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Article ; Online: Infrared multiple photon dissociation spectroscopy of trapped ions.

Polfer, Nick C

2011 Volume 40, Issue 5, Page(s) 2211–2221

Abstract: This tutorial review presents the technique of infrared multiple-photon dissociation (IRMPD) spectroscopy of mass-selected trapped ions. This requires coupling of a tunable infrared laser with mass spectrometry instrumentation. IRMPD spectroscopy has ... ...

Abstract	This tutorial review presents the technique of infrared multiple-photon dissociation (IRMPD) spectroscopy of mass-selected trapped ions. This requires coupling of a tunable infrared laser with mass spectrometry instrumentation. IRMPD spectroscopy has recently blossomed due to the emergence of widely tunable free electron lasers, as well as on-going developments of benchtop lasers. The merits of different trapping approaches in mass spectrometry are discussed in the light of photodissociation experiments. This tutorial discusses current capabilities, as well as limitations of the technique.
MeSH term(s)	Ions/chemistry ; Lasers ; Photons ; Spectrophotometry, Infrared/instrumentation ; Spectrophotometry, Infrared/methods
Chemical Substances	Ions
Language	English
Publishing date	2011-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/c0cs00171f
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Article: Infrared multiple photon dissociation spectroscopy of trapped ions

Polfer, Nick C

Chemical Society reviews. 2011 Apr. 18, v. 40, no. 5

2011

Abstract	This tutorial review presents the technique of infrared multiple-photon dissociation (IRMPD) spectroscopy of mass-selected trapped ions. This requires coupling of a tunable infrared laser with mass spectrometry instrumentation. IRMPD spectroscopy has recently blossomed due to the emergence of widely tunable free electron lasers, as well as on-going developments of benchtop lasers. The merits of different trapping approaches in mass spectrometry are discussed in the light of photodissociation experiments. This tutorial discusses current capabilities, as well as limitations of the technique.
Keywords	dissociation ; instrumentation ; ions ; lasers ; mass spectrometry ; photolysis ; photons
Language	English
Dates of publication	2011-0418
Size	p. 2211-2221.
Publishing place	The Royal Society of Chemistry
Document type	Article
ZDB-ID	1472875-8
ISSN	1460-4744 ; 0306-0012
ISSN (online)	1460-4744
ISSN	0306-0012
DOI	10.1039/c0cs00171f
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Article ; Online: Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance.

Polfer, Nick C / Oomens, Jos

Mass spectrometry reviews

2009 Volume 28, Issue 3, Page(s) 468–494

Abstract: The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The ... ...

Abstract	The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
MeSH term(s)	Gases/chemistry ; Ions/analysis ; Ions/chemistry ; Mass Spectrometry/methods ; Metals/analysis ; Metals/chemistry ; Proteins/analysis ; Proteins/chemistry ; Spectrophotometry, Infrared/methods ; Water/chemistry
Chemical Substances	Gases ; Ions ; Metals ; Proteins ; Water (059QF0KO0R)
Language	English
Publishing date	2009-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.20215
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Article: Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

Polfer, Nick C / Oomens, Jos

Mass spectrometry reviews. 2009 May, v. 28, no. 3

2009

Abstract	The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.
Language	English
Dates of publication	2009-05
Size	p. 468-494.
Publishing place	Wiley Subscription Services, Inc., A Wiley Company
Document type	Article
ZDB-ID	1491946-1
ISSN	1098-2787 ; 0277-7037
ISSN (online)	1098-2787
ISSN	0277-7037
DOI	10.1002/mas.20215
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Article: Reaction products in mass spectrometry elucidated with infrared spectroscopy.

Polfer, Nick C / Oomens, Jos

Physical chemistry chemical physics : PCCP

2007 Volume 9, Issue 29, Page(s) 3804–3817

Abstract: Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of ... ...

