Fragmentation of phosphopeptides by atmospheric pressure MALDI and ESI/Ion trap mass spectrometry

Nanoparticle-based applications by atmospheric pressure matrix assisted desorption/ionization mass spectrometry

Recently, the development of atmospheric pressure matrix assisted desorption/ionization mass spectrometry (AP MALDI MS) has made contributions not only to biomolecule analysis but also to spatial distribution. This has positioned AP MALDI as a powerful tool in multiple domains, thanks to its comprehensive advantages compared to conventional MALDI MS. These developments have addressed challenges associated with previous AP MALDI analysis systems, such as optimization of apparatus settings, synthesis of novel matrices, preconcentration and isolation strategies before analysis. Herein, applications in different fields using AP MALDI MS were described, including peptide and protein analysis, metabolite analysis, pharmaceutical analysis, and mass spectrometry imaging.

Free Radical-Initiated Peptide Sequencing Mass Spectrometry for Phosphopeptide Post-translational Modification Analysis

Free radical-initiated peptide sequencing mass spectrometry (FRIPS MS) was employed to analyze a number of representative singly or doubly protonated phosphopeptides (phosphoserine and phosphotyrosine peptides) in positive ion mode. In contrast to collision-activated dissociation (CAD) results, a loss of a phosphate group occurred to a limited degree for both phosphoserine and phosphotyrosine peptides, and thus, localization of a phosphorylated site was readily achieved. Considering that FRIPS MS supplies a substantial amount of collisional energy to peptides, this result was quite unexpected because a labile phosphate group was conserved. Analysis of the resulting peptide fragments revealed the extensive production of a-, c-, x-, and z-type fragments (with some minor b- and y-type fragments), suggesting that radical-driven peptide fragmentation was the primary mechanism involved in the FRIPS MS of phosphopeptides. Results of this study clearly indicate that FRIPS MS is a promising tool for the characterization of post-translational modifications such as phosphorylation. Graphical Abstract.

Detection of a phosphorylated glycine-serine linker in an IgG-based fusion protein

Molecular mass determination by electrospray ionization mass spectrometry of a recombinant IgG-based fusion protein (mAb1-F) produced in human embryonic kidney (HEK) cells demonstrated the presence of a dominant +79 Da product variant. Using LC-MS tryptic peptide mapping analysis and collision-induced dissociation (CID) and electron-transfer/higher-energy collision dissociation fragmentations, the modification was localized to the C-terminal serine residue of a glycine-serine linker [(G₄S)₂] of a fused heavy chain containing in total 2 (G₄S)₂-linkers. The modification was identified as a phosphorylation (+79.97 Da) by the presence of a 98 Da neutral loss reaction with CID, by spiking a synthetic phosphoserine peptide, and by dephosphorylation with alkaline phosphatase. A thermolysin digest combined with higher-energy collision dissociation (HCD) positioned the phosphoserine to one specific glycine-serine linker of the fused heavy chain, and the relative level of phosphorylated linker was determined to be 11.3% and 0.4% by LC-MS when the fusion protein was transiently expressed in HEK or in stably transformed Chinese hamster ovary cells, respectively. This observation demonstrates that fusions with glycine-serine linker sequences should be carefully evaluated during drug development to prevent the introduction of a phosphorylation site in therapeutic fusion proteins.

A targeted proteomics approach to the quantitative analysis of ERK/Bcl-2-mediated anti-apoptosis and multi-drug resistance in breast cancer

Apoptosis suppression caused by overexpression of anti-apoptotic proteins is a central factor to the acquisition of multi-drug resistance (MDR) in breast cancer. As a highly conserved anti-apoptotic protein, Bcl-2 can initiate an anti-apoptosis response via an ERK1/2-mediated pathway. However, the details therein are still far from completely understood and a quantitative description of the associated proteins in the biological context may provide more insights into this process. Following our previous attempts in the quantitative analysis of MDR mechanisms, liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics was continually employed here to describe ERK/Bcl-2-mediated anti-apoptosis. A targeted proteomics assay was developed and validated first for the simultaneous quantification of ERK1/2 and Bcl-2. In particular, ERK isoforms (i.e., ERK1 and ERK2) and their differential phosphorylated forms including isobaric ones were distinguished. Using this assay, differential protein levels and site-specific phosphorylation stoichiometry were observed in parental drug-sensitive MCF-7/WT cancer cells and drug-resistant MCF-7/ADR cancer cells and breast tissue samples from two groups of patients who were either suspected or diagnosed to have drug resistance. In addition, quantitative analysis of the time course of both ERK1/2 and Bcl-2 in doxorubicin (DOX)-treated MCF-7/WT cells confirmed these findings. Overall, we propose that targeted proteomics can be used generally to resolve more complex cellular events.

Mass spectrometric real-time monitoring of an enzymatic phosphorylation assay using internal standards and data-handling freeware

RATIONALE

Continuous-flow reaction detection systems (monitoring enzymatic reactions with mass spectrometry (MS)) lack quantitative values so far. Therefore, two independent internal standards (IS) are implemented in a way that the online system stability can be observed, quantitative conversion values for substrate and product can be obtained and they can be used as mass calibration standards for high MS accuracy.

METHODS

An application previously developed for the MS detection of peptide phosphorylation by cAMP-dependent protein kinase A (PKA) (De Boer et al., Anal. Bioanal. Chem. 2005, 381, 647-655) was transferred to a continuous-flow reaction detection system. This enzymatic reaction, involving enzyme activation as well as the transfer of a phosphate group from ATP to a peptide substrate, was used to prove the compatibility of a quantitative enzymatic assay in a continuous-flow real-time system (connected to MS).

