Determination of the relative energies of activation for the dissociation of aromatic versus aliphatic phosphopeptides by ESI-FTICR-MS and IRMPD

Multimodal Tandem Mass Spectrometry Techniques for the Analysis of Phosphopeptides

Collisionally activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), ultraviolet photodissociation (UVPD), electron capture dissociation and electron detachment dissociation (EDD) experiments were conducted on a set of phosphopeptides, in a Fourier transform ion cyclotron resonance mass spectrometer. The fragmentation patterns were compared and varied according to the fragmentation mechanisms and the composition of the peptides. CAD and IRMPD produced similar fragmentation profiles of the phosphopeptides, while UVPD produced a large number of complementary fragments. Electron-based dissociation techniques displayed lower fragmentation efficiencies, despite retaining the labile phosphate group, and drastically different fragmentation profiles. EDD produced complex spectra whose interpretation proved challenging.

Facile Determination of Phosphorylation Sites in Peptides Using Two-Dimensional Mass Spectrometry

Detection and characterization of phosphopeptides by infrared multiphoton dissociation two-dimensional mass spectrometry (IRMPD 2DMS) is shown to be particularly effective. A mixture of phosphopeptides was analyzed by 2DMS without any prior separation. 2DMS enables the data independent analysis of the mixture and the correlation of the fragments to their precursor ions. The extraction of neutral loss lines corresponding to the loss of phosphate under IRMPD fragmentation allows the selective identification of phosphopeptides. Resonance of the 10.6 μm infrared radiation with the vibrational modes of the phosphate functional group produced efficient absorption and high cleavage coverage of the phosphopeptides at much lower irradiation fluence than for nonphosphorylated peptides improving discrimination. Additionally, the localization of the phosphate group was determined.

Applications of Infrared Multiple Photon Dissociation (IRMPD) to the Detection of Posttranslational Modifications

Infrared multiple photon dissociation (IRMPD) spectroscopy allows for the derivation of the vibrational fingerprint of molecular ions under tandem mass spectrometry (MS/MS) conditions. It provides insight into the nature and localization of posttranslational modifications (PTMs) affecting single amino acids and peptides. IRMPD spectroscopy, which takes advantage of the high sensitivity and resolution of MS/MS, relies on a wavelength specific fragmentation process occurring on resonance with an IR active vibrational mode of the sampled species and is well suited to reveal the presence of a PTM and its impact in the molecular environment. IRMPD spectroscopy is clearly not a proteomics tool. It is rather a valuable source of information for fixed wavelength IRMPD exploited in dissociation protocols of peptides and proteins. Indeed, from the large variety of model PTM containing amino acids and peptides which have been characterized by IRMPD spectroscopy, specific signatures of PTMs such as phosphorylation or sulfonation can be derived. High throughput workflows relying on the selective fragmentation of modified peptides within a complex mixture have thus been proposed. Sequential fragmentations can be observed upon IR activation, which do not only give rise to rich fragmentation patterns but also overcome low mass cutoff limitations in ion trap mass analyzers. Laser-based vibrational spectroscopy of mass-selected ions holding various PTMs is an increasingly expanding field both in the variety of chemical issues coped with and in the technological advancements and implementations.

Benzoxazine Formation Mechanism Evaluation by Direct Observation of Reaction Intermediates

Benzoxazine formation is a fundamental step in the preparation of polybenzoxazine resins, and a detailed description of the mechanism governing the formation of benzoxazine and side products is vital for improving the properties and performance of these resins. Determination of the nature and properties of reaction intermediates is not trivial. Therefore, a Mannich-type condensation of aniline, formaldehyde, and phenol was evaluated as a potential method to form benzoxazine. Coupling positive mode electrospray ionization mass spectrometry (ESI(+)-MS) with infrared multiple photon dissociation (IRMPD) spectroscopy allowed unambiguous determination of an iminium-based mechanism and the direct observation of iminium intermediates. The benzoxazine formation mechanism was indirectly confirmed by the observation of side products that are relevant to the polymerization step, and directly confirmed by the identification of four distinct reaction intermediates that were completely characterized by IRMPD spectroscopy. The benzoxazine monomer was also shown to undergo isomerization under standard ESI-MS analysis conditions, suggesting the presence of a mixture of three isomers during their usual ESI-MS analysis.