Abstract	Determining the structure and dynamics of large biologically relevant molecules is one of the key challenges facing biology. Although X-ray crystallography (XRD) and nuclear magnetic resonance (NMR) yield accurate structural information, they are of limited use when sample quantities are low. Mass spectrometry (MS) on the other hand has been very successful in analyzing biological molecules down to atto-mole quantities and has hence begun to challenge XRD and NMR as the key technology in the life sciences. This trend has been further assisted by the development of MS techniques that yield structural information on biomolecules. Of these techniques, collision-induced dissociation (CID) and hydrogen/deuterium exchange (HDX) are among the most popular. Despite advances in applying these techniques, little direct experimental evidence had been available until recently to verify their proposed underlying reaction mechanisms. The possibility to record infrared spectra of mass-selected molecular ions has opened up a novel avenue in the structural characterization of ions and their reaction products. On account of its high pulse energies and wide wavelength tunability, the free electron laser for infrared experiments (FELIX) at FOM Rijnhuizen has been shown to be ideally suited to study trapped molecular ions with infrared photo-dissociation spectroscopy. In this paper, we review recent experiments in our laboratory on the infrared spectroscopic characterization of reaction products from CID and HDX, thereby corroborating some of the reaction mechanisms that have been proposed. In particular, it is shown that CID gives rise to linear fragment ion structures which have been proposed for some time, but also yields fully cyclical ring structures. These latter structures present a possible challenge for using tandem MS in the sequencing of peptides/proteins, as they can lead to a scrambling of the amino acid sequence information. In gas-phase HDX of an amino acid it is shown that the structure can be changed from a charge solvated to a zwitterionic structure, thereby demonstrating that HDX can be an invasive technique, in fact changing the structure of the analyte. These results emphasize that more fundamental work is required in order to understand the underlying mechanisms in two of the most important structural techniques in MS.
MeSH term(s)	Enkephalin, Leucine/analysis ; Enkephalin, Leucine/metabolism ; Gases/analysis ; Gases/chemistry ; Gases/metabolism ; Mass Spectrometry/instrumentation ; Peptides/analysis ; Peptides/chemistry ; Peptides/metabolism ; Spectrophotometry, Infrared/instrumentation ; Spectrophotometry, Infrared/methods
Chemical Substances	Gases ; Peptides ; Enkephalin, Leucine (58822-25-6)
Language	English
Publishing date	2007-08-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1476244-4
ISSN	1463-9084 ; 1463-9076
ISSN (online)	1463-9084
ISSN	1463-9076
DOI	10.1039/b702993b
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Article ; Online: Periodicity of monoisotopic mass isomers and isobars in proteomics.

Yu, Long / Xiong, Yan-Mei / Polfer, Nick C

Analytical chemistry

2011 Volume 83, Issue 20, Page(s) 8019–8023

Abstract: We report trends in the theoretically derived number of compositionally distinct peptides (i.e., peptides made up of different amino acid residues) up to a nominal mass of 1000. A total of 21 amino acid residues commonly found in proteomics studies are ... ...

Abstract	We report trends in the theoretically derived number of compositionally distinct peptides (i.e., peptides made up of different amino acid residues) up to a nominal mass of 1000. A total of 21 amino acid residues commonly found in proteomics studies are included in this study, 19 natural, nonisomeric amino acid residues as well as oxidated methione and acetamidated cysteine. The number of possibilities is found to increase in an exponential fashion with increasing nominal mass, and the data show a periodic oscillation that starts at mass ~200 and continues throughout to 1000. Note that similar effects are reported in the companion article on fragment ions from electron capture/transfer dissociation (ECD/ETD) (Mao et al. Anal. Chem.2011, DOI: 10.1021/ac201619t). The spacing of this oscillation is ~15 mass units at lower masses and ~14 mass units at higher nominal masses. This correlates with the most common mass differences between the amino acid building blocks. In other words, some mass differences are more common than others, thus determining the periodicity in this data. From an analytical point of view, nominal masses with a larger number of compositionally distinct peptides include a substantial number of isomers, which cannot be separated based on mass. Consequently, even ultrahigh mass accuracy (i.e., 0.5 ppm) does not lead to a substantially enhanced rate of identification. Conversely, for adjacent nominal masses with a lower number of isomers, moderately accurate mass (i.e., 10 ppm) gives a higher degree of certainty in identification. These effects are limited to the mass range between 200 and 500 Da. At higher masses, the percentage of uniquely identified peptides drops off to close to zero, independent of nominal mass, due the inherently high number of isomers. While the exact number of isobars/isomers at each nominal mass depends on the amino acid building blocks that are considered, the periodicity in the data is found to be remarkably robust; for instance, inclusion of phosphorylated residues barely affects the pattern at lower masses (i.e., <500 Da).
MeSH term(s)	Amino Acids/chemistry ; Isomerism ; Mass Spectrometry ; Molecular Weight ; Peptides/chemistry ; Proteomics
Chemical Substances	Amino Acids ; Peptides
Language	English
Publishing date	2011-10-15
Publishing country	United States
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/ac201624t
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Article ; Online: Hybrid quadrupole mass filter∕quadrupole ion trap∕time-of-flight-mass spectrometer for infrared multiple photon dissociation spectroscopy of mass-selected ions.

Gulyuz, Kerim / Stedwell, Corey N / Wang, Da / Polfer, Nick C

The Review of scientific instruments

2011 Volume 82, Issue 5, Page(s) 54101

Abstract: ... C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed ...

