Tandem mass spectrometry of leucine enkephalin and physalaemin using a hybrid instrument

Large-Scale Metabolite Analysis of Standards and Human Serum by Laser Desorption Ionization Mass Spectrometry from Silicon Nanopost Arrays

The unique challenges presented by metabolomics have driven the development of new mass spectrometry (MS)-based techniques for small molecule analysis. We have previously demonstrated silicon nanopost arrays (NAPA) to be an effective substrate for laser desorption ionization (LDI) of small molecules for MS. However, the utility of NAPA-LDI-MS for a wide range of metabolite classes has not been investigated. Here we apply NAPA-LDI-MS to the large-scale acquisition of high-resolution mass spectra and tandem mass spectra from a collection of metabolite standards covering a range of compound classes including amino acids, nucleotides, carbohydrates, xenobiotics, lipids, and other classes. In untargeted analysis of metabolite standard mixtures, detection was achieved for 374 compounds and useful MS/MS spectra were obtained for 287 compounds, without individual optimization of ionization or fragmentation conditions. Metabolite detection was evaluated in the context of 31 metabolic pathways, and NAPA-LDI-MS was found to provide detection for 63% of investigated pathway metabolites. Individual, targeted analysis of the 20 common amino acids provided detection of 100% of the investigated compounds, demonstrating that improved coverage is possible through optimization and targeting of individual analytes or analyte classes. In direct analysis of aqueous and organic extracts from human serum samples, spectral features were assigned to a total of 108 small metabolites and lipids. Glucose and amino acids were quantitated within their physiological concentration ranges. The broad coverage demonstrated by this large-scale screening experiment opens the door for use of NAPA-LDI-MS in numerous metabolite analysis applications.

Leucine enkephalin--a mass spectrometry standard

The present article reviews the mass spectrometric fragmentation processes and fragmentation energetics of leucine enkephalin, a commonly used peptide, which has been studied in detail and has often been used as a standard or reference compound to test novel instrumentation, new methodologies, or to tune instruments. The main purpose of the article is to facilitate its use as a reference material; therefore, all available mass spectrometry-related information on leucine enkephalin has been critically reviewed and summarized. The fragmentation mechanism of leucine enkephalin is typical for a small peptide; but is understood far better than that of most other compounds. Because ion ratios in the MS/MS spectra indicate the degree of excitation, leucine enkephalin is often used as a thermometer molecule in electrospray or matrix-assisted laser desorption ionization (ESI or MALDI). Other parameters described for leucine enkephalin include collisional cross-section and energy transfer; proton affinity and gas-phase basicity; radiative cooling rate; and vibrational frequencies. The lowest-energy fragmentation channel of leucine enkephalin is the MH(+)  → b(4) process. All available data for this process have been re-evaluated. It was found that, although the published E(a) values were significantly different, the corresponding Gibbs free energy change showed good agreement (1.32 ± 0.07 eV) in various studies. Temperature- and energy-dependent rate constants were re-evaluated with an Arrhenius plot. The plot showed good linear correlation among all data (R(2)  = 0.97), spanned over a 9 orders of magnitude range in the rate constants and yielded 1.14 eV activation energy and 10(11.0)  sec(-1) pre-exponential factor. Accuracy (including random and systematic errors, with a 95% confidence interval) is ±0.05 eV and 10(±0.5)  sec(-1), respectively. The activation entropy at 470 K that corresponds to this reaction is -38.1 ± 9.6 J mol(-1)  K(-1). We believe that these re-evaluated values are by far the most accurate activation parameters available at present for a protonated peptide and can be considered as "consensus" values; results on other processes might be compared to this reference value.

