Applied Biosystems 5500 QTRAP - nanoLC and CapLC ESI MS/MS System
Phosphopeptide analysis by nano-LC/MS/MS:
The analysis of phosphopeptides from complex protein mixtures remains a challenging procedure. APAF uses an Applied Biosystems 4000 Q-Trap hybrid quadrupole linear ion-trap instrument. This instrument is well suited to the analysis of post-translational modifications as diagnostic fragment ions can be detected by precursor ion scanning. In this scan type, Q1 is scanned across a mass range and ions are fragmented in Q2. Q3 is set to transmit only the mass of the diagnostic fragment, (-79 m/z in the case of a phosphopeptide). In a follow-up experiment, precursor ions are selected from fragmentation and product ions scanned out of the ion-trap to provide MS/MS sequence information. Often the site of phosphorylation can be determined from this spectra.