RESULTS

Moreover (using internal standards), the critical parameter reaction temperature (including solution density variations depending on temperature) was studied in the continuous-flow mixing system. Furthermore, two substrates (malantide and kemptide), two enzyme types (catalytic subunit of PKA and complete PKA) and one inhibitor were tested to determine system robustness and long-term availability. Even spraying solutions that contained significant amount of MS contaminants (e.g. the polluted catalytic subunit) resulted in quantifiable MS signal intensities. Subsequent recalculations using the internal standards led to results representing the power of this application.

CONCLUSIONS

The presented methodology and the data evaluation with available Achroma freeware enable the direct coupling of biochemical assays with quantitative MS detection. Monitoring changes such as temperature, reaction time, inhibition, or compound concentrations can be observed quantitatively and thus enzymatic activity can be calculated.

An investigation of heat shock protein 27 and P-glycoprotein mediated multi-drug resistance in breast cancer using liquid chromatography-tandem mass spectrometry-based targeted proteomics

One missing puzzle piece to study heat shock protein 27 (HSP27) in P-glycoprotein (P-gp) mediated multi-drug resistance (MDR) was the amount of HSP27 and the extent of its phosphorylation in the biological context. Liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based targeted proteomics allows researchers to monitor associated proteins and their modification simultaneously and quantitatively. In this study, a targeted proteomics assay was first developed and validated for the quantification of HSP27 and its phosphorylated forms. Using this assay, the level of HSP27 was determined in non-tumoral cells MCF-10A, parental drug-sensitive cancer cells MCF-7/WT and drug-resistant cancer cells MCF-7/ADR. A decrease of HSP27 expression was observed in P-gp overexpressed MCF-7/ADR cells. A quantitative time-course analysis of both HSP27 and P-gp in doxorubicin (DOX)-treated MCF-7/WT cells also implied that HSP27 may participate in the P-gp modulation. Furthermore, stoichiometry of site-specific HSP27 phosphorylation indicated that DOX treatment rapidly induced the HSP27 phosphorylation at Ser82. Moreover, conventional analytical methods were also performed for a comparison.

BIOLOGICAL SIGNIFICANCE

LC/MS/MS-based targeted proteomics turns out to be a promising quantification approach for the study of proteins in the preclinical and clinical environment. Unfortunately, rare studies applied this technology to detect multiple associated proteins or protein modification in one experiment. This study demonstrated the potential of LC/MS/MS-based targeted proteomics to understand the cell events in a more accurate context of biological system. By the quantitative time-course analysis of HSP27 and its phosphorylated forms at sites of Ser15 and Ser82, the possible role of HSP27 in P-gp mediated MDR was suggested. Further development of targeted proteomics in future may provide more insight into signal transduction pathways upon perturbation of a protein network or changes to a panel of proposed biomarkers in a given disease state.

A novel Aurora-A-mediated phosphorylation of p53 inhibits its interaction with MDM2

PURPOSE

Crosstalk between Aurora-A kinase and p53 has been proposed. While the genetic amplification of Aurora-A has been observed in many human cancers, how p53 is regulated by Aurora-A remains ambiguous. In this study, Aurora-A-mediated phosphorylation of p53 was analyzed by mass spectrometry in order to identify a new phosphorylation site. Subsequently, the functional consequences of such phosphorylation were examined.

EXPERIMENTAL DESIGN

In vitro phosphorylation of p53 by Aurora-A was performed and the phosphorylated protein was then digested with trypsin and enriched for phosphopeptides by immobilized metal affinity chromatography. Subsequently, a combination of β-elimination and Michael addition was applied to the phosphopeptides in order to facilitate the identification of phosphorylation sites by MS. The functional consequences of the novel phosphorylation of p53 on the protein-protein interactions, protein stability and transactivation activity were then examined using co-immunoprecipitation, Western blotting and reporter assays.

RESULTS

Ser-106 of p53 was identified as a novel site phosphorylated by Aurora-A. A serine-to-alanine mutation at this site was found to attenuate Aurora-A-mediated phosphorylation in vitro. In addition, phosphate-sensitive Phos-tag SDS-PAGE was used to confirm that the Ser-106 of p53 is in vivo phosphorylated by Aurora-A. Finally, co-immunoprecipitation studies suggested that Ser-106 phosphorylation of p53 decreases its interaction with MDM2 and prolongs the half-life of p53.

CONCLUSIONS

The inhibition of the interaction between p53 and MDM2 by a novel Aurora-A-mediated p53 phosphorylation was identified in this study and this provides important information for further investigations into the interaction between p53 and Aurora-A in terms of cancer biology.

Comparison of CID, ETD and metastable atom-activated dissociation (MAD) of doubly and triply charged phosphorylated tau peptides

The fragmentation behavior of the 2+ and 3+ charge states of eleven different phosphorylated tau peptides was studied using collision-induced dissociation (CID), electron transfer dissociation (ETD) and metastable atom-activated dissociation (MAD). The synthetic peptides studied contain up to two known phosphorylation sites on serine or threonine residues, at least two basic residues, and between four and eight potential sites of phosphorylation. CID produced mainly b-/y-type ions with abundant neutral losses of the phosphorylation modification. ETD produced c-/z-type ions in highest abundance but also showed numerous y-type ions at a frequency about 50% that of the z-type ions. The major peaks observed in the ETD spectra correspond to the charge-reduced product ions and small neutral losses from the charge-reduced peaks. ETD of the 2+ charge state of each peptide generally produced fewer backbone cleavages than the 3+ charge state, consistent with previous reports. Regardless of charge state, MAD achieved more extensive backbone cleavage than CID or ETD, while retaining the modification(s) in most cases. In all but one case, unambiguous modification site determination was achieved with MAD. MAD produced 15-20% better sequence coverage than CID and ETD for both the 2+ and 3+ charge states and very different fragmentation products indicating that the mechanism of fragmentation in MAD is unique and complementary to CID and ETD.

