CPC G01N 33/6842 (2013.01) [C07K 1/22 (2013.01); C07K 1/36 (2013.01); C40B 30/04 (2013.01); G01N 33/56977 (2013.01); G01N 33/6818 (2013.01); G01N 33/6848 (2013.01); G01N 2333/70539 (2013.01)] | 20 Claims |
1. A mass spectrometry method, the method comprising:
obtaining a sample comprising unlabeled isolated peptides from an MHC-I or HLA-I complex or an MHC-II or HLA-II complex;
adding one or more labeled peptides to the sample to form a single mixed sample comprising the labeled peptides and the unlabeled isolated peptides;
processing the single mixed sample with an LC-MS/MS system, comprising:
i) processing the single mixed sample in discovery mode to detect and identify one or more of the unlabeled isolated peptides and the one or more labeled peptides in the single mixed sample;
ii) wherein, when the one or more labeled peptides are detected, processing the same mixed sample with the LC-MS/MS system in targeted mode, thereby detecting and identifying the one or more labeled peptides; and
iii) wherein the LC-MS/MS system toggles between processing the mixed sample in discovery mode and processing the mixed sample in targeted mode in the same LC-MS/MS run,
thereby detecting both labeled and unlabeled peptides in the single mixed sample.
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