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MassLynx does not include peaks of interest from the DDA inclusion list - WKB54097

Article number: 54097
This article is a portion of a Troubleshooting Path.  To see links to other articles related to MassLynx data dependent acquisition (DDA) , please select the link below.
MassLynx data dependent acquisition (DDA) questions
Articles containing tips on setting up MassLynx DDA methods, solutions and known workarounds to problems with DDA in MassLynx, answers to DDA questions, and corrections to outdated DDA information in MassLynx Help files
Pages: 3

SYMPTOMS

  • FastDDA method does not acquire masses on the include list

ENVIRONMENT

  • Xevo G2-XS
  • Xevo G3
  • SYNAPT G2-Si
  • Synapt XS
  • MassLynx

CAUSE

There are several known issues with the use of include lists in DDA acquisitions that can prevent them from working as intended.

FIX or WORKAROUND

  1. Ensure that the "Preferentially select peaks on the include list" option is selected.
    • Using the "Only select..." option seems to lead to the noise peaks of the masses on the include list triggering MSMS. That results in bad MSMS data.
  2. Set the units for the "Include peaks within +/-" option to mDa. If you set it to parts per million (ppm), it won't work.
  3. Do not try to define retention times for the masses of interest. Only define a mass. If you also define a target retention time, the include list won't work.

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ADDITIONAL INFORMATION

The MassLynx Help file says that the maximum number of masses that can be defined in an include list is 100. This is not correct, and the Help files need updating.

On the Xevo G3 and Xevo G2-XS (from MassLynx 4.1 SCN 923 onwards), the limit on the number of entries on a DDA include list was removed.

On the Synapt XS and SYNAPT G2-Si (from MassLynx 4.1 SCN 941 onwards), the limit on the number of entries on a DDA include list was increased to 500.

 

id54097, MALDIG2SI, MLYNX, MLYNXV41, SCN923, SCN941, SUPMM, SYNG2SIHD, XEVOG2XSTF

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