Identification of proteins and phosphoproteins using pulsed Q collision induced dissociation (PQD)

Pulsed Q collision induced dissociation (PQD) was developed to facilitate detection of low-mass reporter ions from labeling reagents (e.g., iTRΑQ) in peptide quantification using an LTQ mass spectrometer (MS). Despite the large number of linear ion traps worldwide, the use and optimization of PQD for protein identification have been limited, in part due to less effective ion fragmentation relative to the collision induced dissociation (CID). PQD expands the m/z coverage of fragment ions to the lower m/z range by circumventing the typical low mass cut-off of an ion trap MS. Since database searching relies on the matching between theoretical and observed spectra, it is not clear how ion intensity and peak number might affect the outcomes of a database search. In this report, we systematically evaluated the attributes of PQD mass spectra, performed intensity optimization, and assessed the benefits of using PQD on the identification of peptides and phosphopeptides from an LTQ. Based on head-to-head comparisons between CID (higher intensity) and PQD (better m/z coverage), peptides identified using PQD generally have Xcorr scores lower than those using CID. Such score differences were considerably diminished by the use of 0.1% m-nitrobenzyl alcohol (m-NBA) in mobile phases. The ion intensities of both CID and PQD were adversely affected by increasing m/z of the precursor, with PQD more sensitive than CID. In addition to negating the 1/3 rule, PQD enhances direct bond cleavage and generates patterns of fragment ions different from those of CID, particularly for peptides with a labile functional group (e.g., phosphopeptides). The higher energy fragmentation pathway of PQD on peptide fragmentation was further compared to those of CID and the quadrupole-type activation in parallel experiments.

Modelling of the gas-phase phosphate group loss and rearrangement in phosphorylated peptides

The gas-phase dissociation of phosphorylated peptides was modelled using a combination of quantum mechanics and the Rice-Ramsperger-Kassel-Marcus theory. Potential energy surfaces and unimolecular reaction rates for several low-energy fragmentation and rearrangement pathways were estimated, and a general mechanism was proposed. The neutral loss of the phosphoric acid was mainly an outcome of the intramolecular nucleophilic substitution mechanism. The mechanism involves a nucleophilic attack of the phosphorylated amino acid N-terminal carbonyl oxygen on β-carbon, yielding a cyclic five-membered oxazoline product ion. Regardless of the proton mobility, the pathway was charge directed either by a mobile proton or by a positively charged side chain of some basic residue. Although the mechanistic aspects of the phosphate loss are not influenced by the proton mobility environment, it does affect ion abundances. Results suggest that under the mobile proton environment, the interplay between phosphoric acid neutral loss product ion and backbone cleavage fragments should occur. On the other hand, when proton mobility is limited, neutral loss product ion may predominate. The fragmentation dynamics of phosphoserine versus phosphothreonine containing peptides suggests that H(3)PO(4) neutral loss from phosphothreonine containing peptides is less abundant than that from their phosphoserine containing analogs. During the low-energy CID of phosphorylated peptides in the millisecond time range, typical for ion trap instruments, a phosphate group rearrangement may happen, resulting in an interchange between the phosphorylated and the hydroxylated residues. Unimolecular dissociation rate constants imply the low abundance of such scrambled product ions.

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.

An experimental approach to enhance precursor ion fragmentation for metabolite identification studies: application of dual collision cells in an orbital trap

Recent advancements in mass spectrometry including data-dependent scanning and high-resolution mass spectrometry have aided metabolite profiling for non-radiolabeled xenobiotics. However, narrowing down a site of metabolism is often limited by the quality of the collision-induced dissociation (CID)-based precursor ion fragmentation. An alternative dissociation technique, higher energy collisional dissociation (HCD), enriches compound fragmentation and yields 'triple-quadrupole-like fragmentation'. Applying HCD along with CID and data-dependent scanning could enhance structural elucidation for small molecules. Liquid chromatography/multi-stage mass spectrometry (LC/MS(n) ) experiments with CID and HCD fragmentation were carried out for commercially available compounds on a hybrid linear ion trap orbital trap mass spectrometer equipped with accurate mass measurement capability. The developed method included stepped normalized collision energy (SNCE) parameters to enhance MS fragmentation without tuning for individual compounds. All the evaluated compounds demonstrated improved fragmentation under HCD as compared with CID. The results suggest that an LC/MS(n) method that incorporated both SNCE HCD- and CID-enabled precursor ion fragmentation afforded comprehensive structural information for the compounds under investigation. A dual collision cell approach was remarkably better than one with only CID MS(n) in an orbital trap. It is evident that such an acquisition method can augment the identification of unknown metabolites in drug discovery by improving fragmentation efficiency of both the parent compound and its putative metabolite(s).

Inline pneumatically assisted atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry

Atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) is known to suffer from poor ion transfer efficiencies as compared to conventional vacuum MALDI (vMALDI). To mitigate these issues, a new AP-MALDI ion source utilizing a coaxial gas flow was developed. Nitrogen, helium, and sulfur hexafluoride were tested for their abilities as ion carriers for a standard peptide and small drug molecules. Nitrogen showed the best ion transport efficiency, with sensitivity gains of up to 1900% and 20% for a peptide standard when the target plate voltage was either continuous or pulsed, respectively. The addition of carrier gas not only entrained the ions efficiently but also deflected background species and declustered analyte-matrix adducts, resulting in higher absolute analyte signal intensities and greater signal-to-noise (S/N) ratios. With the increased sensitivity of pneumatically assisted (PA) AP-MALDI, the limits of detection of angiotensin I were 20 or 3 fmols for continuous or pulsed target plate voltage, respectively. For analyzing low-mass analytes, it was found that very low gas flow rates (0.3-0.6 l min(-1)) were preferable owing to increased fragmentation at higher gas flows. The analyte lability, type of gas, and nature of the extraction field between the target plate and mass spectrometer inlet were observed to be the most important factors affecting the performance of the in-line PA-AP-MALDI ion source.