Ultraviolet, Infrared, and High-Low Energy Photodissociation of Post-Translationally Modified Peptides

Mass spectrometry-based methods have made significant progress in characterizing post-translational modifications in peptides and proteins; however, certain aspects regarding fragmentation methods must still be improved. A good technique is expected to provide excellent sequence information, locate PTM sites, and retain the labile PTM groups. To address these issues, we investigate 10.6 μm IRMPD, 213 nm UVPD, and combined UV and IR photodissociation, known as HiLoPD (high-low photodissociation), for phospho-, sulfo-, and glyco-peptide cations. IRMPD shows excellent backbone fragmentation and produces equal numbers of N- and C-terminal ions. The results reveal that 213 nm UVPD and HiLoPD methods can provide diverse backbone fragmentation producing a/x, b/y, and c/z ions with excellent sequence coverage, locate PTM sites, and offer reasonable retention efficiency for phospho- and glyco-peptides. Excellent sequence coverage is achieved for sulfo-peptides and the position of the SO₃ group can be pinpointed; however, widespread SO₃ losses are detected irrespective of the methods used herein. Based on the overall performance achieved, we believe that 213 nm UVPD and HiLoPD can serve as alternative options to collision activation and electron transfer dissociations for phospho- and glyco-proteomics. Graphical Abstract ᅟ.

Targeted Annotation of S-Sulfonylated Peptides by Selective Infrared Multiphoton Dissociation Mass Spectrometry

Protein S-sulfinylation (R-SO₂^-) and S-sulfonylation (R-SO₃^-) are irreversible oxidative post-translational modifications of cysteine residues. Greater than 5% of cysteines are reported to occupy these higher oxidation states, which effectively inactivate the corresponding thiols and alter the electronic and physical properties of modified proteins. Such higher oxidation states are reached after excessive exposure to cellular oxidants, and accumulate across different disease states. Despite widespread and functionally relevant cysteine oxidation across the proteome, there are currently no robust methods to profile higher order cysteine oxidation. Traditional data-dependent liquid chromatography/tandem mass spectrometry (LC/MS/MS) methods generally miss low-occupancy modifications in complex analyses. Here, we present a data-independent acquisition (DIA) LC/MS-based approach, leveraging the high IR absorbance of sulfoxides at 10.6 μm, for selective dissociation and discovery of S-sulfonated peptides. Across peptide standards and protein digests, we demonstrate selective infrared multiphoton dissociation (IRMPD) of S-sulfonated peptides in the background of unmodified peptides. This selective DIA IRMPD LC/MS-based approach allows identification and annotation of S-sulfonated peptides across complex mixtures while providing sufficient sequence information to localize the modification site.

Phosphoproteomics with Activated Ion Electron Transfer Dissociation

The ability to localize phosphosites to specific amino acid residues is crucial to translating phosphoproteomic data into biological meaningful contexts. In a companion manuscript ( Anal. Chem. 2017 , DOI: 10.1021/acs.analchem.7b00213 ), we described a new implementation of activated ion electron transfer dissociation (AI-ETD) on a quadrupole-Orbitrap-linear ion trap hybrid MS system (Orbitrap Fusion Lumos), which greatly improved peptide fragmentation and identification over ETD and other supplemental activation methods. Here we present the performance of AI-ETD for identifying and localizing sites of phosphorylation in both phosphopeptides and intact phosphoproteins. Using 90 min analyses we show that AI-ETD can identify 24,503 localized phosphopeptide spectral matches enriched from mouse brain lysates, which more than triples identifications from standard ETD experiments and outperforms ETcaD and EThcD as well. AI-ETD achieves these gains through improved quality of fragmentation and MS/MS success rates for all precursor charge states, especially for doubly protonated species. We also evaluate the degree to which phosphate neutral loss occurs from phosphopeptide product ions due to the infrared photoactivation of AI-ETD and show that modifying phosphoRS (a phosphosite localization algorithm) to include phosphate neutral losses can significantly improve localization in AI-ETD spectra. Finally, we demonstrate the utility of AI-ETD in localizing phosphosites in α-casein, an ∼23.5 kDa phosphoprotein that showed eight of nine known phosphorylation sites occupied upon intact mass analysis. AI-ETD provided the greatest sequence coverage for all five charge states investigated and was the only fragmentation method to localize all eight phosphosites for each precursor. Overall, this work highlights the analytical value AI-ETD can bring to both bottom-up and top-down phosphoproteomics.

Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides

In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types (a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.

Radical-directed dissociation of peptides and proteins by infrared multiphoton dissociation and sustained off-resonance irradiation collision-induced dissociation with Fourier transform ion cyclotron resonance mass spectrometry

RATIONALE

Recent experiments utilizing photodissociation in linear ion traps have enabled significant development of Radical-Directed Dissociation (RDD) for the examination of peptides and proteins. The increased mass accuracy and resolution available in Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) should enable further progress in this area. Preliminary experiments with photoactivated radicals are reported herein.

METHODS

A 266 nm Nd:YAG laser is coupled to a FTICR or linear ion trap mass spectrometer. Radical peptides and proteins are generated by ultraviolet photodissociation (PD) and further activated by collisions or infrared photons.

RESULTS

A 266 nm UV laser and an IR laser can be simultaneously coupled to a 15 Tesla FTICR mass spectrometer. The ultra-low-pressure environment in FTICR-MS makes collisional cooling less competitive, and thus more secondary fragments are generated by UVPD than in linear ion traps. Activation by sustained off-resonance irradiation collision-induced dissociation (SORI-CID) or infrared multiphoton dissociation (IRMPD) also yields additional secondary fragmentation relative to CID in an ion trap. Accurate identification of RDD fragments is possible in FTICR-MS.

CONCLUSIONS

Relative to linear ion trap instruments, PD experiments in FTICR-MS are more difficult to execute due to poor ion cloud overlap and the low pressure environment. However, the results can be more easily interpreted due to the increased resolution and mass accuracy.

Photodissociation mass spectrometry: new tools for characterization of biological molecules

Photodissociation mass spectrometry combines the ability to activate and fragment ions using photons with the sensitive detection of the resulting product ions by mass spectrometry. This combination affords a versatile tool for characterization of biological molecules. The scope and breadth of photodissociation mass spectrometry have increased substantially over the past decade as new research groups have entered the field and developed a number of innovative applications that illustrate the ability of photodissociation to produce rich fragmentation patterns, to cleave bonds selectively, and to target specific molecules based on incorporation of chromophores. This review focuses on many of the key developments in photodissociation mass spectrometry over the past decade with a particular emphasis on its applications to biological molecules.

Structures of biomolecular ions in the gas phase probed by infrared light sources

Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.

Tandem mass spectrometry strategies for phosphoproteome analysis

Protein phosphorylation is involved in nearly all essential biochemical pathways and the deregulation of phosphorylation events has been associated with the onset of numerous diseases. A multitude of tandem mass spectrometry (MS/MS) and multistage MS/MS (i.e., MS(n) ) strategies have been developed in recent years and have been applied toward comprehensive phosphoproteomic analysis, based on the interrogation of proteolytically derived phosphopeptides. However, the utility of each of these MS/MS and MS(n) approaches for phosphopeptide identification and characterization, including phosphorylation site localization, is critically dependant on the properties of the precursor ion (e.g., polarity and charge state), the specific ion activation method that is employed, and the underlying gas-phase ion chemistries, mechanisms and other factors that influence the gas-phase fragmentation behavior of phosphopeptide ions. This review therefore provides an overview of recent studies aimed at developing an improved understanding of these issues, and highlights the advantages and limitations of both established (e.g., CID) and newly maturing (e.g., ECD, ETD, photodissociation, etc.) yet complementary, ion activation techniques. This understanding is expected to facilitate the continued refinement of existing MS/MS strategies, and the development of novel MS/MS techniques for phosphopeptide analysis, with great promise in providing new insights into the role of protein phosphorylation on normal biological function, and in the onset and progression of disease. © 2011 Wiley Periodicals, Inc., Mass Spec Rev 30:600-625, 2011.

