Sequence-specific fragmentation generated by matrix-assisted laser desorption/ionization in a quadrupole ion trap/reflectron time-of-flight device

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

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.

Characterization of moenomycin antibiotic complex by multistage MALDI-IT/RTOF-MS and ESI-IT-MS

Flavomycin is a commercially available antimicrobial growth promoter and an authorized additive for feeding stuffs in the EU and in the USA. As most antibiotically active products biosynthesized by microorganisms, it contains not only a single active compound but is a complex mixture of structurally closely related substances. Multistage matrix-assisted laser desorption/ionization-ion trap/reflectron time-of-flight mass spectrometry (MALDI-IT/RTOF-MS) and liquid chromatography-electrospray ionization-ion trap-mass spectrometry (LC-ESI-IT-MS) were utilized for a detailed analysis of the constituents of the Flavomycin complex based on low-energy collision induced dissociation (CID). An optimal sample preparation for negative ion vacuum MALDI-MS for this compound class was developed. The MALDI-IT/RTOF-MS2 and -MS3 analysis starting with the precursor [M - H]- ions of these interesting phosphoglycolipids, named moenomycins, yielded a large variety of product ions that facilitated the structural characterization of this class of compounds. Based on the derived CID fragmentation pathway of the five known major constituents, namely moenomycin A, moenomycin A12, moenomycin C4, moenomycin C3. and moenomycin C1, four not yet described moenomycin-type constituents could be characterized. They were assigned as 4F-demethyl-6E-O-de-beta-D-glucopyranosyl-moenomycin A, 6B-N-de(2-hydroxy-5-oxo-1-cyclopenten-1-yl)-moenomycin A, 6B-hydroxy-6B-de[N-(2-hydroxy-5-oxo-1-cyclopenten-1-yl)amino]-moenomycin A, and 6C-hydroxy-moenomycin A. In addition, a moenomycin A carrying an oxygen in the moenocinol-group was found, which is most probably a chemical degradation product. These new compounds were verified by LC-ESI-IT-MS.

An optimized protocol for nano-LC-MALDI-TOF-MS coupling for the analysis of proteolytic digests of glycoproteins

Matrix-assissted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) analyses of complete proteolytic digests are often hampered by contaminations and the complexity of the sample. This results in suppression effects and the formation of adducts which are difficult to assign, thus leading to low scores in database searches. In particular, signals of post-translationally modified peptides such as glycopeptides are often of low intensity or completely suppressed. Online liquid chromatography electrospray ionization mass spectrometry (ESI-MS) can, in part, overcome this problem, but the analytes are completely consumed during the run. Coupling of nano-flow HPLC (nano-LC), microfractionation and MALDI-TOF-MS combines separation and high-sensitivity UV detection with the possibility of collecting fractionated peptides and preserving the sample for detailed mass spectrometric analyses. Here we report on an optimized protocol for nano-LC-MALDI-TOF-MS analyses of glycoproteins. This protocol improves spectral quality, resulting in better protein identification scores in database searches. Furthermore, post-translationally modified peptides could be detected with higher sensitivity by changing the experimental conditions, allowing assignment, localization and characterization of the respective carbohydrate substituents.

Photoinduced dissociation of electrospray-generated ions in an ion trap/time-of-flight mass spectrometer using a pulsed CO2 laser

An ion trap/time-of-flight (IT/TOF) mass spectrometer was developed and applied to infrared multiphoton dissociation (IRMPD) studies of ions generated by electrospray ionization. A pulsed 10.6- micro m laser beam from a CO(2) laser was used for excitation of trapped ions. Results from IRMPD of peptide ions show that this method provides useful information related to the amino acid sequence of analyzed peptides. Comparative studies show that IRMPD spectra are similar to those obtained using a 266-nm UV laser beam for excitation. However, in contrast to multiple-pulse excitation required at 266 nm, the energy of a single laser pulse in IRMPD is sufficient to induce dissociation of peptide ions. The laser power is practically an exclusive parameter that must be controlled in order to obtain IRMPD spectra that will provide the optimal structural information. It is further demonstrated that the IRMPD IT/TOF technique has the potential to probe the structural features of larger ions that cannot be readily fragmented by collision-induced dissociation (CID). A multiply charged ion of equine cytochrome c is successfully fragmented in a single laser pulse experiment. The IRMPD IT/TOF technique is also shown to be a promising tool for studying dissociation kinetics of peptide and protein ions. Unlike other methods that usually monitor the dissociation ion kinetics in a dissociation time frame of greater than milliseconds, the IT/TOF can promptly detect all product ions generated by the dissociation process, and thus monitor the dissociation process of peptides and proteins in a sub-millisecond time frame. This instrument allows us to determine the dissociation rates of cytochrome c ions using high-energy photoexcitation. It is found that the charge state of the protein ion has a significant effect on dissociation kinetics, which is consistent with that found under low-energy excitation experiments. It is shown that the increase in energy of a laser pulse from 130 to 180 mJ changes the dissociation rate constant for the +12 ion from k = 2.4 x 10(3) x s(-1) to k = 7.3 x 10(4) x s(-1). The +8 ion following excitation at 130 mJ dissociates slower with a rate constant of k = 2.6 x 10(2) x s(-1). The rate difference observed is attributed to conformational differences among the ions with different charge states.