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).

Time-resolved observation of product ions generated by 157 nm photodissociation of singly protonated phosphopeptides

Vacuum UV photodissociation tandem mass spectra of singly charged arginine-terminated phosphopeptides were recorded at times ranging from 300 ns to ms after photoexcitation, to investigate when the phosphate group falls off from the precursor and product ions and whether loss of phosphate can be eliminated in tandem mass spectra. For peptide ions containing phosphoserine and phosphothreonine, little loss of 98 Da from the product ions was observed up to 1 micros after photoexcitation. However, neutral losses from the precursor ions were considerable just 300 ns after photoactivation. Loss of 98 Da from product ions first appears about 1 micros after laser irradiation and becomes more common 13 micros after photoexcitation. Consistent with previous reports, phosphotyrosine was more stable than either phosphoserine or phosphothreonine.

Optimized Orbitrap HCD for quantitative analysis of phosphopeptides

Despite the tremendous commercial success of radio frequency quadrupole ion traps for bottom-up proteomics studies, there is growing evidence that peptides decorated with labile post-translational modifications are less amenable to low-energy, resonate excitation MS/MS analysis. Moreover, multiplexed stable isotope reagents designed for MS/MS-based quantification of peptides rely on accurate and robust detection of low-mass fragments for all precursors. Collectively these observations suggest that beam-type or tandem in-space MS/MS measurements, such as that available on traditional triple quadrupole mass spectrometers, may provide beneficial figures of merit for quantitative proteomics analyses. The recent introduction of a multipole collision cell adjacent to an Orbitrap mass analyzer provides for higher energy collisionally activated dissociation (HCD) with efficient capture of fragment ions over a wide mass range. Here we describe optimization of various instrument and post-acquisition parameters that collectively provide for quantification of iTRAQ-labeled phosphorylated peptides isolated from complex cell lysates. Peptides spanning a concentration dynamic range of 100:1 are readily quantified. Our results indicate that appropriate parameterization of collision energy as a function of precursor m/z and z provides for optimal performance in terms of peptide identification and relative quantification by iTRAQ. Using this approach, we readily identify activated signaling pathways downstream of oncogenic mutants of Flt-3 kinase in a model system of human myeloid leukemia.

Metastable atom-activated dissociation mass spectrometry: leucine/isoleucine differentiation and ring cleavage of proline residues

Extensive backbone fragmentation resulting in a-, b-, c-, x-, y- and z-type ions is observed of singly and doubly charged peptide ions through their interaction with a high kinetic energy beam of argon or helium metastable atoms in a modified quadrupole ion trap mass spectrometer. The ability to determine phosphorylation-sites confirms the observation with previous reports and we report the new ability to distinguish between leucine and isoleucine residues and the ability to cleave two covalent bonds of the proline ring resulting in a-, b-, x-, y-, z- and w-type ions. The fragmentation spectra indicate that fragmentation occurs through nonergodic radical ion chemistry akin to electron capture dissociation (ECD), electron transfer dissociation (ETD) and electron ionization dissociation mechanisms. However, metastable atom-activated dissociation mass spectrometry demonstrates three apparent benefits to ECD and ETD: (1) the ability to fragment singly charged precursor ions, (2) the ability to fragment negatively charged ions and (3) the ability to cleave the proline ring that requires the cleavage of two covalent bonds. Helium metastable atoms generated more fragment ions than argon metastable atoms for both substance P and bradykinin regardless of the precursor ion charge state. Reaction times less than 250 ms and efficiencies approaching 5% are compatible with on-line fragmentation, as would be desirable for bottom-up proteomics applications.

Phosphopeptide fragmentation and analysis by mass spectrometry

Reversible phosphorylation is a key event in many biological processes and is therefore a much studied phenomenon. The mass spectrometric (MS) analysis of phosphorylation is challenged by the substoichiometric levels of phosphorylation and the lability of the phosphate group in collision-induced dissociation (CID). Here, we review the fragmentation behaviour of phosphorylated peptides in MS and discuss several MS approaches that have been developed to improve and facilitate the analysis of phosphorylated peptides. CID of phosphopeptides typically results in spectra dominated by a neutral loss of the phosphate group. Several proposed mechanisms for this neutral loss and several factors affecting the extent at which this occurs are discussed. Approaches are described to interpret such neutral loss-dominated spectra to identify the phosphopeptide and localize the phosphorylation site. Methods using additional activation, such as MS(3) and multistage activation (MSA), have been designed to generate more sequence-informative fragments from the ion produced by the neutral loss. The characteristics and benefits of these methods are reviewed together with approaches using phosphopeptide derivatization or specific MS scan modes. Additionally, electron-driven dissociation methods by electron capture dissociation (ECD) or electron transfer dissociation (ETD) and their application in phosphopeptide analysis are evaluated. Finally, these techniques are put into perspective for their use in large-scale phosphoproteomics studies.

Phosphorylated serine and threonine residues promote site-specific fragmentation of singly charged, arginine-containing peptide ions