Shedding light on the frontier of photodissociation

The development of new ion activation/dissociation methods is motivated by the need for more versatile ways to characterize structures of ions, especially in the growing arena of biological mass spectrometry in which better tools for determining sequences, modifications, interactions, and conformations of biopolymers are essential. Although most agree that collision-induced dissociation (CID) remains the gold standard for ion activation/dissociation, recent inroads in electron- and photon-based activation methods have cemented their role as outstanding alternatives. This article will focus on the impact of photodissociation, including its strengths and drawbacks as an analytical tool, and its potential for further development in the next decade. Moreover, the discussion will emphasize photodissociation in quadrupole ion traps, because that platform has been used for one of the greatest arrays of new applications over the past decade.

Analytical strategies in mass spectrometry-based phosphoproteomics

Phosphoproteomics, the systematic study of protein phosphorylation events and cell signaling networks in cells and tissues, is a rapidly evolving branch of functional proteomics. Current phosphoproteomics research provides a large toolbox of strategies and protocols that may assist researchers to reveal key regulatory events and phosphorylation-mediated processes in the cell and in whole organisms. We present an overview of sensitive and robust analytical methods for phosphopeptide analysis, including calcium phosphate precipitation and affinity enrichment methods such as IMAC and TiO(2). We then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large-scale experiments for studies of phosphorylation-mediated protein regulation.

Top-down protein fragmentation by infrared multiphoton dissociation in a dual pressure linear ion trap

Infrared multiphoton dissociation (IRMPD) was implemented in a novel dual pressure linear ion trap for rapid top-down proteomics. The high pressure cell provided improved trapping and isolation efficiencies while the isotopic profiles of 10+ charged ions could be resolved by mass analysis in the low pressure cell that enabled effective top down protein identification. Striking differences between IRMPD in the low pressure cell and CID in the high pressure cell were observed for proteins ranging from 8.6 to 29 kDa. Because of secondary dissociation, IRMPD yielded product ions in significantly lower charge states as compared to CID, thus facilitating more accurate mass identification and streamlining product ion assignment. This outcome was especially useful for database searching of larger proteins (approximately 29 kDa) as IRMPD substantially improved protein identification and scoring confidence. Also, IRMPD showed an increased selectivity toward backbone cleavages N-terminal to proline and C-terminal to acidic residues (especially for the lowest charge states), which could be useful for a priori spectral predictions and enhanced database searching for protein identification.

HPLC/MS/MS-based approaches for detection and quantification of eicosanoids

Eicosanoids are oxygenated, endogenous, unsaturated fatty acids derived from arachidonic acid. Detection and quantification of these compounds are of great interest because they play important roles in a number of significant diseases, including asthma, chronic obstructive pulmonary disease (COPD), cardiovascular disease, and cancer. Because the endogenous levels of eicosanoids are quite low, sensitive and specific analytical methods are required to reliably quantify these compounds. High-performance liquid chromatography mass spectrometry (HPLC/MS) has emerged as one of the main techniques used in eicosanoid profiling. Herein, we describe the main LC/MS techniques and principles as well as their application in eicosanoid analysis. In addition, a protocol is given for extracting eicosanoids from biological samples, using bronchoalveolar lavage fluid (BALF) as an example. The method and instrument optimization procedures are presented, followed by the analysis of eicosanoid standards using reverse phase HPLC interfaced with an ion trap mass spectrometer (LC/MS/MS). This protocol is intended to provide a broad description of the field for readers looking for an introduction to the methodologies involved in eicosanoid quantification.

