8. Spectrum Search
Selecting the spectrum search button in the toolbar is used to perform a database search of the currently displayed spectrum. A window will open and display the relevant search parameters for the search engine selected in the settings page (the default search engine is Mascot). Currently, users may select Mascot, Comet, or X!Tandem. Note, each engine must be properly installed and configured before use (see sections below “Installing COMET, X!Tandem” and “Configuring Comet, X!Tandem and Mascot for use with mzStudio“).
For a Mascot search, login with your credentials:
Enter your search parameters:
And hit submit.
If there is a significant hit, y and b ions will be annotated in the specturm, and a single ID frame will pop up in the mzStudio GUI.
Go to sourceforge, and download comet_2016013.zip. Extract files to an appropriate directory. https://sourceforge.net/projects/comet-ms/files/
comet_2016013.zip
Go to the X!Tandem ftp site and download tandem-win-17-02-01-4.zip. Extract files to an appropriate directory. ftp://ftp.thegpm.org/projects/tandem/source/
tandem-win-17-02-01-4.zip
To configure search engines with mzStudio, navigate to the settings file in your multiplierz directory, which will be found at
C:\Users<your username>.multiplierz\settings.txt
To enable Comet and X!Tandem, indicate the path of the respective executable(s) in the ‘comet directory’ or ‘xtandem directory’ fields. To enable Mascot, set the ‘mascot server’ field to the URL of your Mascot server (e.g., http://my_server.com/mascot), set the ‘mascot version’ field to the appropriate version number (e.g., 2.5) and, if you have Mascot security enabled, the ‘mascot security’ field to 1.
As mentioned above, to set up mzStudio to perform Mascot searches, go to your “.multiplierz” folder in your User directory and open Settings.txt with notepad or another text editor:
C:\Users\sbf.DRAGON.multiplierz
(Note, the directory will be specific to your user account).
Open Settings.txt
Enter your Mascot Server IP address, version, and other settings (see Mascot user’s guide for further information about each setting):
#Mascot mascot server=http://cys.dfci.harvard.edu/mascot mascot version=2.4 mascot ms2=1 mascot security=1 mascot var_mods=1 mascot max hits=100000 mascot ion cutoff=5 mascot bold red=False mascot show input query=True mascot rank one only=True mascot pep quant=False mascot retain DAT=False mascot genbank=False mascot sub-set hits=True mascot protein summary=False mascot p2g=False mascot mzid=False mascot same-set hits=True
Open the settings.txt file as described above, and set the path to your COMET executable: #Comet comet directory=C:\Users\sbf.DRAGON\Downloads\comet_2016013\comet.2016013.win64.exe
Open the settings.txt file as described above, and set the path to your X!Tandem executable: #XTandem xtandem directory=C:\Users\sbf.DRAGON\Downloads\tandem-win64-17-02-01-4\tandem.exe