In order to investigate gas-phase fragmentation reactions of phosphorylated peptide ions, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) tandem mass (MS/MS) spectra were recorded from synthetic phosphopeptides and from phosphopeptides isolated from natural sources. MALDI-TOF/TOF (TOF: time-of-flight) spectra of synthetic arginine-containing phosphopeptides revealed a significant increase of y ions resulting from bond cleavages on the C-terminal side of phosphothreonine or phosphoserine. The same effect was found in ESI-MS/MS spectra recorded from the singly charged but not from the doubly charged ions of these phosphopeptides. ESI-MS/MS spectra of doubly charged phosphopeptides containing two arginine residues support the following general fragmentation rule: Increased amide bond cleavage on the C-terminal side of phosphorylated serines or threonines mainly occurs in peptide ions which do not contain mobile protons. In MALDI-TOF/TOF spectra of phosphopeptides displaying N-terminal fragment ions, abundant b-H(3)PO(4) ions resulting from the enhanced dissociation of the pSer/pThr-X bond were detected (X denotes amino acids). Cleavages at phosphoamino acids were found to be particularly predominant in spectra of phosphopeptides containing pSer/pThr-Pro bonds. A quantitative evaluation of a larger set of MALDI-TOF/TOF spectra recorded from phosphopeptides indicated that phosphoserine residues in arginine-containing peptides increase the signal intensities of the respective y ions by almost a factor of 3. A less pronounced cleavage-enhancing effect was observed in some lysine-containing phosphopeptides without arginine. The proposed peptide fragmentation pathways involve a nucleophilic attack by phosphate oxygen on the carbon center of the peptide backbone amide, which eventually leads to cleavage of the amide bond.

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.

On-chip solid-phase extraction pre-concentration/focusing substrates coupled to atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry for high sensitivity biomolecule analysis

Atmospheric pressure matrix-assisted laser desorption/ionization (AP-MALDI) has proven a convenient and rapid method for ion production in the mass spectrometric (MS) analysis of biomolecules. AP-MALDI and electrospray ionization (ESI) sources are easily interchangeable in most mass spectrometers. However, AP-MALDI suffers from less-than-optimal sensitivity due to ion losses during transport from the atmosphere into the vacuum of the mass spectrometer. Here, we study the signal-to-noise ratio (S/N) gains observed when an on-chip dynamic pre-concentration/focusing approach is coupled to AP-MALDI for the MS analysis of neuropeptides and protein digests. It was found that, in comparison with conventional AP-MALDI targets, focusing targets showed (1) a sensitivity enhancement of approximately two orders of magnitude with S/N gains of 200-900 for hydrophobic substrates, and 150-400 for weak cation-exchange (WCX) substrates; (2) improved detection limits as low as 5 fmol/microL for standard peptides; (3) significantly reduced matrix background; and (4) higher inter-day reproducibility. The improved sensitivity allowed successful tandem mass spectrometric (MS/MS) sequencing of dilute solutions of a derivatized tryptic digest of a protein standard, and enabled the first reported AP-MALDI MS detection of neuropeptides from Aedes aegypti mosquito heads.

Amazing stability of phosphate-quaternary amine interactions

We have previously used MALDI mass spectrometry to highlight ammonium- or guanidinium-aromatic interactions via cation-pi bonding and ammonium- or guanidinium-phosphate interactions through salt bridge formation. In the present work, the gas-phase stability and dissociation pathways of the interaction between phosphorylated peptides and compounds containing quaternary amines are demonstrated using electrospray ionization mass spectrometry. The presence of one quaternary amine in a compound is enough to form a noncovalent complex with a phosphorylated residue. However, if two quaternary amines are present in one molecule, the electrostatic interactions of the quaternary amines with the phosphate results in a "covalent-like" stability, and these bonds can withstand fragmentation by collision-induced dissociation at energies similar to those that fragment covalent bonds. Such interactions are important in accounting for physiological, pathophysiological, and pharmacological effects of many therapeutic compounds and small molecules containing quaternary amines or phosphates.

Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry

Proteomics has been proposed as one of the key technologies in the postgenomic era. So far, however, the comprehensive analysis of cellular proteomes has been a challenge because of the dynamic nature and complexity of the multitude of proteins in cells and tissues. Various approaches have been established for the analyses of proteins in a cell at a given state, and mass spectrometry (MS) has proven to be an efficient and versatile tool. MS-based proteomics approaches have significantly improved beyond the initial identification of proteins to comprehensive characterization and quantification of proteomes and their posttranslational modifications (PTMs). Despite these advances, there is still ongoing development of new technologies to profile and analyze cellular proteomes more completely and efficiently. In this review, we focus on MS-based techniques, describe basic approaches for MS-based profiling of cellular proteomes and analysis methods to identify proteins in complex mixtures, and discuss the different approaches for quantitative proteome analysis. Finally, we briefly discuss novel developments for the analysis of PTMs. Altered levels of PTM, sometimes in the absence of protein expression changes, are often linked to cellular responses and disease states, and the comprehensive analysis of cellular proteome would not be complete without the identification and quantification of the extent of PTMs of proteins.

Development of an integrated chromatographic system for on-line digestion and characterization of phosphorylated proteins

The development of an integrated chromatographic system for complete phosphoprotein analysis is described. The digestion of phosphoproteins with trypsin- or pronase-based monolithic bioreactors is carried out on-line with selective enrichment on a TiO(2) trap and separation of the produced phosphopeptides by reversed-phase liquid chromatography-multiple mass spectrometry (RPLC/MS(n)). A detailed study on the selective extraction of peptides with different degrees of phosphorylation on TiO(2) cartridges is discussed. This analytical strategy has been optimized using beta-casein as a standard phosphoprotein, and then applied to the identification of phosphorylation sites in insulin-like grow factor-binding protein 1 (IGFBP-1) isolated from amniotic fluid.