Ultraviolet photodissociation at 266 nm of phosphorylated peptide cations

Ultraviolet (UV) photodissociation (PD) experiments using 266 nm light were performed for a series of phosphopeptide cations in a Fourier transform mass spectrometer. The objective of the experiments was to determine whether 266 nm UV irradiation on the phosphopeptide cations would induce unique peptide backbone dissociation. In addition, the general behavior of the phosphate loss (-80 or -98 Da) was monitored, particularly for those phosphopeptides with a phosphotyrosine residue that itself is a UV chromophore. For phosphopeptides with a UV chromophore, their photodissociation behavior was very similar to that of low-energy sustained off-resonance irradiation collisionally activated dissociation (SORI-CAD), with a few exceptions. For example, b- and y-type peptide backbone fragments were prevalent, and their dephosphorylation behavior was consistent with that of the SORI-CAD results. For phosphoserine peptides, the loss of a phosphate group was always observed. On the other hand, for phosphotyrosine peptides, the phosphate loss was found to be dependent on the presence of a basic amino group in the sequence and the charge state of the precursor ions, in agreement with the CAD results in the literature. However, hydrogen atom loss or aromatic side chain loss, which is known to be the excited state specific fragmentation pathway, was rarely observed in our 266 nm UV PD experiments, in contrast to the previous UV PD literature (particularly at 220 nm). The mechanism for these observations is described in terms of dominant internal conversion followed by intramolecular vibrational energy redistribution (IVR).

Improved infrared multiphoton dissociation of peptides through N-terminal phosphonite derivatization

A strategy for improving the sequencing of peptides by infrared multiphoton dissociation (IRMPD) in a linear ion trap mass spectrometer is described. We have developed an N-terminal derivatization reagent, 4-methylphosphonophenylisothiocyanate (PPITC), which allows the attachment of an IR-chromogenic phosphonite group to the N-terminus of peptides, thus enhancing their IRMPD efficiencies. After the facile derivatization process, the PPITC-modified peptides require shorter irradiation times for efficient IRMPD and yield extensive series of y ions, including those of low m/z that are not detected upon traditional CID. The resulting IRMPD mass spectra afford more complete sequence coverage for both model peptides and tryptic peptides from cytochrome c. We compare the effectiveness of this derivatization/IRMPD approach to that of a common N-terminal sulfonation reaction that utilizes 4-sulfophenylisothiocyanate (SPITC) in conjunction with CID and IRMPD.

Comparison of infrared multiphoton dissociation and collision-induced dissociation of supercharged peptides in ion traps

The number and types of diagnostic ions obtained by infrared multiphoton dissociation (IRMPD) and collision-induced dissociation (CID) were evaluated for supercharged peptide ions created by electrospray ionization of solutions spiked with m-nitrobenzyl alcohol. IRMPD of supercharged peptide ions increased the sequence coverage compared with that obtained by CID for all charge states investigated. The number of diagnostic ions increased with the charge state for IRMPD; however, this trend was not consistent for CID because the supercharged ions did not always yield the greatest number of diagnostic ions. Significantly different fragmentation pathways were observed for the different charge states upon CID or IRMPD with the latter yielding far more immonium ions and often fewer uninformative ammonia, water, and phosphoric acid neutral losses. Pulsed-Q dissociation resulted in an increase in the number of internal product ions, a decrease in sequence-informative ions, and reduced overall ion abundances. The enhanced sequence coverage afforded by IRMPD of supercharged ions was demonstrated for a variety of model peptides, as well as for a tryptic digest of cytochrome c.

Atmospheric pressure thermal dissociation of phospho- and sulfopeptides

Several phospho- and sulfopeptides were subjected to atmospheric pressure thermal dissociation (APTD), which was effected by passing peptide ions generated by electrosonic spray ionization (ESSI) through a heated coiled metal tube. Sequence informative fragment ions including a-, b-, c-, and y-types of ions were observed with increased relative intensities under APTD compared with collision-induced dissociation (CID), performed inside the ion trap. A certain degree of preservation of phosphate and sulfate ester moieties was observed for some fragments ions under APTD. The neutral fragments generated outside the mass spectrometer were further analyzed via on-line corona discharge to provide rich and complementary sequence information to that provided by the fragment ions directly obtained from APTD, although complete losses of the modification groups were noted. Improved primary sequence information for phospho- and sulfopeptides was typically obtained by analyzing both ionic and neutral fragments from APTD compared with fragment ions from CID alone. Localization of the modification sites of phospho- and sulfopeptides was achieved by combining the structural information acquired from APTD and CID.

