Can skyline be used to quantify TMT-labeled glycans? The concept would be similar to quantification of TMT-peptdies, using the reporter ions to produce abundances for multiplexed samples. Thanks. Joe
Mike MacCoss responded:
Hi Joe, Skyline is designed to integrate chromatographic data. So while it is possible to generate XICs from the reporter ions of TMT labeled molecules it wouldn't provide much specificity and you would need to acquire the MS/MS data systematically like with PRM or DIA. So if you were collecting your TMT data by PRM it is technically possible but this is not the normal strategy used for TMT.