AP/MALDI-MS complete characterization of the proteolytic fragments produced by the interaction of insulin degrading enzyme with bovine insulin

The prominent role that insulin degrading enzyme (IDE) has in the clearance of insulin as well as of other molecules such as amyloid-beta has recently drawn much interest in the scientific community toward this protease. In order to give an insight into the manner of interaction of IDE with its substrates, several papers have focused on the structure of the IDE/insulin complex. In this scenario, although the cleavage sites involved in the interaction of insulin with IDE are known, a convenient experimental method that is able to identify in a complete and unambiguous way, all the peptide fragments generated by such interaction has yet to be found. MS-based experiments have often represented to be invaluable tools for the assessment of the cleavage sites, but the reported MS-spectra always show a partial coverage of all the peptide fragments generated by the enzyme interaction, lacking a complete characterization. In this work, we report a new experimental procedure by which an unambiguous as well as complete assignment of all the peptide fragments generated by the interaction of insulin with IDE is described. Atmospheric pressure/matrix-assisted laser desorption ionization (AP/MALDI) mass spectra are reported and the data recorded, together with the introduction of a reduction/alkylation step, allows us to fully characterize the cleavage sites of the bovine insulin interacting with IDE. Different experimental conditions are screened and some insights into the IDE/insulin system regarding preference of the cleavage and its dependence on particular experimental conditions used are also given. Investigation on the tendency that different insulin fragments have toward aggregation is also carried out. Good reproducibility, global and unambiguous assignment, low time-consuming experimental procedure, and requirements of enzyme in small amounts are some of the advantages of the proposed AP/MALDI based approach.

Homeodomain-interacting protein kinase-2 (HIPK2) phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77 and modulates its DNA binding affinity

The chromosomal high-mobility group A (HMGA) proteins, composed of HMGA1a, HMGA1b and HMGA2, play important roles in the regulation of numerous processes in eukaryotic cells, such as transcriptional regulation, DNA repair, RNA processing, and chromatin remodeling. The biological activities of HMGA1 proteins are highly regulated by their post-translational modifications (PTMs), including acetylation, methylation, and phosphorylation. Recently, it was found that the homeodomain-interacting protein kinase-2 (HIPK2), a newly identified serine/threonine kinase, co-immunoprecipitated with, and phosphorylated, HMGA1 proteins. However, the sites and the biological significance of the phosphorylation have not been elucidated. Here, we found that HIPK2 phosphorylates HMGA1a at Ser-35, Thr-52, and Thr-77, and HMGA1b at Thr-41 and Thr-66. In addition, we demonstrated that cdc2, which is known to phosphorylate HMGA1 proteins, could induce the phosphorylation of HMGA1 proteins at the same Ser/Thr sites. The two kinases, however, exhibited different site preferences for the phosphorylation: The preference for HIPK2 phosphorylation followed the order of Thr-77 > Thr-52 > Ser-35, whereas the order for cdc2 phosphorylation was Thr-52 > Thr-77 > Ser-35. Moreover, we found that the HIPK2-phosphorylated HMGA1a reduced the binding affinity of HMGA1a to human germ line promoter, and the drop in binding affinity induced by HIPK2 phosphorylation was lower than that introduced by cdc2 phosphorylation, which is consistent with the notion that the second AT-hook in HMGA1a is more important for DNA binding than the third AT-hook.

Infrared multiphoton dissociation for enhanced de novo sequence interpretation of N-terminal sulfonated peptides in a quadrupole ion trap

Infrared multiphoton dissociation (IRMPD) of N-terminal sulfonated peptides improves de novo sequencing capabilities in a quadrupole ion trap mass spectrometer. Not only does IRMPD promote highly efficient dissociation of the N-terminal sulfonated peptides but also the entire series of y ions down to the y(1) fragment may be detected due to alleviation of the low-mass cutoff problem associated with conventional collisional activated dissociation (CAD) methods in a quadrupole ion trap. Commercial de novo sequencing software was applied for the interpretation of CAD and IRMPD MS/MS spectra collected for seven unmodified peptides and the corresponding N-terminal sulfonated species. In most cases, the additional information obtained by N-terminal sulfonation in combination with IRMPD provided significant improvements in sequence identification. The software sequence tag results were combined with a commercial database searching algorithm to interpret sequence information of a tryptic digest on alpha-casein s1. Energy-variable CAD studies confirmed a 30-40% reduction in the critical energies of the N-terminal sulfonated peptides relative to unmodified peptides. This reduction in dissociation energy facilitates IRMPD in a quadrupole ion trap.

Analytical methodologies for the detection and structural characterization of phosphorylated proteins

Phosphorylation of proteins is a frequent post-translational modification affecting a great number of fundamental cellular functions in living organisms. Because of its key role in many biological processes, much effort has been spent over the time on the development of analytical methodologies for characterizing phosphoproteins. In the past decade, mass spectrometry-based techniques have emerged as a viable alternative to more traditional methods of phosphorylation analysis, providing accurate information for a purified protein on the number of the occurring phosphate groups and their exact localization on the polypeptide sequence. This review summarizes the analytical methodologies currently available for the analysis of protein phosphorylation, emphasizing novel mass spectrometry (MS) technologies and dedicated biochemical procedures that have been recently introduced in this field. A formidable armamentarium is now available for selective enrichment, exaustive structural characterization and quantitative determination of the modification degree for phosphopeptides/phosphoproteins. These methodologies are now successfully applied to the global analysis of cellular proteome repertoire according a holistic approach, allowing the quantitative study of phosphoproteomes on a dynamic time-course basis. The enormous complexity of the protein phosphorylation pattern inside the cell and its dynamic modification will grant important challenges to future scientists, contributing significantly to deeper insights into cellular processes and cell regulation.

Atmospheric Pressure Molecular Imaging by Infrared MALDI Mass Spectrometry

An atmospheric pressure (AP) MALDI imaging interface was developed for an orthogonal acceleration time-of-flight mass spectrometer and utilized to analyze peptides, carbohydrates, and other small biomolecules using infrared laser excitation. In molecular imaging experiments, the spatial distribution of mock peptide patterns was recovered with a detection limit of approximately 1 fmol/pixel from a variety of MALDI matrixes. With the use of oversampling for the image acquisition, a spatial resolution of 40 microm, 5 times smaller than the laser spot size, was achieved. This approach, however, required that the analyte was largely removed at the point of analysis before the next point was interrogated. Native water in plant tissue was demonstrated to be an efficient natural matrix for AP infrared laser desorption ionization. In soft fruit tissues from bananas, grapes, and strawberries, potassiated ions of the most abundant metabolites, small carbohydrates, and their clusters produced the strongest peaks in the spectra. Molecular imaging of a strawberry skin sample revealed the distribution of the sucrose, glucose/fructose, and citric acid species around the embedded seeds. Infrared AP MALDI mass spectrometric imaging without the addition of an artificial matrix enables the in vivo investigation of small biomolecules and biological processes (e.g., metabolomics) in their natural environment.

