4000 qtrap hybrid triple quadrupole linear ion trap mass spectrometer

Fifty-four glycoproteins with a high confidence of identity were selected for protein profiling by targeted LC-MS/MS. One signature peptide per protein was used in the assay with 1, 2 or 3 SRM transition(s) per peptide being monitored.
Two separate LC-MS/MS runs of trypsin digested peptides were made for each sample representing proteins monitored in fractions A and B., using a 4000 QTRAP hybrid triple quadrupole/linear ion trap mass spectrometer (Applied Biosystems, CA, USA) operating in positive ion mode. Peptides were first separated by a Shimadzu series 10AD VP LC system (Shimadzu, Columbia, MD) using C18 3 µm 300 Å, 100x1mm column (ACE, Reading, UK) and a mobile phase gradient of 10 to 45% acetonitrile in water both with 0.1% formic acid over 15 min at 100 µL/min flow rate. Multiple reaction monitoring (MRM) transitions were monitored and acquired at unit resolution in both Q1 and Q3 and were used to trigger enhanced product ion (EPI) scan in the linear ion trap of the QTRAP in the mass range m/z 100-1500 to confirm the surrogate peptide sequence. The optimised values for curtain gas, collision gas, GS1 and GS2 were 10, 9, 30 and 45 arbitrary units respectively. The heated capillary temperature was maintained at 450°C and the ESI voltage was kept at 4200 V.
All MRM and EPI data were processed with Analyst software 1.4.2.