A new tandem mass spectrometer for photofragment spectroscopy of cold, gas-phase molecular ions.
ABSTRACT We present here the design of a new tandem mass spectrometer that combines an electrospray ion source with a cryogenically cooled ion trap for spectroscopic studies of cold, gas-phase ions. The ability to generate large ions in the gas phase without fragmentation, cool them to approximately 10 K in an ion trap, and perform photofragment spectroscopy opens up new possibilities for spectroscopic characterization of large biomolecular ions. The incorporation of an ion funnel, together with a number of small enhancements, significantly improves the sensitivity, signal stability, and ease of use compared with the previous instrument built in our laboratory.
A new tandem mass spectrometer for photofragment spectroscopy of cold,
gas-phase molecular ions
Annette Svendsen, Ulrich J. Lorenz, Oleg V. Boyarkin, and Thomas R. Rizzo
Laboratoire de Chimie Physique Moléculaire, Ecole Polytechnique Fédérale de Lausanne,
EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
?Received 1 May 2010; accepted 8 June 2010; published online 20 July 2010?
We present here the design of a new tandem mass spectrometer that combines an electrospray ion
source with a cryogenically cooled ion trap for spectroscopic studies of cold, gas-phase ions. The
ability to generate large ions in the gas phase without fragmentation, cool them to ?10 K in an ion
trap, and perform photofragment spectroscopy opens up new possibilities for spectroscopic
characterization of large biomolecular ions. The incorporation of an ion funnel, together with a
number of small enhancements, significantly improves the sensitivity, signal stability, and ease of
use compared with the previous instrument built in our laboratory. © 2010 American Institute of
Since the mid-1980s, considerable interest has been fo-
cused on spectroscopic investigations of isolated biological
molecules in the gas phase.1–13The motivation for many of
these studies has been to understand the intrinsic spectro-
scopic and conformational properties of biologically related
molecules and to test the ability of theory to predict these
properties accurately. While amino acids and small peptides
can be volatilized thermally and studied in the cold environ-
ment of a supersonic expansion, the extension of this ap-
proach to larger molecules is made difficult by their thermal
During this same period, the extension of mass spectro-
metric techniques to biological molecules has literally ex-
ploded with the advent of ionization techniques such as
ionization,15which can put molecules of virtually any mass
into the gas phase with little or no fragmentation. Many
groups have recently begun to capitalize on these develop-
ments by performing spectroscopic studies of electrosprayed
The major advantage of supersonic molecular beam
techniques for spectroscopic studies is the low internal tem-
peratures that can be achieved, which greatly simplifies the
spectra of large molecules and reveals sharp spectral features
related to their structure. The challenge for spectroscopic
studies of larger biological molecules is thus to find ways to
cool the ions produced by electrospray to similar internal
temperatures. Gerlich25,26has pioneered the use of high-
order multipole rf ion traps for cooling molecules of astro-
physical interest, and we have recently shown that these
techniques can be coupled with electrospray ionization and
molecules.13,22–24,27Building on this initial work, we report
here a second-generation apparatus for spectroscopic studies
of electrospray-generated ions, which greatly improves on
the performance of the original machine. While our focus is
on applications to biological molecules, this apparatus may
also be well suited for studies of synthetic polymers,
transition-metal complexes, or nanoparticles.
Figure 1 shows an overview of the tandem mass spec-
trometer designed for photofragment spectroscopy of cold,
biomolecular ions. The major components of this apparatus
are a nanospray-based mass-selective ion source, a cryogenic
multipole rf ion trap, and a mass-selective ion detection sys-
tem. The ion optical elements are housed in a vacuum cham-
ber divided into seven differentially pumped stages. The fol-
lowing sections describe this apparatus in detail.
A. Nanospray source
Figure 2 shows the details of the front end of the appa-
ratus comprising a nanospray source, an ion funnel, and a
hexapole ion guide. The nanospray source ?Proxeon, ES070,
Odense, Denmark? consists of a metalized borosilicate
needle ?1 ?m inner diameter ?ID? tip?, which serves as the
ion emitter ?not shown in Fig. 2?. The needle is connected to
a sample reservoir ?a microcentrifuge tube? through a metal
holder such that the liquid is contained in a closed volume.
