AB QSTAR/QTRAP

How do I load data from my AB QSTAR/QTRAP instrument?

There are two choices for converting WIFF files from either the QSTAR or QTRAP instruments.

1. MSX

Once installed, wiff files will be converted and loaded into PEAKS automatically.

Installation
Contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it if you would like to use this tool. We can easily send you the download link for the installer.

Requirements

  • Installed on the same computer as PEAKS
  • Installed on the same computer as Analyst
  • Analyst QS for QSTAR (1.1 or later), Analyst 1.4.1 for QTRAP (or later)

    • **Extra Note About MSX Preferences**
    There are some options you can configure for MSX data loading. To do this, go to Preferences -> Instrument -> ABI (.wiff) AB files may contain several samples. By default, these samples are not merged into one data set.
  • Select “yes” if you would like PEAKS to merge all the samples into one data set.
  • Select “Survey Spectrum Centroiding” if centroiding has been performed before loading the data into PEAKS.
  • Select “Product Spectrum Centroiding” if centroiding has been performed on the product spectrum before loading into PEAKS.
    • This is important to insure PEAKS performs optimally.

    2. mzWIFF

    This is a command line tool. Some manual labour is required outside of PEAKS to convert the file. It creates a mzxml file that can then be loaded into PEAKS.

    Installation

  • The download information is provided here.

    Requirements

  • Installed on the same computer as PEAKS
  • Installed on the same computer as Analyst
  • Analyst QS for QSTAR (1.1 or later), Analyst 1.4.1 for QTRAP (or later)

    • command Line Usage Instructions

  • Start by opening a command line window
  • (Start Menu -> Programs -> Accessories -> Command Prompt)
  • Change the directory to the location of the mzwiff.exe file.
  • For example, type: cd Desktop
  • (If you installed it on your desktop)
  • Convert it to mzXML
  • For example type: mzwiff.exe -mzXML c:\data\filename.wiff c:\data\filename.mzxml
  • The mzXML file will appear at the location specified in: c:\data\filename.mzxml

    • After the data has been converted, load it up!

  • Once all of that is complete, start PEAKS and select 'New Project' from the 'File' menu.
  • Give the new project a name and select the "Add data files..." button.
  • Browse to the location of the desired file and select it.
  • Multiple files can be loaded in as one sample by using the SHIFT or CTRL keys as multiple files are selected.
  • Press Open.
  • Complete the fields marked Instrument Vendor and Instrument Type.
  • Select whole sample or whole project, as most likely all files were produced by the same instrument.
  • Press OK to have the file loaded into PEAKS.
  • In the top left panel, marked Project View, a number of icons will appear.
  • First the Project node, then the Sample node and lastly the file node.
  • As the project loads, the file node will appear as a green outlined icon .
  • Wait until this icon turns solid green , this represents the file is completely loaded into PEAKS and is ready for processing.
  • For small files, users may not even notice the outlined icon, but larger files may take a short period of time to load.

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