Laser-induced dissociation of phosphorylated peptides using matrix assisted laser desorption/ionization tandem time-of-flight mass spectrometry

Reversible phosphorylation is one of the most important posttranslational modifications of cellular proteins. Mass spectrometry is a widely used technique in the characterization of phosphorylated proteins and peptides. Similar to nonmodified peptides, sequence information for phosphopeptides digested from proteins can be obtained by tandem mass analysis using either electrospray ionization or matrix assisted laser desorption/ionization (MALDI) mass spectrometry. However, the facile loss of neutral phosphoric acid (H3PO4) or HPO3 from precursor ions and fragment ions hampers the precise determination of phosphorylation site, particularly if more than one potential phosphorylation site or concensus sequence is present in a given tryptic peptide. Here, we investigated the fragmentation of phosphorylated peptides under laser-induced dissociation (LID) using a MALDI-time-of-flight mass spectrometer with a curved-field reflectron. Our data demonstrated that intact fragments bearing phosphorylated residues were produced from all tested peptides that contain at least one and up to four phosphorylation sites at serine, threonine, or tyrosine residues. In addition, the LID of phosphopeptides derivatized by N-terminal sulfonation yields simplified MS/MS spectra, suggesting the combination of these two types of spectra could provide an effective approach to the characterization of proteins modified by phosphorylation.

The fragmentation of ethoxylated surfactants by AP-MALDI-QIT

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry has become an important technique to characterize the chemical structure of industrial polymer materials. MALDI methods have been developed to address a broad variety of different polymer materials containing different chemistries. One of the key aspects of the typical MALDI experiment is the generation of intact ions. The development of Atmospheric Pressure (AP) MALDI quadrupole ion trap (QIT) instruments has opened another channel to obtaining MS/MS experiments for polymer samples. These experiments provide a new method to obtain chemical structure information from MALDI experiments. Collision-Induced Dissociation (CID) provides an improved MALDI MS/MS experiment that can be done on readily available mass spectrometers. AP MALDI QIT techniques have been successfully applied to a variety of synthetic polymers. This work explores the applicability of AP MALDI QIT methods to relatively low molecular weight ethoxylated surfactants. In these experiments we show the CID fragmentation mass spectra on some ethoxylated surfactants, and demonstrate the existence of analyte matrix clusters.

UV photodissociation of phospho-seryl-containing peptides: laser stabilization of the phospho-seryl bond with multistage mass spectrometry

Protonated precursor ions of phosphorylated peptides containing a tyrosyl residue have been subjected to UV laser-induced dissociation (LID) at a wavelength of 220 nm and to collision-induced dissociation (CID) in an ion trap. As expected, neutral loss of the phosphate group is one of the predominant fragmentation channels during CID together with H2O elimination. In contrast, LID leads mainly to the homolytic cleavage of the tyrosyl side chain and a restrained loss of the phosphate group. Interestingly, the intensity of the dephosphorylated fragment ion is greatly minimized when CID is carried out next on the radical precursor ion of the singly and doubly charged species.

A deflection system to reduce the interference from post-source decay product ions in photodissociation tandem time-of-flight mass spectrometry

A deflection system consisting of four deflectors was designed and used to reduce the interference from post-source decay (PSD) product ions in photodissociation (PD) tandem time-of-flight (TOF) mass spectrometry. For simple protonated peptides generated by matrix-assisted laser desorption/ionization, the presence of PSD product ions at the laser irradiation spot was found to noticeably alter the minor peaks in the PD spectra even though the major ones were hardly affected. Other benefits from the use of the deflection system such as the improvement in the resolving power in PSD tandem mass spectra are discussed.

Manipulating the fragmentation patterns of phosphopeptides via gas-phase boron derivatization: determining phosphorylation sites in peptides with multiple serines

Trivalent boron species readily react with protonated phosphopeptides to give addition products with the loss of boron ligands. In the present study, trimethoxyborane (TMB), diisopropoxymethylborane (DIPM), and diethylmethoxyborane (DEMB) were allowed to react with four phosphopeptides, VsSF, LSsF, LsGASA, and VSGAsA (lower-case s indicates phosphoserine). Each of the phosphopeptides contains one serine that is phosphorylated and one that is not. Under collision-activated dissociation (CAD) conditions, the boron-derivatized peptides give fragmentation patterns that differ significantly from that of the protonated phosphopeptide. The patterns vary, depending on the number of labile (i.e., alkoxy) ligands on the boron. In general, boron derivatization increases the yield of phosphate-containing sequence ions, but dramatic effects are only seen with certain reagent/peptide combinations. However, the suite of reagents provides a means of altering and increasing the information content of phosphopeptide CAD spectra.

Study of the fragmentation patterns of the phosphate-arginine noncovalent bond

Our previous work has highlighted the role of certain amino acid residues, mainly two or more adjacent arginine on one peptide and two or more adjacent glutamate, or aspartate, or a phosphorylated residue on the other in the formation of noncovalent complexes (NCX) between peptides. In the present study, we employ ESI-MS to investigate the gas-phase stability and dissociation pathways of the NCX of a basic peptide VLRRRRKRVN, an epitope from the third intracellular loop of the dopamine D(2) receptor, with the phosphopetide SVSTDpTpSAE, an epitope from the cannabinoid CB1 carboxyl terminus. ESI-MS/MS analysis of the NCX between VLRRRRKRVN and SVSTDpTpSAE suggests two dissociation pathways for the NCX. The major pathway is the disruption of the electrostatic interactions between the Arg residues and the phosphate groups, while an alternative pathway is also recorded, in which the complex is dissociated along the covalent bond between the oxygen from either Thr or Ser and HPO(3). To verify the alternative pathway, we have used an ion trap instrument to conduct MS(3) analysis on the product ions of both dissociation pathways.