In order to facilitate flow through the needle, this volume can
be pressurized. The sample holder is mounted on a xyz trans-
lational stage but electrically insulated such that the needle
tip can be biased at 500–1000 V with respect to ground.
Ions produced by nanospray are transferred into vacuum
through a capillary made from an 11.5 cm long stainless steel
tube ?0.5 mm ID, 2 mm outer diameter ?OD?? inserted into a
copper block, which can be heated to 250 °C by two 100 W
cartridge heaters ?Prang?Partner AG, Pfungen, Switzer-
land?. The copper block is surrounded by a polyether ether
ketone jacket that isolates it thermally and electrically from
the source flange into which the parts are mounted. The cap-
illary is typically biased at 100–200 V.
REVIEW OF SCIENTIFIC INSTRUMENTS 81, 073107 ?2010?
0034-6748/2010/81?7?/073107/7/$30.00 © 2010 American Institute of Physics
B. Ion funnel
The capillary is followed by an ion funnel, which is a rf
ion guide that effectively collects and focuses the divergent
stream of ions exiting the capillary. The design of the funnel
is based on those of Smith and co-workers.28,29It consists of
100 stainless steel plates, 0.5 mm thick, separated by 0.5 mm
thick Teflon spacers. The first section of the funnel has 57
plates, all having a central aperture of 25.4 mm diameter.
The 20th plate of this section ?located ?2 cm from the fun-
nel entrance? has been modified slightly to disperse the jet of
neutrals exiting the capillary. This jet-disrupter plate has
been cut such that it has a disk of diameter 6.5 mm located in
the center of the 25.4 mm aperture and connected to the
remainder of the plate by four 0.5 mm wide stripes forming
a cross. The second section consists of 42 plates with an
aperture diameter that decreases uniformly from 25.4 to
2.5 mm. The last plate has a 1.5 mm hole that serves as the
conductance limit between two consecutive differential
The electrical connections to the funnel are made by way
of a custom-made zero-insertion-force ?ZIF? socket ?Tactic
Electronics, Plano, TX?, into which a small tab on each plate
inserts. Onto the opposite side of the ZIF socket is soldered a
circuit board containing two networks of capacitors and re-
sistors, shown schematically in Fig. 3. One network connects
all odd-numbered plates to one phase of a rf potential with a
dc potential gradient superimposed, while the second net-
work connects all even-numbered plates to the other phase of
the rf potential combined with the dc potential gradient. The
peak-to-peak rf potential is typically 35 V. The dc potential
for the first electrode is 190 V and that for the last electrode
in the series is 10 V, resulting in a dc gradient of 18 V/cm.
The jet disrupter and the conductance limit plate ?i.e., the last
plate of the funnel? are connected separately and carry only a
dc potential. The jet disrupter is normally held at 150 V
while the conductance limit plate is biased at 14 V. The pres-
sure in the ion funnel region is 1.5 mbar and is maintained by
a rotary vane pump ?Alcatel, Annecy, France? with a pump-
ing speed of 60 m3/h.
C. Hexapole ion guide or trap
Ions leaving the funnel enter a 17 cm long hexapole ion
guide ?Analytica of Branford, Branford, CT? made of six
gold-coated ceramic rods of 2 mm diameter positioned on an
inscribed diameter of 4 mm. Two 4 MHz rf signals of oppo-
site phase are used to drive the device; typical values for the
amplitude and the dc offset are 100–200 V and 10 V, respec-
A dc lens placed at the exit of the hexapole guide allows
the guide to also be used as a trap, depending on how the
lens is biased. By applying a sufficiently high voltage to this
lens, ions are reflected at the exit and lose enough kinetic
energy through collisions with the background gas that they
cannot escape over the potential barrier at the hexapole en-
trance. To trap ions, the exit electrode is biased at 10 V above
the dc offset of the ion guide whereas the applied voltage to
transmit ions is 5 V below the dc offset.
22pole ion trap
FIG. 1. Overview of the tandem photofragment mass spectrometer.
FIG. 2. Detailed view of the ion source region. For clarity, only every fourth
plate of the ion funnel is shown.
