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2.3. The Toolbar

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sficarro edited this page Aug 19, 2017 · 1 revision

mzStudio Toolbar items

mzStudio

In order, the toolbar icons are as follows:

(1) Open a data file (same as File Menu/Open MS Data File (New Tab))

(2) Search for MS2 spectra.

  • Enter mz and tolerance. Click locate. A grid appears:

  • Click on the row label to jump to the listed scan.

(3) Perform an XIC (same as menu item XIC/XIC)

  • See wiki section "Extracted ion chromatograms"

(4) Open mzPepCalc.

  • mzPepCalc is a very useful tool for calculating fragment ion masses.

  • See wiki section on mzPepCalc for more details.

(5) Jump to scan.

  • Enter scan number to navigate to this scan in the data file.

(6) SQLite Icon – “Make database”.

  • Allows for import and visualization of search result peptide-spectrum-matches with a powerful sqlite interface.
  • See wiki section "Importing Search Results" for more details.

(7) Set XIC time range

  • Opens dialog to set the displayed time range. Enter start time, stop time or start time – stop time.

(8) Set spectrum m/z display range

  • Opens dialog to set the displayed m/z range. Enter Start mz-stop mz to display the range, or Center, Width to center on an m/z with the selected width.

(9) Set Spectrum Intensity Scale

  • Opens dialog; allows spectrum to be re-scaled to the specified intensity.

(10) Toggle for XIC traces (new window vs. overlay)

  • This button toggles how new XIC traces are added to the main XIC window. By default, they are displayed in new windows; this button toggles to allow new traces to overlay the last window.

(11) View spectrum list

  • Displays the current spectrum in text format. Can be copied to clipboard with Ctrl-V.

(12) Perform Spectrum Search

  • Allows database search of currently displayed spectrum with Mascot, COMET, or X!Tandem.
  • See wiki section "Database Searching Spectra" for more details

(13) Set fragment ion label tolerance

  • This sets the tolerance for labeling fragment ions. Entering ‘0’ uses the instrument default (0.02 Da for FTMS instruments, 0.5 Da for all others).

(14) Copy current window to Clipboard

  • Copies the current mzStudio Spectrum/XIC window to the clipboard for pasting into other applications.

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