Shifting unoccupied spectral space in mass spectrum of peptide fragment ions

Ions near the high-end border of a mass defect distribution plot for native peptide fragment ions have potential as signature markers that are based on mass-to-charge ratio determination. The specificity of these marker ions, including phosphoryl ions, can be improved by removing interfering isobaric ions from the border region on the distribution plot. These interfering ions are rich in Asp and Glu content. The masses of amino acid residues and peptides are rescaled from the IUPAC scale (¹²C=12 u as the mass reference) to the averagine scale (averagine mass=111 u* as the mass reference with zero mass defect; u*: the mass unit on the averagine scale), using a scaling factor of 0.999493894. It is theoretically predicted that esterification of Asp and Glu side-chain carboxylates with n-butanol can achieve a sufficient retreat of the high-end border on a mass defect distribution plot based on the use of mass spectrometers with better-than-medium resolution. Theoretical calculations and laboratory experiments are performed to examine effects of various esterifications on the averagine-scale mass defect distribution of peptide fragment ions and on the specificity of two positive phosphoryl ions: the phosphotyrosine immonium ion and a cyclophosphoramidate ion.     

Neutral fragment mass spectra via ambient thermal dissociation of peptide and protein ions

A novel method for the fragmentation of peptide and protein ions at atmospheric pressure outside the mass spectrometer is described. Peptide/protein ions generated by electrosonic spray ionization (ESSI) are carried through a heated coiled metal tube where they fragment. Fragment ions of types a, b, and y are observed for peptides such as angiotensin II and bradykinin. In the case of phosphopeptides, informative b and y ions which preserve the labile phosphate groups are observed in the negative ion mode, which is potentially useful in the location of phosphorylation sites in proteins through chemical analysis of phosphopeptides. The thermal dissociation method extends to proteins such as ubiquitin and myoglobin, giving rise to y-type and other fragment ions. The most important feature of this method is that it also allows characterization of the neutral fragments arising from thermal dissociation by use of on-line corona discharge ionization. This neutral re-ionization experiment is much easier to perform outside the mass spectrometer than as conventionally done, in vacuum. It yields increased structural information from the resulting mass spectra in both the positive and the negative ion modes.     

Evidence for structural variants of a- and b-type peptide fragment ions using combined ion mobility/mass spectrometry

Tandem mass spectrometry (MS/MS) of peptides plays a key role in the field of proteomics, and an understanding of the fragmentation mechanisms involved is vital for data interpretation. Not all the fragment ions observed by low-energy collision-induced dissociation of protonated peptides are readily explained by the generally accepted structures for a- and b-ions. The possibility of a macrocyclic structure for b-type ions has been recently proposed. In this study, we have undertaken investigations of linear protonated YAGFL-NH(2), N-acetylated-YAGFL-NH(2), and cyclo-(YAGFL) peptides and their fragments using a combination of ion mobility (IM) separation and mass spectrometry. The use of IM in this work both gives insight into relative structural forms of the ion species and crucial separation of isobaric species. Our study provides compelling evidence for the formation of a stable macrocyclic structure for the b(5) ion generated by fragmentation of protonated linear YAGFL-NH(2). Additionally we demonstrate that the a(4) ion fragment of protonated YAGFL-NH(2) has at least two structures; one of which is attributable to a macrocyclic structure on the basis of its subsequent fragmentation. More generally, this work emphasizes the value of combined IM-MS/MS in probing the detailed fragmentation mechanisms of peptide ions, and illustrates the use of combined ion mobility/collisional activation/mass spectrometry analysis in achieving an effective enhancement of the resolution of the mobility separator.     

Hybrid tandem mass spectrometry of electrospray-produced peptide ions

The collision-induced decomposition spectra of electrospray-produced molecule ions were investigated on a hybrid tandem mass spectrometer. The molecular mass of the peptides investigated ranged from m/z 409 (as the singly protonated molcule ion) to 1758 (as the singly, doubly and triply protonated molecules). The effect of changing the center-of-mass collision energy by changing either the laboratory collision energy or the mass of the target gas was investigated. The spectra of all ions investigated showed a large number of sequence ions representative of the peptides' structures.     

Doubly charged fragment ions in the field ionization mass spectra of alkylbenzenes

It is shown that the radical [C₆H₅C_mH_2m]²⁺ fragment ions found in the field ionization mass spectra of alkylbenzenes are formed via a different adsorption state of the singly charged species than in the case of the formation of [M]²⁺ molecular ions. It is further demonstrated that the primary fragmentation of molecules by the cleavage of C? C bonds results not only from decompositions of molecular ions in the gas phase but also from surface reactions.     