10 nF10 nF10 nF
10 nF10 nF10 nF
FIG. 3. Schematic drawing of the electrical circuits for connecting the ion
073107-2Svendsen et al.Rev. Sci. Instrum. 81, 073107 ?2010?
The hexapole guide spans two differential pumping sec-
tions and has a 3.5 cm long closed section in the middle
pumped only from the ends. This construction is made in
order to limit the conductance between the two pumping
stages. A 60 l/s turbomolecular pump ?Pfeiffer, TMU 071 P,
Nashua, NH? backed by a 5 m3/h rotary vane pump
?Pfeiffer, DUO 5? maintains a pressure of 7?10−3mbar at
the entrance side of the ion guide. The terminal end of the
hexapole is evacuated by a 500 l/s turbomolecular pump
?Pfeiffer TMU 521 P? backed by a 0.9 m3/h membrane
pump ?Pfeiffer, MVP 015–4?, maintaining a pressure of 1
The capillary, ion funnel, and hexapole guide are all
mounted on a homemade flange that is bolted to a conflat
flange on the ion source vacuum chamber. All electrical con-
nections from the source elements are made to gold-coated
pins mounted on this assembly, and inside the vacuum cham-
ber the pins contact homemade spring-loaded connectors,
which in turn are connected to electrical feedthroughs on the
chamber flanges. With this design, the source components
can easily be removed from the chamber as a single unit
without disengaging electrical connections, thereby greatly
facilitating the cleaning of the source.
D. Gate valve
A homebuilt gate valve separates the source chamber
from the rest of the machine. This valve, which is modeled
after the design of Pittman and O’Connor,30allows venting
the source region to atmospheric pressure while maintaining
the rest of the mass spectrometer under high vacuum condi-
tions. Consequently, the gate valve speeds up the source
cleaning procedure, as only the high-pressure regions of the
apparatus need to be vented.An advantage of this valve com-
pared to those commercially available is that its blade is
electrically isolated and hence can be used as an electrostatic
ion lens. Moreover, the assembly is made such that the sepa-
ration of ion optical elements is kept at a minimum ?2 mm?.
The combination of these two features leads to a high ion
transmission through the valve.30
E. Mass selection and octupole ion guide
The next element along the ion path is a quadrupole
mass filter with a m/z range of 2–2000 amu ?Extrel, Pitts-
burgh, PA?. After mass selection, the ions enter an electro-
static quadrupole ion deflector ?Extrel?, which deflects the
ions 90° in one of two opposite directions, depending on how
it is biased. When traveling in one direction, ions are de-
tected by a channel electron multiplier combined with a con-
version dynode ?DeTech, 402-A-H, Palmer, MA?. This de-
tector is mainly used for diagnostic purposes and to obtain a
mass spectrum of the sprayed solution. When deflected in the
opposite direction, ions enter a 40 cm long octupole ion
guide ?Extrel?, which directs them further downstream.
The quadrupole mass filter, quadrupole deflector, and
channeltron detector are all housed in the same differential
pumping stage. The region is pumped by a 500 l/s turbomo-
lecular pump ?Pfeiffer, TMU 521 P? backed by a 0.9 m3/h
membrane pump ?Pfeiffer, MVP 015–4?, resulting in a pres-
sure of 2?10−7mbar.
The octupole guide is installed in a pumping stage of its
own evacuated by a 500 l/s turbomolecular pump backed by
a 0.9 m3/h membrane pump. The octupole device can be
operated either as a guide or an ion trap. In trapping mode,
the octupole entrance and exit lenses are held at potentials
somewhat higher than the potential on the octupole axis. To
trap the continuous stream of incoming ions, the ion kinetic
energy must be dissipated, and this is achieved through col-
lisions with a He buffer gas introduced into the chamber
through a leak valve mounted externally on a flange. Under
trapping conditions, the pressure is raised to 2?10−4mbar,
which requires lowering the rotation speed of the turbo pump
in order to maintain an acceptable backing pressure. If the rf
device serves as a guide only, no buffer gas is present, and
the pressure is 10−8mbar.
F. Cryogenic 22-pole ion trap
A second quadrupole deflector placed after the octupole
guide diverts the ions 90° in one of two opposite directions.
