samples.

Workflows


Quantitative Metabolomics & Lipidomics



Complex Mixture Analysis



Quantitative LC/GC-MS analysis
of Compound Classes



MALDI & DESI Imaging



Top-Down & Middle-Down Analysis



CDMS:
Individual Ion Counting



Protein Analysis (BioPharma)



FTMS Simulator (Protein-grade!)



Custom
Workflows


Advanced Modular Software

 

Peak-by-Peak suite: a set of computational modules with a graphic user interface to process transients or mass spectra configured into a basic (essential functionality) or expert (full functionality) editions.

 

Editions

Workflows

Quantitative Metabolomics & Lipidomics

In-depth processing and quantitative analysis of mass spectrometry metabolomics and lipidomics data

Key features
 

  • A multi-vendor platform for data processing and analysis from diverse mass spectrometers, supporting both LC-MS and GC-MS, with an automated recognition of meta-information
  • Data processing based on the target and semi-target databases of individual compounds of interest
  • Aligning of LC-MS experiments with or without extracted feature lists: targeted and untargeted approaches
  • Accurate peak picking and diverse mass accuracy evaluation and re-calibration procedures
  • Reliable feature extraction via experimental data matching with the simulated isotopic envelopes
  • Quantification of compounds (area under the curve): absolute, standard, and semi-quantification
  • Elemental formula assignment by accurate mass, with a similarity score ranking vs the simulated data
  • Support for batch file processing of large data sets: practically any number of LC-MS datasets
  • Comparative analysis of extracted features via a dynamic global result matrix, user-defined output reports

MALDI & DESI Imaging

Process, analyze, and visualize MSI data – no matter the file size or the MS platform.

Key features
 

  • A multi-vendor platform for MSI data processing and analysis from diverse MS instruments, including
  • OrbitrapTM FTMS, FT-ICR MS, MRT MS, TOF MS, and QQQ MS with and without ion mobility
  • A direct data import of major vendor file types accompanied by import of MSI data in the imzML file format
  • Support for MALDI and DESI sources (MassTech, Spectroglyph, TransMIT, and others)
  • Automatic recognition of acquisition modes (MS, MS/MS, SIM, etc.), ion sources, and ion polarity
  • Data validation and correction (re-calibration) through several mass accuracy evaluation capabilities
  • Basic and advanced mass spectra and time-domain transient processing with user-defined parameters
  • Instant visualization (click & see) and processing of images: normalization, noise reduction, hotspot removal
  • Regions of interest (ROI) definition, analysis and geometry handling, comparative analysis
  • Co-localization and overlay of (multi-mode) images, image weighted transparency and many color options

Protein Analysis (BioPharma)

In-depth processing and quantitative analysis of mass spectrometry protein analysis data

Key features
 

  • Advanced and proprietary mass spectrometry solutions for mAb analysis, including complex ADCs/AOCs
  • Integration of intact mass and middle-up mass spectrometry approaches
  • Sensitivity boost: data averaging of LC-MS,direct infusion MS data from multiple experiments (replicates)
  • Targeted (direct) deconvolution via simulation of mass spectra from proteoform sequences and modifications
  • High-resolution (FLASH Deconv) and low-resolution (UniDec) untargeted deconvolution, charge state grouping
  • Recalibration of intact (MS data) mass spectra and mass accuracy evaluation procedures
  • Annotation and quantification of proteoforms (via area under the curve in LC-MS)
  • Graphical output (high quality images), interactive and PDF reports with mass spectral data and peak lists
  • User-defined automation options for data input, processing, and reporting

Complex Mixture Analysis

Advanced processing and analysis of (very) complex mixtures mass spectrometry data

Key features
 

  • Integration and processing of mass spectra of practically any size (.RAW, .d folders, and .H5 files)
  • Open file formats for time-domain transients & mass spectra: H5, DAT, MGF, mzXML, and mzML
  • Visual comparison of time-domain transients and mass spectra from separate data sets
  • Spectral and time-domain transient averaging for higher sensitivity and dynamic range in MS & LC-MS
  • Processing of LC-MS data for complex mixtures analysis, e.g., in petroleomics and biofuels applications
  • Narrow m/z window (SIM) stitching of the unreduced and reduced data for enhanced performance
  • Advanced peak picking and baseline correction, noise thresholding, mass spectral data reduction
  • Mass scale calibration equations, including iterative re-calibration for complex mixtures analysis