Synthesis and conformational properties of phosphopeptides related to the human tau protein

In the brains of Alzheimer's disease patients, the tau protein dissociates from the axonal microtubule and abnormally aggregates to form a paired helical filament (PHF). One of the priorities in Alzheimer research is to determine the effects of abnormal phosphorylation on the local structure. A series of peptides corresponding to isolated regions of tau protein have been successfully synthesized using Fmoc-based chemistry and their conformations were determined by 1H NMR spectroscopy and circular dichroism (CD) spectroscopy. Immunodominant peptides corresponding to tau-(256-273), tau-(350-367) and two phosphorylated derivatives in which a single Ser was phosphorylated at positions 262 and 356, respectively, were the main focus of the study. A direct alteration of the local structure after phosphorylation constitutes a new strategy through which control of biological activity can be enforced. In our study on Ser262 in R1 peptide and Ser356 in R4 peptide, phosphorylation modifies both the negative charge and the local conformation nearby the phosphorylation sites. Together, these structural changes indicate that phosphorylation may act as a conformational switch in the binding domain of tau protein to alter specificity and affinity of binding to microtubule, particularly in response to the abnormal phosphorylation events associated with Alzheimer's disease.

Atmospheric pressure MALDI-FTMS of normal and chemically modified RNA

Atmospheric pressure (AP) MALDI has been combined with Fourier transform mass spectrometry (FTMS) to obtain the unambiguous characterization of RNA samples modified by solvent accessibility reagents used in structural studies of RNA and protein-RNA complexes. The formation of cation adducts typical of MS analysis of nucleic acids was effectively reduced by extensive washing of the anionic analytes retained onto the probe surface by strong interactions with a cationic layer of poly(diallyldimethylammonium chloride) (PADMAC). This rapid desalting procedure allowed for the detection of DNA and RNA samples in high femtomole quantities distributed over a 4 x 4 mm sample well. AP MALDI-FTMS was shown to provide high-resolution spectra for analytes as large as approximately 6.4 kDa with little or no evidence of metastable decomposition. The absence of significant metastable decay observed for precursor ions selected for tandem experiments offered a further measure of the low energy content typical of ions generated by AP MALDI. This feature proved to be very beneficial in the characterization of chemically modified RNA samples, which become particularly prone to base losses upon alkylation. The high resolution offered by FTMS enabled the application of a data-reduction algorithm capable of rejecting any signal devoid of plausible isotopic distribution, thus facilitating the analysis of complex analyte mixtures produced by nuclease treatment of RNA substrates. Proper selection of nucleases and digestion conditions can ensure the production of hydrolytic fragments of manageable size, which could extend the range of applicability of this bottom-up strategy to the structural investigation of very large RNA and protein-RNA complexes.

Quantitation of Lysergic Acid Diethylamide in Urine Using Atmospheric Pressure Matrix-Assisted Laser Desorption/Ionization Ion Trap Mass Spectrometry

A quantitative method was developed for analysis of lysergic acid diethylamide (LSD) in urine using atmospheric pressure matrix-assisted laser desorption/ionization ion trap mass spectrometry (AP MALDI-ITMS). Following solid-phase extraction of LSD from urine samples, extracts were analyzed by AP MALDI-ITMS. The identity of LSD was confirmed by fragmentation of the [M + H](+) ion using tandem mass spectrometry. The quantification of LSD was achieved using stable-isotope-labeled LSD (LSD-d(3)) as the internal standard. The [M + H](+) ion fragmented to produce a dominant fragment ion, which was used for a selected reaction monitoring (SRM) method for quantitative analysis of LSD. SRM was compared with selected ion monitoring and produced a wider linear range and lower limit of quantification. For SRM analysis of samples of LSD spiked in urine, the calibration curve was linear in the range of 1-100 ng/mL with a coefficient of determination, r(2), of 0.9917. This assay was used to determine LSD in urine samples and the AP MALDI-MS results were comparable to the HPLC/ ESI-MS results.

Atmospheric Pressure MALDI with Pulsed Dynamic Focusing for High-Efficiency Transmission of Ions into a Mass Spectrometer

The atmospheric pressure (AP) matrix-assisted laser desorption/ionization (MALDI) technique described to date has proven to be a convenient and rapid method for soft ionization of biomolecules. However, this technique, like other AP ionization methods, has so far suffered from a low efficiency in transmitting ions from atmospheric pressure into the vacuum of the mass spectrometer (MS). In this work, a novel technique we termed pulsed dynamic focusing, or PDF, which improves the ion transmission efficiency and sensitivity of AP-MALDI by over an order of magnitude, is described. Pulsed dynamic focusing operates on the basis of pulsing a high-voltage extraction field to zero, when ions are just outside of the MS entrance, to allow the intake gas flow of the MS to effectively entrain the ions into the MS. Results from application of the PDF technique to an AP-MALDI ion trap MS demonstrated that in comparison to static AP-MALDI operation (1). up to 2.1 times more ions from a given laser shot could be transferred into the MS, (2). applying higher voltages in combination with the switching scheme yielded up to 1.6-times-higher ion intensities, and (3). a 3-times-larger laser spot area could be utilized. The combination of these factors produced an enhancement in throughput and sensitivity, as measured by the ions detected per unit time, of over 12 times for a digest sample of bovine serum albumin. In addition, the PDF technique proved to make AP-MALDI less sensitive to laser positioning, creating a more robust ion source in comparison to static AP-MALDI.