Along one direction, the deflector is followed by an off-axis
channel electron multiplier equipped with a conversion dyn-
ode ?DeTech, 402-A-H? for ion detection. In the opposite
direction, a stack of five tube lenses, mounted on the quad-
rupole bender, serve to focus and decelerate the ions before
they enter a linear, 22-pole ion trap.
The design of the 22-pole rf ion trap is based on those of
Gerlich.26,31It consists of 22 calibrated stainless steel rods of
1?0.001 mm diameter and 41 mm long positioned on a
circle with an inscribed diameter of 11 mm. One end of each
rod is pressed into a hole in a supporting copper wall, and the
other end ?reduced to 0.5 mm? is loosely supported by a
ceramic sleeve ?OD=1 mm, ID=0.5 mm?, inserted to a
similar hole in the opposite supporting wall. This is done in
an alternating fashion such that each wall electrically con-
tacts one set of 11 rods. These walls each have an 8 mm hole
centered on the trap axis for injection and extraction of ions.
Ion trapping in the radial direction is then achieved by ap-
plying rf potentials of opposite phase to the two end walls.
The trap is equipped with two tube electrodes at each end,
and by applying appropriate potentials to the four electrodes
the ions are confined along the trap axis. To extract ions from
the trap, the potentials on the two electrodes at the exit side
are transiently lowered. Five 0.15 mm thick ring electrodes
of 13 mm ID spaced 6 mm apart, surround the cylindrical
cage of rf electrodes and allow shaping the potential along
the trap axis for manipulation of the ion cloud.
The 22-pole trap is housed in a copper box, two oppos-
ing walls of which support the 22 rods. As these walls con-
duct the rf potential applied to the rods, they are electrically
isolated from the remainder of the box by 1 mm thick sap-
phire plates. To ensure good thermal contact, two 0.1 mm
thick indium foil gaskets are put on each surface of the sap-
phire plates, which are inserted between the supporting walls
and the base plate. The trap assembly is bolted onto a closed-
cycle helium cryostat ?Sumitomo, SRDK-408D-W71D, To-
kyo?, which enables cooling the trap to 4 K, as measured by
073107-3Svendsen et al.Rev. Sci. Instrum. 81, 073107 ?2010?
a silicon diode ?Lakeshore, DT-670B-CU, Westerville, OH?.
An indium gasket is used to make good thermal contact be-
tween the trap and the cryostat. Moreover, the low-
temperature parts of the assembly are shielded against room-
temperature blackbody radiation by an aluminum housing
connected to the first stage of the cryostat, which is at 70 K.
All electrical connections to the trap are precooled to this
temperature. To provide continuous control of the trap tem-
perature in the range from 4 to 320 K, a 50 W cartridge
heater ?Lakeshore, HTR-50? is installed on the top of the
Ions in the trap are cooled both internally and transla-
tionally to low temperature through collisions with cold He
buffer gas. The He gas is injected into the trap volume using
a pulsed valve ?Parker Hannifin, Series 9, Cleveland, OH?
connected to the trap via a 25 mm long Teflon tube. The
buffer gas is thermalized to the temperature of the trap as the
He atoms undergo many collisions with the trap walls and
rods before escaping the trap volume through the entrance or
After ejection from the trap, the ions are focused by a
lens stack consisting of three tube electrodes. These lenses
are mounted on a third quadrupole bender ?Extrel? that de-
flects the ion beam 90° into the last section of the apparatus:
the detection chamber.
The two quadrupole benders, lens stacks, and the 22-
pole trap are located in the same differential pumping stage,
which is evacuated by a 500 l/s turbomolecular pump
?Pfeiffer TMU 521 P? backed by a 5 m3/h scroll pump ?Ed-
wards, XDS5, Crawley, England?. The pumps maintain a
background pressure below 2?10−9mbar while the average
pressure is ?5?10−6mbar when He buffer gas is pulsed
into the trapping volume.
G. Mass-selected ion detection
The last differentially pumped vacuum stage houses a
quadrupole mass filter ?Extrel? and channel electron multi-
plier combined with a conversion dynode ?DeTech, 402-
A-H? for mass-selective ion detection. The section is pumped
by a 260 l/s turbomolecular pump ?Pfeiffer TMU 261 P?
backed by the same 5 m3/h scroll pump used for the
previous stage. The background pressure is below 2
?10−9mbar but rises to ?10−8mbar when helium is pulsed
into the 22-pole trap in the neighboring vacuum stage.
