An Automated Matrix-Assisted Laser Desorption/Ionization Quadrupole Fourier Transform Ion
Cyclotron Resonance Mass Spectrometer for
“Bottom-Up” Proteomics
posted on 2003-06-03, 00:00authored byAnsgar Brock, David M. Horn, Eric C. Peters, Christopher M. Shaw, Christer Ericson, Qui T. Phung, Arthur R. Salomon
Here we describe a new quadrupole Fourier transform ion
cyclotron resonance hybrid mass spectrometer equipped
with an intermediate-pressure MALDI ion source and
demonstrate its suitability for “bottom-up” proteomics.
The integration of a high-speed MALDI sample stage, a
quadrupole analyzer, and a FT-ICR mass spectrometer
together with a novel software user interface allows this
instrument to perform high-throughput proteomics experiments. A set of linearly encoded stages allows subsecond positioning of any location on a mircotiter-sized
target with up to 1536 samples with micrometer precision
in the source focus of the ion optics. Such precise control
enables internal calibration for high mass accuracy MS
and MS/MS spectra using separate calibrant and analyte
regions on the target plate, avoiding ion suppression
effects that would result from the spiking of calibrants into
the sample. An elongated open cylindrical analyzer cell
with trap plates allows trapping of ions from 1000 to 5000
m/z without notable mass discrimination. The instrument
is highly sensitive, detecting less than 50 amol of angiotensin II and neurotensin in a μLC MALDI MS run under
standard experimental conditions. The automated tandem
MS of a reversed-phase separated bovine serum albumin
digest demonstrated a successful identification for 27
peptides covering 45% of the sequence. An automated
tandem MS experiment of a reversed-phase separated
yeast cytosolic protein digest resulted in 226 identified
peptides corresponding to 111 different proteins from
799 MS/MS attempts. The benefits of accurate mass
measurements for data validation for such experiments
are discussed.