Abstract	We present a laboratory-constructed mass spectrometer optimized for recording infrared multiple photon dissociation (IRMPD) spectra of mass-selected ions using a benchtop tunable infrared optical parametric oscillator∕amplifier (OPO∕A). The instrument is equipped with two ionization sources, an electrospray ionization source, as well as an electron ionization source for troubleshooting. This hybrid mass spectrometer is composed of a quadrupole mass filter for mass selection, a reduced pressure (∼10(-5) Torr) quadrupole ion trap (QIT) for OPO irradiation, and a reflectron time-of-flight drift tube for detecting the remaining precursor and photofragment ions. A helium gas pulse is introduced into the QIT to temporarily increase the pressure and hence enhance the trapping efficiency of axially injected ions. After a brief pump-down delay, the compact ion cloud is subjected to the focused output from the continuous wave OPO. In a recent study, we implemented this setup in the study of protonated tryptophan, TrpH(+), as well as collision-induced dissociation products of this protonated amino acid [W. K. Mino, Jr., K. Gulyuz, D. Wang, C. N. Stedwell, and N. C. Polfer, J. Phys. Chem. Lett. 2, 299 (2011)]. Here, we give a more detailed account on the figures of merit of such IRMPD experiments. The appreciable photodissociation yields in these measurements demonstrate that IRMPD spectroscopy of covalently bound ions can be routinely carried out using benchtop OPO setups.
Language	English
Publishing date	2011-05
Publishing country	United States
Document type	Journal Article
ZDB-ID	209865-9
ISSN	1089-7623 ; 0034-6748
ISSN (online)	1089-7623
ISSN	0034-6748
DOI	10.1063/1.3585982
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Article ; Online: Diagnostic NH and OH vibrations for oxazolone and diketopiperazine structures: b2 from protonated triglycine.

Wang, Da / Gulyuz, Kerim / Stedwell, Corey N / Polfer, Nick C

Journal of the American Society for Mass Spectrometry

2011 Volume 22, Issue 7, Page(s) 1197–1203

Abstract: We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b(2) from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, ...

Abstract	We present infrared multiple photon dissociation (IRMPD) spectra in the hydrogen stretching region of the simplest b fragment, b(2) from protonated triglycine, contrasted to that of protonated cyclo(Gly-Gly). Both spectra confirm the presence of intense, diagnostic vibrations linked to the site of proton attachment. Protonated cyclo(Gly-Gly) serves as a reference spectrum for the diketopiperazine structure, showing a diagnostic O-H(+) stretch of the protonated carbonyl group at 3585 cm(-1). Conversely, b(2) from protonated triglycine exhibits a strong band at 3345 cm(-1), associated with the N-H stretching mode of the protonated oxazolone ring structure. Other weaker N-H stretches can also be discerned, such as the amino NH(2) and amide NH bands. These results demonstrate the usefulness of the hydrogen stretching region, and hence benchtop optical parametric oscillator/amplifier (OPO/A) set-ups, in making structural assignments of product ions in collision-induced dissociation (CID) of peptides.
MeSH term(s)	Diketopiperazines/chemistry ; Mass Spectrometry/methods ; Molecular Conformation ; Oligopeptides/chemistry ; Oxazolone/chemistry ; Piperazines/chemistry ; Protons ; Spectrophotometry, Infrared ; Vibration
Chemical Substances	Diketopiperazines ; Oligopeptides ; Piperazines ; Protons ; Oxazolone (15646-46-5) ; 2,5-dioxopiperazine (240L69DTV7) ; glycyl-glycyl-glycine (CVK73ZDQ8B)
Language	English
Publishing date	2011-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1073671-2
ISSN	1879-1123 ; 1044-0305
ISSN (online)	1879-1123
ISSN	1044-0305
DOI	10.1007/s13361-011-0147-3
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Zs.MO 241: Show issues

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Article ; Online: Alkali metal complexes of the dipeptides PheAla and AlaPhe: IRMPD spectroscopy.

Polfer, Nick C / Oomens, Jos / Dunbar, Robert C

Chemphyschem : a European journal of chemical physics and physical chemistry

2008 Volume 9, Issue 4, Page(s) 579–589

Abstract: ... establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C-terminal hydroxyl ... a threefold chelation geometry. This third site may be either the C-terminal carbonyl oxygen, or the N ...