Chromogenic cross-linker for the characterization of protein structure by infrared multiphoton dissociation mass spectrometry

We have developed a new IR chromogenic cross-linker (IRCX) to aid in rapidly distinguishing cross-linked peptides from unmodified species in complex mixtures. By incorporating a phosphate functional group into the cross-linker, one can take advantage of its unique IR absorption properties, affording selective infrared multiphoton dissociation (IRMPD) of the cross-linked peptides. In a mock mixture of unmodified peptides and IRCX-cross-linked peptides (intramolecularly and intermolecularly cross-linked), only the peptides containing the IRCX modification were shown to dissociate upon exposure to 50 ms of 10.6-microm radiation. LC-IRMPD-MS proved to be an effective method to distinguish the cross-linked peptides in a tryptic digest of IRCX-cross-linked ubiquitin. A total of four intermolecular cross-links and two dead-end modifications were identified using IRCX and LC-IRMPD-MS. IRMPD of these cross-linked peptides resulted in secondary dissociation of all primary fragment ions containing the chromophore, producing a series of unmodified b- or y-type ions that allowed the cross-linked peptides to be sequenced without the need for collision-induced dissociation.

Structural characterization of monohydroxyeicosatetraenoic acids and dihydroxy- and trihydroxyeicosatrienoic acids by ESI-FTICR

The fragmentation characteristics of monohydroxyeicosatetraenoic acids and dihydroxy- and trihydroxyeicosatrienoic acids were investigated by electrospray ionization Fourier transform ion cyclotron resonance (FTICR) mass spectrometry using sustained off-resonance irradiation collision-induced dissociation (SORI-CID) and infrared multiphoton dissociation (IRMPD). The fragmentation patterns of these compounds were associated with the number and positions of the hydroxyl substituents. The fragmentation is more complicated with increasing number of the hydroxyl groups of the compounds. In general, the major carbon-carbon cleavage of [M - H](-) ions occurred at the alpha-position to the hydroxyl group, and the carbon-carbon cleavage occurred when there was a double-bond at the beta-position to the hydroxyl group. SORI-CID and IRMPD produced some common fragmentation patterns; however, each technique provided some unique patterns that are useful for structural identification of these compounds. This study demonstrated the application of FTICR via the identification of regioisomers of trihydroxyeicosatrienoic acids in rabbit aorta samples.

A microPLC-based approach for determining kinase-substrate specificity

Phosphorylation is central to signal transduction in living organisms. The specificity of phosphorylation ensures signaling fidelity. Understanding substrate specificity is essential for novel assay development in drug discovery. In this study, we have developed an innovative approach to study protein kinase and its substrate specificity. Using 24 micro parallel liquid chromatography, we studied the reaction kinetics for two different peptide substrates commonly associated with protein kinase A (PKA): Kemptide (Leu-Arg-Arg-Ala-Ser-Leu-Glu) and CREBtide (Lys-Arg-Arg-Glu-Ile-Leu-Ser-Arg-Arg-Pro-Ser-Tyr-Arg). The phosphorylation of each substrate was monitored in real time, and the kinetic parameters (V(max), K(m), k(cat), and k(cat) K(m)) were determined for a variety of initial conditions. The results from several kinetic experiments indicated that Kemptide had higher V(max) and k(cat) values compared to CREBtide under the same assay conditions. However, both substrates had a similar k cat)/K(m) value, suggesting that both substrates have similar specificity constants for PKA. We further analyzed the reaction kinetics of ATP for both PKA/substrate complexes. Interestingly, we found that there was a fivefold difference in the specificity constants for ATP affinity to the two complexes, suggesting that even though the sequence differences between the two substrates do not affect their independent interactions with PKA, the differences do have a secondary effect on each enzyme's interaction with ATP and significantly alter the ATP consumption and thus phosphorylation. This novel approach has a broad application for studying enzyme functions and enzyme/substrate specificity.