Analysis of recombinant and modified proteins by capillary zone electrophoresis coupled with electrospray ionization tandem mass spectrometry

A method for rapid characterization of recombinant and modified proteins with known sequences is described. The analytical system consists of a capillary zone electrophoresis (CZE) instrument coupled to an electrospray ionization ion trap tandem mass spectrometer via a sheath-flow interface. Following the procedure consists of proteolytic fragmentation, CZE peptide separation, tandem mass spectrometry (MS-MS) analysis of separated peptides, sequence database search and monitoring of the specific peptides, C 125 S mutated interleukin 2 (S-125-IL2) and bovine beta-casein were characterized as a model of recombinant protein and naturally modified protein, respectively. A tryptic peptide mixture derived from the synthetic salmon calcitonin (s-CT) was also analyzed to test the performance of the system. Although a conventional sheath-flow interface with much higher flow-rate compared to the microspray interface and nanospray interface was used, the proteins were identified at the low picomole level.

A critical investigation of the effects of the radio frequency potential on the trapping of externally injected ions in ion trap mass spectrometry

The sensitivity of all ion trap mass spectrometry (ITMS) methods is dependent on the trapping efficiency of the instrument. For ITMS instruments utilizing external ion sources, such as laser desorption, trapping efficiency is known to depend on the phase and amplitude of the radio frequency (RF) potential applied to the ring electrode at the time of ion introduction. It is remarkable that, in a considerable body of literature, no consensus exists regarding the effects of these parameters on the efficacy of trapping externally generated ions. In this paper, a summary of the literature is presented in order to highlight significant discrepancies. New laser desorption ion trap mass spectrometry (LD-ITMS) data are also presented, from which conclusions are drawn in our effort to clarify some of the confusion. Copyright 1999 John Wiley & Sons, Ltd.

Mass spectrometry in protein studies from genome to function

The demands for highly sensitive and specific analytical techniques in biochemistry, molecular biology and biotechnology are met by new developments in mass spectrometry. Femto- to attomole sensitivity and mass accuracy in a low parts per million range can now be routinely obtained. Mass spectrometry, already accepted for studies of protein secondary modifications, must, in the future, be expected to be an important tool in protein studies on all levels, ranging from proteome analysis to studies of protein higher order structures and protein interaction.

Factors that influence the observed fast fragmentation of peptides in matrix-assisted laser desorption

Fragmentation processes that occur very early during matrix-assisted laser desorption ionization (MALDI) of peptides are examined by utilization of delayed pulsed ion extraction with a linear time-of-flight mass spectrometer. The oxidized B chain of bovine insulin (MW=3495. 95 u), which produces a wide range of fragment ions, is utilized as a probe to examine the effects of several experimental parameters on this process. Experimental evidence suggests that this MALDI process is not prompt fragmentation and involves metastable ion decay that is quite different from that which is observed with postsource decay experiments. This conclusion is based upon the significant differences observed in the fragmentation products produced by the two techniques. This metastable ion decay process also appears to be over within the minimum pulse delay period (320 ns) that is possible with the current pulsed ion extraction hardware. These two observations suggest that either different activation processes are involved in the two techniques or that the much different time frame of the methods influences the observed ion decay pathways. This fast MALDI metastable ion fragmentation also is shown to be influenced by both the MALDI matrix and the laser fluence.

Developments in matrix-assisted laser desorption/ionization peptide mass spectrometry

Most characteristics of matrix-assisted laser desorption/ionization (MALDI) are ideal for the analysis of biomolecules. New preparation techniques have dramatically increased mass accuracy and resolution, making MALDI a high-performance mass spectrometric technique for peptide mass analysis. Attempts to obtain amino acid sequence information by MALDI have been partially successful. The technique has been put to novel uses in protein primary structure characterization.

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)

Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been responsible for solving many problems in structural biology. Mass analysis is now used routinely to confirm proper expression and processing of proteins, and to locate and identify post-translational modifications. Innovative advances in instrumentation have led to higher mass resolution and mass accuracy. New sample preparation methods are likewise yielding higher sensitivity plus greater tolerance for buffer components that have in the past suppressed signals at higher concentrations. Advancements in the technique have also led to new or improved applications in many areas, including peptide sequencing and the identification of proteins by database searching with peptide masses. Instruments with lower cost, smaller size, and higher performance are making mass measurements available to an increasing number of laboratories. MALDI-MS is poised to continue to improve in performance and in its usefulness for current and new applications.