Abstract	Complexes of PheAla and AlaPhe with alkali metal ions Na(+) and K(+) are generated by electrospray ionization, isolated in the Fourier-transform ion cyclotron resonance (FT-ICR) ion trapping mass spectrometer, and investigated by infrared multiple-photon dissociation (IRMPD) using light from the FELIX free electron laser over the mid-infrared range from 500 to 1900 cm(-1). Insight into structural features of the complexes is gained by comparing the obtained spectra with predicted spectra and relative free energies obtained from DFT calculations for candidate conformers. Combining spectroscopic and energetic results establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C-terminal hydroxyl does not complex the metal ion and is in the endo conformation. It is also likely that the aromatic ring of Phe always chelates the metal ion in a cation-pi binding configuration. Along with the amide CO and ring chelation sites, a third Lewis-basic group almost certainly chelates the metal ion, giving a threefold chelation geometry. This third site may be either the C-terminal carbonyl oxygen, or the N-terminal amino nitrogen. From the spectroscopic and computational evidence, a slight preference is given to the carbonyl group, in an RO(a)O(t) chelation pattern, but coordination by the amino group is almost equally likely (particularly for K(+)PheAla) in an RO(a)N(t) chelation pattern, and either of these conformations, or a mixture of them, would be consistent with the present evidence. (R represents the pi ring site, O(a) the amide oxygen, O(t) the terminal carbonyl oxygen, and N(t) the terminal nitrogen.) The spectroscopic findings are in better agreement with the MPW1PW91 DFT functional calculations of the thermochemistry compared with the B3LYP functional, which seems to underestimate the importance of the cation-pi interaction.
MeSH term(s)	Computer Simulation ; Dipeptides/chemistry ; Metals, Alkali/chemistry ; Models, Chemical ; Organometallic Compounds/chemistry ; Spectrophotometry, Infrared/methods ; Thermodynamics
Chemical Substances	Dipeptides ; Metals, Alkali ; Organometallic Compounds ; alanylphenylalanine (3061-90-3) ; phenylalanylalanine (3918-87-4)
Language	English
Publishing date	2008-03-14
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	1439-7641
ISSN (online)	1439-7641
DOI	10.1002/cphc.200700700
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Article ; Online: Infrared spectroscopy of [XFeC24H12]+ (X = C5H5, C5(CH3)5) complexes in the gas phase: experimental and computational studies of astrophysical interest.

Simon, Aude / Joblin, Christine / Polfer, Nick / Oomens, Jos

The journal of physical chemistry. A

2008 Volume 112, Issue 37, Page(s) 8551–8560

Abstract: ... IRMPD) spectra of [XFeC 24H 12] (+) (X = C 5H 5 or Cp, C 5(CH 3) 5 or Cp*) complexes in the gas phase ... The isomers in which the XFe unit is coordinated to an outer ring of C 24H 12 (+) (Out isomers) were ... The effect of the coordination of Fe in weakening the bands of C 24H 12 (+) in the 1000-1600 cm (-1) region ...

Abstract	We report the first experimental mid-infrared (700-1600 cm (-1)) multiple-photon dissociation (IRMPD) spectra of [XFeC 24H 12] (+) (X = C 5H 5 or Cp, C 5(CH 3) 5 or Cp) complexes in the gas phase obtained using the free electron laser for infrared experiments. The experimental results are complemented with theoretical infrared (IR) absorption spectra calculated with methods based on density functional theory. The isomers in which the XFe unit is coordinated to an outer ring of C 24H 12 (+) (Out isomers) were calculated to be the most stable ones. From the comparison between the experimental and calculated spectra, we could derive that, (i) for [CpFeC 24H 12] (+) complexes, the (1)A Out isomer appears to be the best candidate to be formed in the experiment but the presence of the (1)A In higher energy isomer in minor abundance is also plausible; and (ii) for [CpFeC 24H 12] (+) complexes, the three calculated Out isomers of similar energy are likely to be present simultaneously, in qualitative agreement with the observed dissociation patterns. This study also emphasizes the threshold effect in the IRMPD spectrum below which IR bands cannot be observed and evidence strong mode coupling effects in the [XFeC 24H 12] (+) species. The effect of the coordination of Fe in weakening the bands of C 24H 12 (+) in the 1000-1600 cm (-1) region is confirmed, which is of interest to search for such complexes in interstellar environments.
MeSH term(s)	Astronomical Phenomena ; Astronomy ; Computer Simulation ; Ferrous Compounds/chemistry ; Gases/chemistry ; Lasers ; Mass Spectrometry/methods ; Models, Chemical ; Molecular Conformation ; Photochemistry ; Spectrophotometry, Infrared/methods ; Stereoisomerism
Chemical Substances	Ferrous Compounds ; Gases
Language	English
Publishing date	2008-09-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1520-5215
ISSN (online)	1520-5215
DOI	10.1021/jp801517q
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