Surface-induced dissociation of peptides and protein complexes in a quadrupole/time-of-flight mass spectrometer

A novel in-line surface-induced dissociation (SID) device was designed and implemented in a commercial QTOF instrument (Waters/Micromass QTOF II). This new setup allows efficient SID for a broad range of molecules. It also allows direct comparison with conventional collision-induced dissociation (CID) on the same instrument, taking advantage of the characteristics of QTOF instrumentation, including extended mass range, improved sensitivity, and better resolution compared with quadrupole analyzers and ion traps. Various peptides and a noncovalent protein complex have been electrosprayed and analyzed with the new SID setup. Here we present SID of leucine enkephalin, fibrinopeptide A, melittin, insulin chain-B, and a noncovalent protein complex from wheat, heat shock protein 16.9. The SID spectra were also compared to CID spectra. With the SID setup installed, ion transmission proved to be efficient. SID fragmentation patterns of peptides are, in general, similar to CID, with differences in the relative intensities of some peaks such as immonium ions, backbone cleavage b- versus y-type ions, and y- versus y-NH3 ions, suggesting enhanced accessibility to high-energy/secondary fragmentation channels with SID. Furthermore, these results demonstrate that the in-line SID setup is a valid substitute for CID, with potential advantages for activation of singly/multiply charged peptides and larger species such as noncovalent protein complexes.

Fragmentation characteristics of neuropeptides related to chromogranin B and proenkephalin B using fast atom bombardment and collision-induced dissociation

This study deals with the mass spectral characterization of selected neuropeptides related to chromogranin B and proenkephalin B precursor proteins using fast atom bombardment (FAB) ionization in combination with low- and high-energy collision-induced dissociation. Fragmentation pathways were investigated using linked scan and tandem mass spectrometric techniques. First-order FAB mass spectra and product ion spectra of [M+H]+ ions are discussed and analysed for structure-specific information. In the high-energy product ion spectra, abundant y and c ions are found to be indicative of the presence of proline and threonine residues, respectively. With regard to side chain specific ions, diagnostic d and w ions are found, which support the presence of leucine, glutamic acid and glutamine at specific positions in the amino acid sequence.

Collision energy effects on the collision-induced dissociation of multiply charged melittin

The fragmentation of the melittin 4+ ion has been studied over a range of collision energies from 28 eV to 12 keV in a four-sector mass spectrometer. Patterns of fragmentation and energy conversion were found to be analogous to those observed for singly charged peptides. High numbers of collisions were not required for activation at low energies.

Calibration Point for Electron Ionization MS / MS spectra measured with multiquadrupole mass spectrometers

A protocol for establishing standard instrument conditions for measurement of product ion MS/MS spectra from parent ions produced by electron ionization is presented. Within this protocol, the ion at m/z 231 (C5F9 (+)) from perfluorokerosene or perfluorotributylamine is selected as the parent ion and subjected to collision-induced dissociation. The relative intensities of product ions at m/z 69, 131, and 181 are monitored as a function of collision energy while keeping the target gas pressure constant within the range of 10(-4)-10(-6) torr (measured), or a beam attenuation of approximately 30-70%. The collision energy at which the ion intensities for product ions at m/z 69 and 181 are equal is defined as the calibration point at that collision gas pressure; the intensity of the ion at m/z 131 is very close to this value as well. Electron ionization MS/MS spectra taken at the calibration point using two different multiquadrupole instruments show good reproducibility for several test compounds. The high degree of similarity may aid in the establishment of a MS/MS spectral library.

Origin of the tailing signal on the low-energy side of the main beam in mass-analyzed ion kinetic energy spectra

