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Cross-link Transition Calculator

Cross-link Transition Calculator Support

Welcome to the Cross-link Transition Calculator support board. If you have a question about using Cross-link Transition Calculator, or if you encounter a problem, you can post your questions here.

Support is provided by the creators of the software, as time allows, though we hope others will share their experience as the user community grows.

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Requests

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Inter-Peptide Disulfide Bridge Settings

(1 response)

david schmidt

2023-03-29 06:38

Hi,

I wanted to analyze inter-peptide disulfide bond formation, which could be treated as a CID cleavable cross-link. Could you please tell me the settings for long- and short-arm mass as well as modification A and -B for the disulfide-linked form?

Thank you and best wishes,
David

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Problem_Crosslinktransitioncalculator

(1 response)

Nour Alturihi

2018-02-28 05:19

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