Problem_Crosslinktransitioncalculator

Cross-link Transition Calculator
Problem_Crosslinktransitioncalculator Nour Alturihi  2018-02-28
 
Hi,

I installed your software and I wanted to try to test with your file "input_dss.txt" but it doesn't work.
I had this error message:
 J.A.Yergey, Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337-349






"C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\SkylineIntegration.exe" 30def13f-4991-4c31-a76b-9f09affb572a
 USAGE:
         C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\react2prm_web.exe [options] pepA pepB modA modB xlink-string shortArmMass longArmMass precursorCharge
     or C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\react2prm_web.exe -f /input/file.txt

   [options] specifies:
           -m report theoretical monoisotopic precursor m/z
                            default is to report theoretical most intense isotope m/z

 Input file format:
    short_arm_mass long_arm_mass
    pepA pepB modA modB precursorCharge
    pepA pepB modA modB precursorCharge
      : : : : :

 Download example file and see documentation at http://xlinkdb.gs.washington.edu/xlinkdb/prmTransitionForm.php

 Default is to report most intense isotope precursor m/z based on:
 J.A.Yergey, Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337-349






"C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\SkylineIntegration.exe" 30def13f-4991-4c31-a76b-9f09affb572a
 USAGE:
         C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\react2prm_web.exe [options] pepA pepB modA modB xlink-string shortArmMass longArmMass precursorCharge
     or C:\Users\noura\AppData\Local\Apps\2.0\7Y8H36B2.6W3\4W5974KX.5A0\skyl..tion_e4141a2a22107248_0004.0001_352b8c93f6ba0623\Tools\XLTCalc\react2prm_web.exe -f /input/file.txt

   [options] specifies:
           -m report theoretical monoisotopic precursor m/z
                            default is to report theoretical most intense isotope m/z

 Input file format:
    short_arm_mass long_arm_mass
    pepA pepB modA modB precursorCharge
    pepA pepB modA modB precursorCharge
      : : : : :

 Download example file and see documentation at http://xlinkdb.gs.washington.edu/xlinkdb/prmTransitionForm.php

 Default is to report most intense isotope precursor m/z based on:
 J.A.Yergey, Int. J. Mass Spectrom. Ion Phys. 1983, 52, 337-349




Could you help me?

Thank you so much,

Regards,

Nour AL TURIHI
PhD student
 
 
engj responded:  2018-05-02
Nour,

Sorry for the late reply. I just found out about your post today as I wasn't subscribed to this support board (which I am now). The error message you're seeing is the underlying program's command line help message, repeated a few times, which you should theoretically never get to. Obviously something is wrong but it's unclear to me how this Skyline plug-in would get to this state of returning the messages you see.

I tried reproducing the problem here with the file you uploaded and everything ran as expected. Can you try running this on another installation of Skyline, say on a different computer? I don't know what the problem might be but it would be helpful to know if this is a consistent problem for you across multiple machines. This will help determine whether it's a general tool issue or an issue specific to your current installation. For what it's worth, I just asked another user here to install the cross-link transition calculator plug-in and run it with the input_dss.txt file that you attached and it ran fine in that installation also.

Jimmy