Most of the dc and rf power supplies used for this appa-
ratus are commercially available. Three 20-channel bipolar
??400 VDC? power supplies ?Spectrum Solutions, TD 1400,
Russellton, PA? provide the voltages for all electrostatic ion
optical elements such as lenses, quadrupole benders, the ion
funnel dc gradient, and the capillary. To eject ions from the
traps, the exit lenses of the hexapole, octupole, and the 22-
pole ion traps are switched between two static outputs from
the bipolar supplies. The switching is done in 100 ns with a
home-built metal-oxide-semiconductor field-effect transistor
switch in push-pull configuration.
The rf signals for the ion funnel are generated by a
0.5 MHz generator ?CGC Instruments, RFG50–10, Chem-
nitz, Germany? and has a variable rf amplitude determined
by the magnitude of the voltage delivered to the generator by
an external dc power supply ?FuG Elektronik GmbH, NTN
35–35, Rosenheim, Germany?. The rf signal supplied to the
hexapole ion guide is generated in a similar way but at a
frequency of 4 MHz. In the case of the hexapole guide, a
second external dc voltage, supplied by one of the Spectrum
Solutions power supplies, is fed to the rf generator to control
the dc offset of the rf signal. The rf power supplies driving
the quadrupole mass filters and the octupole guide/trap were
purchased from Extrel and have frequencies of 1.2 and
2.1 MHz, respectively. The rf signals for the 22-pole trap are
generated by a homemade 4 MHz rf generator,32,33and the rf
amplitude is controlled by an external dc power supply ?FuG
Elektronik GmbH, NLN 140M-500?.
The voltages for the conversion dynode and the channel
electron multiplier are delivered by three high voltage power
supplies ?Schulz-Electronic GmbH, AK0072 and AK0002,
Baden-Baden, Germany?, while the high voltage for the
spray needle is supplied by a fourth high voltage supply
?EMCO High Voltage Corporation, Sutter Creek, CA?.
LABVIEW programs were written to control all the elec-
tronics. The computer interface uses a National Instruments
PXI-chassis equipped with several cards providing digital
and analog inputs and outputs, counters, and timers. Analog
?10 V outputs of either 13- or 16-bit resolution are used to
set the output voltages of the different power supplies,
whereas the mass commands for the quadrupole mass filters
are controlled uniquely by 16-bit analog outputs. The analog
inputs are used for readbacks from the power supplies to
monitor their state and to check for faults.
For ion detection, the output signal from one of the
channeltrons is sent through a preamplifier ?Advanced Re-
search Instruments, COMBO-100, Golden, CO? that has both
digital and analog output signals. In digital mode, the
transistor-transistor logic ?TTL? pulses generated by the pre-
amplifier are sent directly to a counter input on one of the
PXI cards, where those arriving within a certain time win-
dow are recorded. In analog mode, the output of the preamp-
lifier is sent to a digitizer card in the PXI chassis, and the
signal within certain a time span is integrated in software.
The accurate timings needed for extracting ions from the
traps and for synchronizing trap emptying with the ion de-
tection time gate are produced by timer outputs from the PXI
chassis. However, all the timings necessary to trigger lasers
in laser experiments are generated by an external delay gen-
erator ?Berkeley Nucleonics, Model 565, San Rafael, CA?,
which also serves as the master clock for running the appa-
The machine was characterized in two ways. To assess
the transmitted ion currents and the efficiency of cooling in
the 22-pole ion trap, we used protonated tyrosine as a bench-
mark, since its UV spectrum is sharp, well understood, and
provides a good monitor of the internal ion temperature.13A
073107-4Svendsen et al.Rev. Sci. Instrum. 81, 073107 ?2010?