The tailing signal on the low-energy side of the precursor ion signal observed during fast atom bombardment (FAB) mass-analyzed ion kinetic energy spectrometric (MIKES) analyses is due largely to ions of higher m/z value than the chosen precursor. The majority of these ions are independent, unfragmented species that emerge from the ion source with less than the full amount of kinetic energy predicted by the source potential. The tailing precursor ion signal observed under helium collision-activated decomposition conditions is too short to account for the protracted MIKES tail (as judged from mass-to-charge ratio-deconvoluted MIKES analyses performed on a BEqQ hybrid instrument), and a tailing precursor signal is not observed under unimolecular decomposition conditions. Measurements of the mass-to-charge ratios of the ionic species comprising the MIKES tail demonstrated that ions higher in mass-to-charge ratio than the chosen precursor are present throughout the tail, with the mass-to-charge ratio increasing as kinetic energy decreases. These ions possess the same momentum as the chosen precursor, and thus were formed prior to the magnetic field. The existence of intact, source-formed [M + H](+) ions with reduced kinetic energy was demonstrated through several types of tandem mass spectrometric experiments. These [M + H](+) ions with reduced kinetic energy do not appear to have undergone collisional deceleration, because they do not possess increased internal energy (as judged by observation of their fragmentation patterns). The kinetic energy profiles of unfragmented FAB-desorbed ions were determined and found to exhibit a tailing character similar in appearance to that of the MIKES tail. The population of ions emerging from the source under FAB conditions thus incorporates the characteristics necessary to account for the MIKES tail, namely, the presence of ions of a mass-to-charge ratio higher than the chosen precursor (due to matrix and other background ions), which possess reduced kinetic energy such that their momentum is identical to that of the selected precursor. These ions may arise via desolvation and declustering processes in the acceleration region of the ion source, or via FAB or chemical ionization processes in regions removed from the FAB target.

Mass spectrometric characterization of bovine chromaffin granule peptides related to chromogranin B

Peptides were extracted from the lysate of isolated bovine chromaffin granules. Following reversed-phase HPLC purification, the fractions were analyzed by FAB/MS. The presence of methionine-enkephalin and leucine-enkephalin was indicated by their chromatographic retention time and by the m/z value of their protonated molecules. As to five new peptides related to chromogranin B, prominent protonated molecules were observed at m/z 1746, 1446, 1333, 977 and 901. Trypsinolysis resulted in a common loss of a component with mass 545, pointing to a structural relationship and a common precursor molecule. The peptide showing a (M+H)+ ion at m/z 1746 could be identified as a novel, recently reported, neuropeptide derived from chromogranin B, whereas the other peptides with (M+H)+ ions at m/z 1446, 1333, 977 and 901 could be characterized as smaller fragments of this peptide. Peptidase-guided sequence analysis and MS/MS analysis provided sequence information.

Collisionally induced fragmentation of protonated oligoalanines and oligoglycines

In a hybrid instrument under minimal multiple-collision conditions, the collision-induced fragmentation of the [M + H]+ ions of tetraalanine and tetraglycine are dominated by the gamma 2 fragment, in distinction to the fragmentation of the [M + H]+ ions of hexa- and octaalanine and -glycine; these latter fragmentations are instead a distribution of b and y ions, and to a lesser extent a ions. This difference may be rationalized on the basis of control of the fragmentation by the most basic site in the peptide, which may be identified by taking internal hydrogen bonding into account. On increasing the collision energy from 10 to 150 eV, a, b and y ions of lower mass appear; and in several cases a peak due to a smaller b ion becomes the base peak. The ion distribution in the spectra of these protonated peptides serves as a baseline from which the effects of conformation on side-group rearrangements and other fragmentations may be explored.

Endothermic ion molecule reactions

Endothermic ion-molecule reactions in a tandem mass spectrometer have been used for a number of years for determining thermodynamic quantities, such as heats of formation and proton affinities, for gaseous ions. Recently, the reactive, endothermic collision has been exploited as an analytical technique for the structural analysis of peptides and other biomolecules. The technique is based upon the endothermic transfer of protons associated with amide bonds to ammonia. This reaction proceeds via a long-lived collision complex. When additional beam energy is supplied, other dissociation channels are opened up, leading to the production of sequence ions for the mass-selected, protonated analyte that are normally observed in high energy collision-induced dissociation spectra. The advantage, however, is that such spectra can be produced at very low beam energies. In this article, the rationale for developing this scheme, and its roots in previous ion-molecule studies, are explored.