Top-Down & Middle-Down Analysis

Advanced processing and analysis of intact, middle-down, and top-down data

Key features
 

  • All the features of the Peak-by-Peak BioPharma workflow for intact mass protein analysis
  • Integration of middle-down, top-down, and bottom-up mass spectrometry approaches
  • Sensitivity boost: data averaging of LC-MS/MS and MS/MS data from multiple experiments (replicates)
  • Targeted (direct) deconvolution via simulation of product ion isotopic envelopes and mass spectra
  • High-resolution (FLASH Deconv and Hardklor) untargeted deconvolution, charge state grouping
  • Recalibration of middle-down and top-down (MS/MS data) mass spectra and mass accuracy evaluation
  • Interactive graphical representation of sequence maps (add proteoforms, remove assignments, etc.)
  • Graphical output (high quality images), interactive and PDF reports with MS/MS data and sequence maps

FTMS Simulator (Protein-grade!)

A software tool to accurately simulate FTMS isotopic envelopes and mass spectra

Key features
 

  • Analyte parameters selection: elemental composition, amino acid sequence, charge carrier, modifications, isotopic enrichment/depletion, number of charge states, and number of isotopologues
  • FTMS experiment parameters: FTMS instrument selection (models of Orbitrap & ICR), resolution setting (@ m/z), add noise, set signal intensity thresholds, set initial phase, sampling rate, and decay rate
  • Data processing parameters: absorption or magnitude FT, unapodized or apodization function, number of zero-fills, full or reduced profile mass spectra, centroids
  • Applicable to (almost) any size molecules – from metabolites to monoclonal antibodies and viruses
  • Applicable to (almost) any complexity mass spectra – from isotopic envelopes to full scale top-down mass spectra
  • Results output and applicability: use simulated data to search experimental data, rank search results by the similarity score (m/z, intensity), save project for future use, create report as a PDF file

Quantitative LC/GC-MS analysis of Compound Classes

In-depth processing and quantitative analysis of mass spectrometry compound classes data

Key features
 

  • All the features of the Peak-by-Peak Metabolomics workflow
  • Input of target and semi-target databases of pre-set and user-defined classes of compounds of interest
  • Quantification of classes of compounds (via area under the curve in LC/GC-MS):
     
    – absolute quantification (labelled compound classes as internal standards, ratio of analyte compound classes signal to the internal standard compound classes)
     
    – semi-quantification (internal standards provide quantitative information, expressed as areas under the curve; information used for other compound classes)
     
    – semi-quantification, standard addition (external calibration)
  • Graphical output (high quality images), interactive and PDF reports with mass spectra and peak lists

CDMS: Individual Ion Counting

An integrated solution enabling individual (single) ion counting approach on OrbitrapTM and ICR FTMS

Key features
 

  • Access to the time-domain transients from OrbitrapTM and ICR FTMS instruments via our proprietary add-on high-performance data acquisition systems – FTMS Boosters
  • Wide range of time-domain data processing parameters: absorption/magnitude FT, apodization function, number of zero-fills, full or reduced profile mass spectra, centroids, visualize transients
  • Advanced time-domain data processing, including STORI (selective temporal overview of resonant ions) approach
  • User-controllable multi-iterative conditional filtering, averaging, and feature detection
  • Charge calibration and charge grouping procedures
  • Results comparison with conventional approaches for time-domain transient analysis (data averaging)

Custom Workflows

Our powerful computational algorithms and flexible graphical user interface (GUI) templates can be configured to match your needs and offer computationally-efficient, fast, and accurate data processing and analysis solutions.

Selected custom workflows
 

  • UVPD spectroscopy
  • Bottom-up glycoproteomics
  • TMT-based multiplexed protein quantitation