spray solution of tyrosine ?Sigma Aldrich? at a concentration
of ?0.2 mM was prepared in a 1:1 mixture of water and
methanol. To characterize the low mass cutoff of the ion
funnel, a solution of primary amines was prepared. It con-
tained a sequence of primary amines from methylamine up to
hexylamine, with the exception of pentylamine, dissolved in
The mass spectra shown in the following section were
acquired by guiding the continuous ion stream through the
hexapole ion guide and scanning the first quadrupole mass
filter while detecting ions on the channeltron behind the first
For experiments involving lasers, the ions of interest
were mass-selected in the first quadrupole mass filter and
collected in the octupole ion trap. An intense pulse of He
buffer gas was injected into the cold 22-pole ion trap, and 1
ms later, a fraction of the ions were transferred from the
octupole to the 22-pole trap. Here, they were cooled to
?10 K through collisions with the cold buffer gas and in-
terrogated with an UV laser pulse. The ions were then re-
leased from the trap, mass-selected in the last quadrupole
mass filter and detected by the channeltron detector. The rep-
etition rate of the described cycle was 20 Hz. To obtain an
UV excitation spectrum, the signal of any UV-induced frag-
ment ion can be recorded as a function of the wavelength.
A. Mass spectra and ion currents
A typical mass spectrum obtained when spraying the ty-
rosine solution is shown in Fig. 4. The most intense peak is
located at a m/z value of 182 amu, corresponding to proto-
nated tyrosine, whereas the smaller peaks at 165 and 136
amu indicate the presence of fragment ions resulting from
loss of neutral NH3or H2O+CO, respectively. These types
of fragment ions were also observed in studies of collision-
induced dissociation of protonated tyrosine.34The scale of
Fig. 4 is indicative of the continuous ion currents transmitted
to the first channeltron detector, however since these count
rates are close to the saturated regime of the detector, they
should be considered as lower limits.
Simulations and experiments have shown that ion fun-
nels have a low-mass cutoff,35–37which depends on several
parameters, such as the ratio of the electrode spacing to the
aperture radius, the rf frequency, and the dc gradient. To
investigate the low-mass cutoff of our ion funnel under nor-
mal operating conditions, we recorded a mass spectrum of a
mixture of primary amines. The spectrum shown in Fig. 5
demonstrates that ions with m/z values of ?40 amu are eas-
ily transmitted through the funnel, while ions down to m/z
=30 amu are transmitted with sufficient efficiency to allow
B. UV excitation spectrum
The presented instrument was designed for spectroscopic
investigations of cold gas-phase ions, and protonated ty-
rosine ions are used to demonstrate how UV excitation spec-
tra are measured and to diagnose the internal ion tempera-
ture. Figure 6?a? shows a mass spectrum of buffer-gas cooled
TyrH+ions that have been trapped in the 22-pole for 12 ms.
Clearly, the spectrum is dominated by TyrH+at m/z
=182 amu, but also a small peak at m/z=186 amu is
present, which is attributed to the formation of TyrH+·He
complexes in the ion trap. The small peak at 165 amu stems
from elimination of NH3from protonated tyrosine, and
among all collision-induced dissociation ?CID? channels this
fragmentation channel has the lowest energy threshold.34The
small peak at 173 amu could not be identified.
-(H2O + CO)
FIG. 4. Mass spectrum of the ions produced when spraying a tyrosine
ion signal [kcounts/s]
FIG. 5. Mass spectrum of a mixture of primary amines.
(a) Laser off
(b) Laser on
FIG. 6. Mass spectra of trapped, buffer-gas cooled TyrH+ions ?m/z
=182 amu?: ?a? UV laser is off; ?b? Same as ?a?, but ions are irradiated by
an UV laser pulse resonant with an electronic transition of TyrH+.
073107-5Svendsen et al.Rev. Sci. Instrum. 81, 073107 ?2010?
Figure 6?b? shows a mass spectrum recorded under the
same conditions as those of Fig. 6?a?, but here the ions were
irradiated by an UV laser pulse resonant with an electronic
transition of TyrH+at 35 081 cm−1prior to extraction of
ions from the trap.24Several fragment ions are clearly pro-
duced upon UV excitation, of which only the major one at
m/z=108 amu, which is the protonated side chain, is not
observed in CID experiments.34It should be noted that a
previous study on protonated tyrosine by Stearns et al.24re-
ported the mass of the major fragment to be 107 amu, but in
fact the mass resolution of that data was not high enough to
distinguish between 107 and 108 amu. The 108 amu frag-
ment was also observed in photofragmentation of room-
temperature protonated tyrosine at 263 nm,38although it is
less intense than the 107 fragment. This may be due to the
higher excitation energy in these experiments.
