a TSQ Vantage triple quadrupole (QQQ) mass spectrometer (Thermo Scientific)
at the University of Washington Proteomics Resource. The mass spectrometer
was coupled to a nanoelectrospray ionization source and a Waters nanoACQUITY
UPLC system. Glycopeptides from 1 μL of original plasma (∼1
μg peptides) were loaded onto a C18 trap column (20 mm long,
75 μm ID) and separated by a 150 mm C18 column (75 μm
ID) over a 60 min 2–35% linear acetonitrile gradient. Spray
voltage was set at 1700 V. Scheduled SRM was performed with 5 min
retention time windows for most of the peptides and an instrument
cycle time of 2000 ± 500 ms. Dwell times were varied depending
on the number of concurrent transitions; in all cases they were at
least 10 ms.