Biology Reference
In-Depth Information
Table 1
Conservative figures of merit of mass analyzers typically used in proteomics
QQQ
3D-IT
QQ-qLIT
TOF-TOF
FT-ICR
LTQ-Orbitrap
Mass range
4,000
4,000
4,000
Unlimited
4,000
6,000
4,500 (R)
Mass accuracy
100 ppm
100 pm
100 ppm
5-10 ppm
<1 ppm
2-5 ppm
Resolution (FWHM)
≥4,000
≥4,000
≥4,000
~25,000 (R)
≥1 × 10
6
≥150,000
Dynamic range
1 × 10
7
1 × 10
3
1 × 10
4
1 × 10
6
1 × 10
3
1 × 10
4
(MS)
n
(MS)
2
(MS)
n
(MS)
3
(MS)
2
(MS)
n
(MS)
n
Sensitivity
Atto-fmol
Picomol
Femtomol
Femtomol
1 × 10
4
1 × 10
4
Scan speed
~1 s
~1 s
4/s
200/s
~1 s
~1 s
T
These values may vary with hybrid configurations from different instrument manufacturers; please check the
manufacturer's technical specifications
R
reflectron,
FWHM
full width at half maximum
Another common application of triple quadrupoles is the quantita-
tive analysis of metabolites or candidate biomarkers by selected or
multiple reaction monitoring. SRM and MRM are particularly use-
ful for targeted quantitative proteomics [
92
,
93
].
FT-ICR mass spectrometers provide the highest recorded mass
resolution (Table
1
). However, stable mass calibration requires
superconducting magnets, which are costly to maintain. Orbitrap
configurations are characterized by high mass resolution (up to
150,000), large space charge capacity, high mass accuracy
(2-5 ppm), a mass/charge range of at least 6,000, and dynamic
range greater than 10
3
[
66
]. The high resolving power of the
Orbitrap is possible because the ions'
m
/
z
value is a function of
frequency, and frequency is a parameter that can be very accurately
measured by existing technology. The ability to obtain accurate
mass measurements on precursor and MS/MS fragment ions in
proteomic experiments is critical to identify and characterize pro-
tein with increased confidence in protein database searches.
Linear ion traps can be used either as ion accumulation devices
or as stand-alone mass spectrometers. They have become very pop-
ular, particularly as front-end stages prior to trapping instruments,
3D ion trap, FT-ICR, and Orbitrap, or as Q3 in a triple-quadrupole
configuration (Fig.
3
). In addition to classical triple quadrupole
scan functions, such as enhanced product ion scan, time-delayed
fragmentation, and enhanced multiply charged scans, the QqLIT
design allows an additional stage of MS/MS after the regular
triple-quadrupole CID [
58
,
59
].
Unlike the quadrupole, the TOF mass analyzer is not a scanning
instrument. The TOF mass analyzer characterizes ions as batches