As demonstrated in Fig. 7, an UV spectrum of the
trapped ions is obtained by recording the number of fragment
ions at m/z=108 amu as a function of the UV wavenumber.
The spectrum shows sharp, well-resolved features in agree-
ment with that previously reported by Stearns et al.24In this
previous study, the two intense lowest energy transitions at
35 081 and 35 111 cm−1were assigned to the band origins
of two different conformers:Aand B.Ahot band transition is
clearly evident to the red of each of these electronic band
origins: at ?40 and −46 cm−1for A and B, respectively. The
intensity of these hot bands implies a vibrational temperature
of ?10 K for TyrH+.13This is consistent with the appear-
ance of the TyrH+·He peak in the mass spectrum of Fig.
6?a?, which suggests an internal temperature below 20 K.39
The UV spectrum of Fig. 7 was recorded with
?105ions in the cold trap, which is an order of magnitude
higher than possible with our previous apparatus.13Storage
of a large number of ions in a cold, 22-pole ion trap can lead
to space charge effects that cause heating of the ion
ensemble.40As estimated from the spectrum, the vibrational
temperature that we achieve with ?105ions in the trap is
still quite low, suggesting that rf heating due to space charge
is not yet significant at this loading level.
V. COMPARISON WITH THE PREVIOUS INSTRUMENT
The apparatus presented here resembles the instrument
previously built in our laboratory,13,41but the new apparatus
has some design enhancements which improves the perfor-
mance. The most important change is in the ion source re-
gion where an ion funnel has been incorporated instead of
the traditional skimmer setup, which is employed in the older
apparatus. According to Smith et al.,42the ion funnel should
improve the transmitted ion current by an order of magni-
tude, and we observe such an increase in the number of cold,
trapped ions: from ?104to ?105. This increased signal level
allows us to increase the quadrupole mass resolution when
necessary at the expense of lowering the ion signal.
Other changes to the design include the addition of a
gate valve that allows venting the ion source region for
cleaning purposes without bringing the entire machine up to
atmosphere, and the addition of a third quadrupole bender,
which provides better optical access to the cold trap by mak-
ing the laser axis shorter. We have also used a more powerful
closed cycle refrigerator, which cools the 22-pole ion trap to
4 K rather than 6 K as in our previous apparatus. We find that
this translates into colder internal ion temperatures by ap-
proximately the same increment.
Finally, having complete software control of the poten-
tials applied to all ion optical elements provides much
greater flexibility and ease for optimizing the ion signals.
A new tandem mass spectrometer designed for photo-
fragment spectroscopy of cold, biomolecular ions has been
described. The instrument comprises a nanospray ion source,
a cryogenically cooled 22-pole trap, and a mass-selective
detection system. An ion funnel in the ion source region
efficiently transmits ions through the high-pressure section of
the apparatus leading to large ion currents downstream. Fur-
thermore, the design of the source and the addition of a gate
valve greatly facilitate cleaning procedures.
The capabilities of the instrument were demonstrated by
recording a photofragmentation spectrum and an UV excita-
tion spectrum of protonated tyrosine. The UV spectrum
showed sharp, well-resolved features indicative of internally
cold ions. Even with a large number of ions ??105? stored in
the cold trap, the vibrational temperature estimated from the
small intensity of hot bands of low-frequency vibrations in
the electronic spectrum was found to be ?10 K.
We gratefully acknowledge financial support for this
work from the Fonds National Suisse ?through Grant Nos.
20-120065 and 206021-117416? and the Ecole Polytechnique
Fédérale de Lausanne ?EPFL?. U.L. thanks the support of a
doctoral fellowship from the “Fonds der Chemischen Indus-
trie” of Germany. A.S. acknowledges financial support from
the Danish Research Agency ?Grant No. 272-06-0312?. The
authors would like to thank K.Asmis and M. P. Gorshkov for
FIG. 7. UV excitation spectrum of protonated tyrosine recorded by moni-
toring the number of fragment ions at m/z=108 amu.
073107-6Svendsen et al.Rev. Sci. Instrum. 81, 073107 ?2010?
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