Parallel Accumulation–Serial
Fragmentation
(PASEF): Multiplying Sequencing Speed and Sensitivity by Synchronized
Scans in a Trapped Ion Mobility Device
In
liquid chromatography-mass spectrometry (LC-MS)-based proteomics,
many precursors elute from the column simultaneously. In data-dependent
analyses, these precursors are fragmented one at a time, whereas the
others are discarded entirely. Here we employ trapped ion mobility
spectrometry (TIMS) on an orthogonal quadrupole time-of-flight (QTOF)
mass spectrometer to remove this limitation. In TIMS, all precursor
ions are accumulated in parallel and released sequentially as a function
of their ion mobility. Instead of selecting a single precursor mass
with the quadrupole mass filter, we here implement synchronized scans
in which the quadrupole is mass positioned with sub-millisecond switching
times at the <i>m</i>/<i>z</i> values of appropriate
precursors, such as those derived from a topN precursor list. We demonstrate
serial selection and fragmentation of multiple precursors in single
50 ms TIMS scans. Parallel accumulation–serial fragmentation
(PASEF) enables hundreds of MS/MS events per second at full sensitivity.
Modeling the effect of such synchronized scans for shotgun proteomics,
we estimate that about a 10-fold gain in sequencing speed should be
achievable by PASEF without a decrease in sensitivity