A typical sequence to acquire the data for PQA characterization is as follows:

  1. A blank injection of the Matrix type.
  2. An injection or several injections of the Unknown type with your peptide.
  3. An injection or several injections of the Unknown type with your peptide after thermal stress.
  4. An injection or several injections of the Unknown type with your peptide spiked with the Pierce Peptide Retention Time Calibration (PRTC) mixture.
  5. TIP

    For more information about the Thermo Scientific Pierce PRTC mixture, refer to the product website.

  6. A blank injection of the Matrix type.
  7. A shutdown injection of the Blank type.
  8. This injection is the only injection that uses the shutdown instrument method (all other injections use the instrument method that collects full-MS data with ddMS2 scans).

TIP

While you are just designing the sequence, injections do not need to have any processing method assigned, but you must specify the injection volumes and rack positions of the samples in the autosampler. For details on how to create a sequence in Chromeleon CDS software and how to specify its parameters, refer to Chromeleon CDS Software User Help.