Spectral counting robust on high mass accuracy mass spectrometers

Mass spectrometry is central to shotgun proteomics, an application that seeks to quantify as much of the total protein complement of a biological sample as possible. The high mass accuracy, resolution, capacity and scan rate of modern mass spectrometers have greatly facilitated this endeavor. The sum of MS to MS/MS transitions in tandem mass spectrometry, the spectral count (SC), of a peptide has been shown to be a reliable estimate of its relative abundance. However, when using SCs, optimal MS configurations are crucial in order to maximize the number of low abundant proteins quantified while keeping the estimates for the highly abundant proteins within the linear dynamic range. In this study, LC/MS/MS analysis was performed using an LTQ‐OrbiTrap on a sample containing many highly abundant proteins. Tuning the LTQ‐OrbiTrap mass spectrometer to minimize redundant MS/MS acquisition and to maximize resolution of the proteome by accurately measured m/z ratios resulted in an appreciable increase in quantified low abundant proteins. An exclusion duration of 90 s and an exclusion width of 10 ppm were found best of those tested. The spectral count of individual proteins was found to be highly reproducible and protein abundance ratios were not affected by the different settings that were applied. We conclude that on a high mass accuracy instrument spectral counting is a robust measure of protein abundance even for samples containing many highly abundant proteins and that tuning dynamic exclusion parameters appreciably improves the number of proteins that can be reliably quantified. Copyright © 2010 John Wiley & Sons, Ltd.     

Surface-induced dissociation of peptide ions in Fourier-transform mass spectrometry

Peptide molecular ion species up to m/z 3055 introduced into a Fourier-transform mass spectrometer can be made to undergo extensive fragmentation by electrically floating the ion cell. The proportion of ions dissociated increases with increasing voltage, with 48 eV producing the highest absolute abundance of fragment ions above m/z 200. At this energy, spectra closely resemble those from photodissociation at 193 nm, indicating an internal energy deposition of 6–7 eV; change of product abundances with kinetic energy resembles a conventional breakdown curve. The precursor ions apparently are electrostatically attracted to strike screen wires across the ion cell entrance, producing daughter ions of low kinetic energy.

     

Studies of peptide a- and b-type fragment ions using stable isotope labeling and integrated ion mobility/tandem mass spectrometry

The structures of peptide a- and b-type fragment ions were studied using synthetic peptides including a set of isomeric peptides, differing in the sequence location of an alanine residue labeled with ¹⁵N and uniformly with ¹³C. The pattern of isotope labeling of second-generation fragment ions derived via a _n and b _n ions (where n=4 or 5) suggested that these intermediates existed in part as macrocyclic structures, where alternative sites of ring opening gave rise to different linear forms whose simple cleavage might give rise to the observed final products. Similar conclusions were derived from combined ion mobility/tandem MS analyses where different fragmentation patterns were observed for isomeric a- or b-type ions that display different ion mobilities. These analyses were facilitated by a new approach to the processing of ion mobility/tandem MS data, from which distinct and separate product ion spectra are derived from ions that are incompletely separated by ion mobility. Finally, an example is provided of evidence for a macrocyclic structure for b _n ions where n=8 or 9.     

Electron impact fragmentation of pyranocoumarin derivatives. Tandem mass spectrometric study of abundant singly and doubly charged fragment ions at high and low collision energy

A series of novel pyranocoumarin derivatives were analysed by electron impact mass spectrometry and tandem mass spectrometry at low aud high collision energy. The collision-induced decomposition tandem mass spectra of the [M ? CH₃]⁺ ions yielded several structurally valuable fragments and those of the [M ? CH₃]²⁺ ions allowed some charge-separation reactions to be recognized.     

