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Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large‐scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to...
Isobaric tagging, via TMT or iTRAQ, is widely used in quantitative proteomics. To date, tandem mass spectrometric analysis of isobarically-labeled peptides with hybrid ion trap–orbitrap (LTQ-OT) instruments has been mainly carried out with higher-energy C-trap dissociation (HCD) or pulsed q dissociation (PQD). HCD provides good fragmentation of the reporter-ions, but peptide sequence-ion recovery...
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