AutoVectis Tools Suite

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The AutoVectis suite contains many useful tools designed to work with mass spectrometry data.  These tools are designed to provide new or improved capability over normal data processing applications.  In many cases, these tools were initially written to solve specific problems encountered by various collaborating labs and organizations.  However they have all been developed so that they can be used together.

We can build special workflows in order to automate specific tasks for your projects.  Some workflows and capabilities are designed into the standard versions of the software.  For example, assigning peaks in top-down fragmentation of proteins using FT-ICR MS combines power and benefits of the Autophaser, Autopiquer, Autoseequer and SeqMap tools to perform a single task in an automated workflow.


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SeqMap – allows users to easily generate protein sequence coverage maps like this.

Current Toolset:

  • Autophaser – absorption mode spectral processing for FT-MS instruments – including for mass spectrometry imaging
    • Includes baseline deviation free absorption mode spectrs
    • Mass recalibration function
    • Simple charge state estimation
    • Designed to make extraction of spectra simple, to ease the production of publication or report figures
  • Peak detection – various options available
    • Basic moving window peak detection
    • Wavelet transform peak detection – works well for MALDI data and for small molecule spectra
    • Autopiquer – proprietary algorithm for high confidence peak detection in large molecule (protein, peptide digest etc.) spectra
  • Top down assignmentAutoseequer matches isotope clusters detected in spectra against in-silico fragmented peak libraries generated by Autofraggeur
  • SeqMap – a tool to make it easy to make and compare sequence coverage maps for proteins
  • Little Imager – a simple tool for the processing of absorption mode mass spectrometry imaging.  Includes the ability to mass calibrate across complete images and to rapidly and easily extract images from specific spectral features
  • Big Picture – Little Imager’s big brother – in development.  Ask for details
  • Isotope labeling deconvolution – NEMESIS was developed to help deconvolve overlapping isotopic distributions resulting from differential heavy and light NEM isotopic labeling of cysteine residues
  • nD KMD – a tool for automatic peak assignment of complex small molecule spectra (such as dissolved organic matter or the products of pyrolysis production of biofuels) or for the sequencing of peptides by MS/MS

We will create video summaries of these tools and their features as soon as we can.  In the mean time, if you would like more information, please get in touch.

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Example output from Little Imager.


The Autophaser suite is written in National Instruments LabVIEW.  LabVIEW is a great tool for writing mass spectrometry software – indeed some companies already write their entire instrument control software in LabVIEW.  Additionally, most universities have LabVIEW licenses – so we’d be happy to work with you to let your own tools work with Autophaser components, or even in place of them.

Although the components of Autophaser have been developed with a view to their use with FT-MS type instruments (FT-ICRs and Orbitraps) we also use them with data from other types of instrument – in particular MALDI-TOF, Q-TOF and IMS-TOF classes.  We are happy to discuss adapting any of the tools to suit a particular problem.