Structure and fragmentation of b2 ions in peptide mass spectra

In a number of cases the b2 ion observed in peptide mass spectra fragments directly to the a1 ion. The present study examines the scope of this reaction and provides evidence as to the structure(s) of the b2 ions undergoing fragmentation to the a1 ion. The b2 ion H-Ala-Gly+ fragments, in part, to the a1 ion, whereas the isomeric b2 ion H-Gly-Ala+ does not fragment to the a1 ion. Ab initio calculations of ion energies show that this different behavior can be rationalized in terms of protonated oxazolone structures for the b2 ions provided one assumes a reverse activation energy of approximately 1 eV for the reaction b2-->a2; such a reverse activation energy is consistent with experimental kinetic energy release measurements. Experimentally, the H-Aib-Ala+ b2 ion, which must have a protonated oxazolone structure, fragments extensively to the a1 ion. We conclude that the proposal by Eckart et al. (J. Am. Soc. Mass Spectrom. 1998, 9, 1002) that the b2 ions which undergo fragmentation to a1 ions have an immonium ion structure is not necessary to rationalize the results, but that the fragmentation does occur from a protonated oxazolone structure. It is shown that the b2-->a1 reaction occurs extensively when the C-terminus residue in the b2 ion is Gly and with less facility when the C-terminus residue is Ala. When the C-terminus residue is Val or larger, the b2-->a1 reaction cannot compete with the b2-->a2 fragmentation reaction. Some preliminary results on the fragmentation of a2 ions are reported.     

Negative ion mass spectrometry: The generation of high concentrations of low energy molecular negative ions at high source pressures

The effect of the addition of argon and other gases upon the intensities of negative ion species formed in an electron impact source has been investigated. The negative ion current generated for a series of aromatic compounds has been investigated as a function both of sample and argon pressure in the ion source of a ZAB-2F mass spectrometer. For all compounds studied, a striking enhancement of molecular negative ion current occurred on increasing either the presure of the sample or of argor. The results are consistent with thermalization of the 50 eV electrons by collisions with neutral molecules in the high pressure ion source and collisional stabilization of the negative ions initially formed. Analytical applications of the technique are discussed.     

Factors influencing the formation of some characteristic fragment ions in the mass spectra of 16-trimethylsilyloxy androstanes

The mass spectra of the trimethylsilyl derivatives of several steroids containing a 16-hydroxy function are presented. The mechanisms giving rise to various characteristic fragment ions were investigated with the aid of deuterium and ¹⁸O-labeling.     

Formation of c1 fragment ions in collision-induced dissociation of glutamine-containing peptide ions: a tip for de novo sequencing

A c1 ion was observed with significant yield in the tandem mass (MS/MS) spectra of peptide ions containing glutamine as the second amino acid residue from the N-terminus. The c1 fragment was generated independently of the N-terminal residue of the peptide, but its abundance was strongly dependent on the side-chain identity. This ion is not a common fragmentation product in low-energy collision-induced dissociation of peptide ions, but it assists in identification of the first two amino acid residues, often difficult due to a low or absent signal from the heaviest y ion. A consecutive fragmentation mechanism is proposed, involving a b2 ion with a six-membered ring as an intermediate, to explain the exceptional stability of the c1 fragment ion. The utility of this information is discussed, especially in de novo sequencing of peptide ions.     

Mass spectroscopy at high mass

Summary High mass in mass spectroscopy is defined as being the region above m/z 10000. Ionization techniques, methods of mass analysis and ion detection are reviewed. A general mechanism of formation of gaseous ions from nonvolatile, thermally labile compounds is put forward. The characteristics in common to all ionization techniques are, it is proposed, the setting-up of a charge at the condensed phase/vacuum interface, and the subsequent field evaporation of ions.

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Massenspektrometrie im hohen Massenbereich

Zusammenfassung Die Definition Hoher Massenbereich in der Massenspektroskopie gilt für Ionen oberhalb von m/z 10000. Es wird eine Übersicht über Ionisierungstechniken, Methoden der Massentrennung und der Ionendetektion gegeben. Ein allgemeingültiger Mechanismus der Bildung von Ionen in der Gasphase aus nicht flüchtigen, thermisch empfindlichen Verbindungen wird vorgestellt. Der Vorschlag beschreibt als gemeinsame Eigenschaft dieser Ionisierungstechniken die Ausbildung einer Ladung an der Grenzschicht zwischen kondensierter Phase und Vakuum bei anschließender feldinduzierter Verdampfung der Ionen.