Infrared multiphoton dissociation and electron-induced dissociation as alternative MS/MS strategies for metabolite identification

A major challenge encountered in mass spectrometric metabolite analysis is the identification and structural characterization of metabolites. Fourier transform ion cyclotron resonance mass spectrometry is a valuable technique for metabolite structural determination because it provides accurate masses and allows for multiple MS/MS fragmentation strategies, including infrared multiphoton dissociation (IRMPD) and electron-induced dissociation (EID). Collision activated dissociation (CAD) is currently the most commonly used MS/MS technique for metabolite structural characterization. In contrast, IRMPD and EID have had very limited, if any, application for metabolite characterization. Here, we explore IRMPD and EID of phosphate-containing metabolites and compare the resulting fragmentation patterns to those of CAD. Our results show that CAD, IRMPD, and EID provide complementary structural information for phosphate-containing metabolites. Overall, CAD provided the most extensive fragmentation for smaller (<600 Da) phosphate-containing metabolites; however, IRMPD generated more extensive fragmentation for larger (>600 Da) phosphate-containing metabolites, particularly for species containing increased numbers of phosphate groups. EID generally provided complementary fragmentation to CAD and showed extensive fragmentation with relatively evenly abundant product ions, regardless of metabolite size. However, EID fragmentation efficiency is lower than those of CAD and IRMPD.

Differentiation of phosphorylated and unphosphorylated peptides by high-performance liquid chromatography-electrospray ionization-infrared multiphoton dissociation in a quadrupole ion trap

Infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap coupled to high-performance liquid chromatography allows the selective dissociation of phosphorylated peptides in mixtures following chromatographic separation. This method is shown to be effective for differentiation of phosphorylated peptides from unphosphorylated ones; only the abundances of the phosphorylated species are appreciably decreased following exposure to 125 ms of 10.6-microm radiation. This LC-IRMPD-MS strategy is demonstrated for a mock mixture of peptides and a tryptic digest of alphaS1-casein. The ability of this technique to differentiate peptides based on phosphorylation state is unaffected by whether the peptides are protonated or sodium-cationized.

Quantitation of Trace Metals in Liquid Samples by Dried-Droplet Laser Ablation Inductively Coupled Plasma Mass Spectrometry

A new, discrete sample introduction approach based on laser ablation (LA) is described for the quantitation of several trace metals in aqueous samples by ICPMS. Dried microdroplets of sample, previously mixed with a sodium acetate matrix, were quantitatively ablated from a polystyrene substrate. Calibration via the method of standard additions or isotope dilution provided accurate results for Ni, Cd, and Pb in drinking water and Se in a yeast extract. Compared to conventional solution nebulization, LA sample introduction provided a 2-7-fold enhancement in absolute sensitivity and transport efficiency of 2-14% for the elements examined. Estimated detection limits are 1-7-fold poorer for the dried-droplet LA technique, primarily a result of degraded precision arising from counting statistics limitations for discrete sample introduction. On the basis of the several-second half-width of the resulting transient signals, sample throughput can be in the range of 250 samples per hour. Additionally, integration of the transient signal should eliminate contributions to elemental fractionation from the LA step. Dried-droplet LA-ICPMS offers several advantages over its counterpart, ETV-ICPMS, with respect to background intensity, throughput, and ease of desorption.

Infrared multiphoton dissociation (IRMPD) and collisionally activated dissociation of peptides in a quadrupole ion trap with selective IRMPD of phosphopeptides

Dissociation of protonated peptides via infrared multiphoton dissociation (IRMPD) provides more extensive sequence information than is obtained with collisionally activated dissociation (CAD) in a quadrupole ion trap due to the lack of the CAD low m/z cutoff and the ability to form secondary and higher order fragments with the non-resonant photoactivation technique. In addition, IRMPD is shown to be useful for the selective dissociation of phosphopeptides over those which are not phosphorylated because the greater photon absorption efficiency of the phosphorylated peptides leads to their more rapid dissociation. Finally, the selectivity of the IRMPD technique for phosphorylated species in complex mixtures is confirmed with the analysis of a mock peptide mixture and a tryptic digest of alpha-casein.