178
M. Dantus and C.L. Kalcic
shaping methods to optimize the cleavage of an acyl-N bond in Ac-Phe-NHMe to
demonstrate the application of femtosecond pulse photodissociation for peptide sequencing [82]. Guyon et al. performed femtosecond pump-probe experiments on
flavin, using the frequency doubled laser at 405 nm for resonant excitation of the
inherent flavin chromophore [83]. Other experiments have interrogated the dissociation pathways of protonated aromatic amino acids and dipeptides using femtosecond pulses at 266 nm [84, 85]. Our work builds upon these previous experiments,
but avoids the need for resonant excitation in the UV.
8.2.2 Experimental Methods
Fs-TOF Experiments on small neutral molecules were carried out using a regeneratively amplified Ti:Al 2 O 3 laser seeded with a broad-band Ti:Al 2 O 3 oscillator.
The output was centered at 800 nm with the maximum pulse energy of 0.8 mJ. The
bandwidth was ∼28 nm (FWHM) resulting in ∼35 fs (FWHM) transform-limited
(TL) pulses. A MIIPS enabled pulse shaper [48] was placed before the amplifier
to eliminate phase distortions from the laser and any optics in the setup, and to deliver arbitrary phases precisely at the target. Para-nitrotoluene (Aldrich > 99 %) was
used without further purification. The fs-TOF experiments were carried out using a
time-of-flight mass spectrometer (TOFMS) with a 0.5 meter field-free drift region
(Fig. 8.3). Sample molecules were effused through an inlet valve into the chamber,
where the pressure was maintained with a three stage differentially pumped system
at 10 −7 Torr with operational flexibility up to 10 −5 Torr during experiments. Pulses
with a 1 kHz repetition rate were focused by a 50 mm lens into the chamber to cause
ionization and fragmentation of the molecules. The energy per pulse was attenuated
to 100 µJ to reach a corresponding peak power density of 4.0 × 10 15 W/cm 2 .
Fs-LID of Trapped Ions Experiments on biomolecules were conducted by using
a custom-built Quantronix (East Setauket, NY) Integra-HE amplified Ti:Al 2 O 3 laser
system. The broadband output of the Ti-Light oscillator is passed through a 128pixel MIIPS-enabled pulse shaper (Biophotonic Solutions Inc, MI) before seeding
a 2-stage amplifier. The system is capable of delivering a 3.0 W output with a repetition rate of 10 kHz. The pulse-shaper is used to measure and compensate phase
distortions accumulated as the laser beam passes through optics in the setup, resulting in transform-limited (TL) pulses with a ∼ 26 nm (FWHM) bandwidth and
∼ 35 fs duration at the sample.
All samples were subjected to electrospray ionization for introduction into a
Thermo Finnigan LCQ Deca XP Plus ion trap mass spectrometer. The LCQ was
modified in-house to accommodate laser irradiation of the trapped ion samples.
A ½ diameter hole was drilled through the vacuum manifold in line with the ion
trap, and a vacuum-sealed laser port was constructed with fused silica window.
A 5 mm hole was drilled all the way through the ring electrode and the quartz
spacers were notched accordingly to provide a clear path for the focused laser beam
M. Dantus and C.L. Kalcic
shaping methods to optimize the cleavage of an acyl-N bond in Ac-Phe-NHMe to
demonstrate the application of femtosecond pulse photodissociation for peptide sequencing [82]. Guyon et al. performed femtosecond pump-probe experiments on
flavin, using the frequency doubled laser at 405 nm for resonant excitation of the
inherent flavin chromophore [83]. Other experiments have interrogated the dissociation pathways of protonated aromatic amino acids and dipeptides using femtosecond pulses at 266 nm [84, 85]. Our work builds upon these previous experiments,
but avoids the need for resonant excitation in the UV.
8.2.2 Experimental Methods
Fs-TOF Experiments on small neutral molecules were carried out using a regeneratively amplified Ti:Al 2 O 3 laser seeded with a broad-band Ti:Al 2 O 3 oscillator.
The output was centered at 800 nm with the maximum pulse energy of 0.8 mJ. The
bandwidth was ∼28 nm (FWHM) resulting in ∼35 fs (FWHM) transform-limited
(TL) pulses. A MIIPS enabled pulse shaper [48] was placed before the amplifier
to eliminate phase distortions from the laser and any optics in the setup, and to deliver arbitrary phases precisely at the target. Para-nitrotoluene (Aldrich > 99 %) was
used without further purification. The fs-TOF experiments were carried out using a
time-of-flight mass spectrometer (TOFMS) with a 0.5 meter field-free drift region
(Fig. 8.3). Sample molecules were effused through an inlet valve into the chamber,
where the pressure was maintained with a three stage differentially pumped system
at 10 −7 Torr with operational flexibility up to 10 −5 Torr during experiments. Pulses
with a 1 kHz repetition rate were focused by a 50 mm lens into the chamber to cause
ionization and fragmentation of the molecules. The energy per pulse was attenuated
to 100 µJ to reach a corresponding peak power density of 4.0 × 10 15 W/cm 2 .
Fs-LID of Trapped Ions Experiments on biomolecules were conducted by using
a custom-built Quantronix (East Setauket, NY) Integra-HE amplified Ti:Al 2 O 3 laser
system. The broadband output of the Ti-Light oscillator is passed through a 128pixel MIIPS-enabled pulse shaper (Biophotonic Solutions Inc, MI) before seeding
a 2-stage amplifier. The system is capable of delivering a 3.0 W output with a repetition rate of 10 kHz. The pulse-shaper is used to measure and compensate phase
distortions accumulated as the laser beam passes through optics in the setup, resulting in transform-limited (TL) pulses with a ∼ 26 nm (FWHM) bandwidth and
∼ 35 fs duration at the sample.
All samples were subjected to electrospray ionization for introduction into a
Thermo Finnigan LCQ Deca XP Plus ion trap mass spectrometer. The LCQ was
modified in-house to accommodate laser irradiation of the trapped ion samples.
A ½ diameter hole was drilled through the vacuum manifold in line with the ion
trap, and a vacuum-sealed laser port was constructed with fused silica window.
A 5 mm hole was drilled all the way through the ring electrode and the quartz
spacers were notched accordingly to provide a clear path for the focused laser beam