     

Accurate mass measurement at enhanced mass-resolution on a triple quadrupole mass-spectrometer for the identification of a reaction impurity and collisionally-induced fragment ions of cabergoline

In this study, accurate mass measurements were made by electrospray ionization (ESI) on a triple quadrupole mass spectrometer operating in enhanced mass-resolution mode (peak width = 0.1 u FWMH), to give qualitative information relating to the pharmaceutical, cabergoline. Accurate mass determinations by ESI-MS were performed on a protonated impurity formed during cabergoline storage. The accurate mass measurement resulted in only one proposed elemental composition for the impurity, using reasonable elemental limits and mass tolerance for the calculation. This information was sufficient to propose a structure for the impurity where ESI-MS/MS proved consistent. The difference between the accurate mass measurement and the exact mass calculated for the proposed structure was 0.8 mmu, with a standard deviation of 0.7 mmu for replicate accurate mass determinations. Accurate mass determinations in ESI-MS/MS provided information on cabergoline fragment ions formed through collisionally-induced dissociation. Since the potential formation of isobaric ions exists for two major cabergoline fragment ions, accurate mass measurement allowed for the determination of the most probable fragment ion structures. The differences between the accurate mass measurements and exact masses calculated for the proposed fragment ions were 1.9 and 2.1 mmu, with standard deviations of 0.4 and 0.8 mmu, respectively, for replicate determinations.     

Electrospray ionization tandem mass spectrometry of model peptides reveals diagnostic fragment ions for protein ubiquitination

In this work, synthetic peptides were used to determine the fragmentation behavior of ubiquitinated peptides and to find ions diagnostic for peptide ubiquitination. The ubiquitin-calmodulin peptide1 was chosen as the model peptide for naturally occurring ubiquitinated proteins cleaved with endoproteinase gluC. In addition, the fragmentation behavior of model ubiquitinated peptides produced by tryptic digestion was also of great interest since the standard protocols for proteomics-based protein identification use trypsin as the protease. Attachment of ubiquitin to a target protein results in a branched structure, but only ions from the ubiquitin side chain (and the lysine to which it is attached) can be used as diagnostic ions, since fragment ions that contain other amino acids from the parent protein will vary in mass. Characteristic b-type fragment ions from the gluC cleavage of the ubiquitin side chain (designated as b ions) were found which involve only the ubiquitin tail (b2, b3, b4, b5 and b6 ions at m/z 189.06, 302.12, 439.18, 552.30 and 651.30, respectively). Maximum production of these ions occurred at a collision energy of 45 eV in a Q-TOF instrument. Although a non-ubiquitinated peptide may produce isobaric fragment ions, it is unlikely that it can produce these ions in combination. With liquid chromatography/tandem mass spectrometry (LC/MS/MS) experiments, ubiquitinated peptides can readily be determined by surveying the reconstructed or extracted ion chromatograms of the diagnostic fragment ions for common peaks. Characteristic ions resulting from tryptic cleavage of the side chain were found in cleavage products with a missed cleavage, resulting in a LRGG- tag instead of a GG- tag. For the LRGG-tagged peptide, diagnostic MS/MS fragment ions (at m/z 270.17 and 384.21) from the ubiquitin tail (b2 and b4, respectively) were found, along with an internal fragment ion (LRGGK-28) at m/z 484.30. These ions should prove useful in precursor-ion scanning experiments for identifying peptides modified by attachment of ubiquitin, and for locating the site of ubiquitin attachment.     

Use of benchtop exactive high resolution and high mass accuracy orbitrap mass spectrometer for screening in horse doping control

Liquid chromatography-mass spectrometry (LC-MS) has been widely used in doping control laboratories over the last two decades. Currently, simple quadrupole, triple quadrupole and ion trap are the most commonly employed analyzers in toxicological analysis. Nevertheless, the main lack of these technologies is the restricted number of target compounds simultaneously screened without loss of sensitivity. In this article we present an innovative screening approach routinely applied in the French horse doping control laboratory based on high resolution (50000) and high mass accuracy (<5 ppm) in full scan MS mode for more than 235 target analytes screened from an initial volume of 5 mL of urine. The sample preparation was classically founded on solid phase extraction by means of reverse phase C18 cartridges. LC-MS analyses were carried out on a Shimadzu binary HPLC pumps linked to a C18 Sunfire column associated with the high resolution exactive benchtop orbitrap mass spectrometer. This screening was performed alternatively in positive-negative ionization mode during the same run. Thus, the identification of compounds of interest was made using their exact mass in positive-negative ionization mode at their expected retention time. All data obtained were processed by ToxID software (ThermoFisherScientific) which is able to identify a molecule by theoretical mass and retention time. In order to illustrate this innovative technology applied in our laboratory, sample preparation, validation data performed on 20 target compounds from 16 different horse urine samples, chromatograms and spectra will be discussed in this paper.