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2. mzStudio Basic Navigation

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sficarro edited this page Aug 13, 2017 · 1 revision

Note: Please see the tutorial document in the repository, this has additional screen captures that may be helpful.

Opening a file

mzStudio currently supports direct access to raw mass spectrometry data files from Thermo, AB-Sciex, and Agilent, as well as multiplierz generated .mgf files.

To open a Thermo raw file, an AB-Sciex wiff or t2d file, or an mgf file, select the “Open MS data file (New Tab)” menu item. This opens a file dialog. Browse to the desired file, and click the Open button.

To open an Agilent file, select the “Open D data file (New Tab)” menu item. This opens a directory dialog. Browse inside the data file folder – here you should see an “AcqData” folder (don’t open this though) - hit the “Select Folder” button.

After opening a file, a TIC is displayed, along with the first spectrum. This is the sourceforge tutorial file 2011-07-29-eno-100fmol-1.raw.

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Basic Navigation

Helpful tip: When typing key commands, make sure the spectrum window has focus. If focus is lost, just left click the mass spectrum – commands will now be sent to the spectrum window!

  • R selects XIC/Spectrum display mode (side-by-side).
  • S selects Spectrum display mode (no XICs).

Mass spectrum navigation

  • +/- go to next or previous scan.
  • < and > go to the next or previous MS1 scan for files with MS1 data.
  • Left click and drag in mass spectrum zooms in on mass range.
  • Right click in mass spectrum window zooms out.
  • Left click in XIC window displays the spectrum for the selected retention time.
  • Typing 1,2,3 displays the mass spectrum on the indicated number of x-axes.
  • L toggles locking the mass range. When locked, the displayed range stays the same moving from scan-to-scan.
  • W toggles the “filter lock”. This applies to targeted MS2 or MSn experiments. When the filter is locked, < and > move to the next scan or previous scan with the same filter.

XIC Navigation

  • Left click & drag in XIC panel zooms in the selected time range.
  • Right click in XIC panel zooms out to the entire time range.
  • Right click & drag in XIC will integrate the selected peak. There are two algorithms that are used: SUM and GUASSIAN. The algorithm is set in the settings page. SUM simply calculates the total of (time[n+1]-time[n]) * [(intensity[n+1]+ intensity[n])/2] across the entire selected peak. Guassian performs a Guassian fit to the selected peak and returns the area of the Guassian. Note, to perform the Guassian fit requires installation of Scipy and numpy+mkl (please see tutorial for installation).

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