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Software tools for FTMS data processing & analysis

Boosting the Information Output

The Spectroswiss software solutions provide a step change in FTMS data quality and processing sophistication, helping you to take on the most complex and challengingapplications. Our computationally-efficient tools are capable of processing large datasets of both, unreduced data (time-domain data or transients and full profile mass spectra) andreduced data (reduced profile and centroided mass spectra). Our application-specificworkflows enable step-by-step data processing and data analysis.

WORKFLOWS

FTMS Simulator

Complex Mixture Analysis

Imaging

Top-Down Analysis

Metabolomics

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

Software Base edition Expert edition
Simulation of FTMS data (The FTMS Isotopic Simulator)
RAW file statistics (data distributions: scan time, IT, charge state) and metadata overview
Mass spectra processing: baseline correction, noise thresholding and peak-picking
Plot multiple mass spectra: experimental and/or simulated data comparison
Mass spectra re-calibration: single mass spectra
Mass spectra re-calibration: LC-MS/GC-MS (1D datasets )
Mass spectra re-calibration: imaging (2D datasets)
Process multiple FTMS experiments:
plot TICs and SICs for each input file
plot single and/or average mass spectra
align LC-MS or LC-MS/MS chromatograms
average data between any files (including between technical replicates)
SIM-window stitching from spectral or time-domain data
SIM-window averaging and stitching
Deconvolution of low-resolution data
Deconvolution of high-resolution data
Data visualization and output: high quality images and/or mass spectra in open file formats

FTMS Simulator

FTMS Simulator

The FTMS Simulator is a software tool to accurately simulate FTMS isotopic envelopes and mass spectra to:
I. search the experimental data with a like-for-like theoretical data using similarity score for ranking the results
II. design FTMS experiments by selecting appropriate instrumentation settings and FT data processing parameters
III. teach the FTMS subject by demonstrating both transients and corresponding mass spectra, containing typical FT artefacts, etc.

 

Key features

  • Analyte parameters: elemental composition, amino acid sequence, charge carrier, modifications, isotopic enrichment/depletion, number of charge states and isotopologues
  • FTMS experiment parameters : FTMS instrument selection (models of OrbitrapTM & ICR), resolution setting (@ m/z), transient sampling rate, add noise, set thresholds
  • Data processing parameters : absorption/magnitude FT, apodization function, number of zerofills, full or reduced profile mass spectra, centroids, visualize transients
  • Use mass spectra : set ratios of intensities, visualize isotopic envelopes, plot multiple envelopes, extract high quality figures, extract data points for analysis
  • Results output : search experimental data, rank search results by the similarity score (m/z, intensity), save project for future use, create report as a PDF file

Imaging

Key features

  • Workflows based on transients acquired with FTMS Booster or provided by manufacturer
  • Data processing of large (e.g., 0.1-1.0 TB) imaging mass spectra datasets (RAW, d. folder)
  • Post-processing of large transient datasets increases FTMS imaging throughput
  • Efficient visualization and processing of practically any size imaging datasets
  • Imaging-grade and scale absorption mode FT (aFT) of phased transients
  • Data averaging over selected areas of images, including via transients, to up sensitivity
  • Recalibration of mass spectra to improve mass accuracy over entire images
  • Super-resolution signal processing for targeted applications: drug profiling
  • Advanced control of processing parameters, including noise analysis
  • Output file formats, imzML, enable further analysis with commercial and open source tools

Metabolomics

Key features

  • Workflows based on full profile mass spectra & transients acquired with FTMS Booster
  • Scan co-indexing between .RAW and transient datasets for every LC/GC-MS run
  • Visualization and processing of practically any size LC/GC-MS datasets (.RAW)
  • Absorption mode FT of phased transients matches the performance of eFT processing
  • Data summation across a number of LC/GC-MS runs, including chromatogram alignment
  • Capabilities of data (mass spectra and transients) averaging within a single and across a number of DDA and DIA proteomics experiments
  • Supporting quantitation workflows via selected ion chromatograms and area calculations
  • Recalibration of mass spectra to improve mass accuracy
  • Super-resolution signal processing for targeted quantitative proteomics applications
  • Advanced control of processing parameters, including noise analysis
  • Automated batch analysis of LC/GC-MS datasets
  • Output file formats enable further analysis with commercial and open source tools

Complex Mixture Analysis

Key features

  • Integration and processing of practically any size .RAW files, .d folders and .H5 files
  • Open file formats for transients & mass spectra : H5, MGF, mzXML, mzML, imzXML
  • Visualization of transients and mass spectra, visual comparison from separate data sets
  • Spectral and transient averaging for high sensitivity and dynamic range
  • Processing of LC-MS data for petroleomics/biofuels/lipidomics applications
  • Basic discrete FT with parallel, multi-CPU computing
  • Advanced FT with pre- and post-processing, including apodization, zero-filling, magnitude and absorption mode FT
  • Noise thresholding, reduced-profile mode mass spectra representation
  • Peak picking with N-points interpolation and efficient baseline correction
  • Mass scale calibration equations, including iterative re-calibration for complex mixtures

Top-Down Protein Analysis

Key features

  • Input of proteoform structural information: sequence and modifications
  • Averaging of LC-MS/MS and MS/MS data from multiple experiments
  • Recalibration of intact mass (MS data) and top-down (MS/MS data) mass spectra
  • Comparison of experimental and simulated isotopic envelopes and mass spectra
  • High-resolution and low-resolution deconvolution
  • Product ion assignment to the deconvolved data
  • Graphic interactive representation of sequence maps

Custom Workflows

Selected custom workflows

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