Targeted analysis of protein citrullination using chemical modification and tandem mass spectrometry

Protein citrullination originates from enzymatic deimination of polypeptide‐bound arginine and is involved in various biological processes during health and disease. However, tools required for a detailed and targeted proteomic analysis of citrullinated proteins in situ, including their citrullination sites, are limited. A widely used technique for detection of citrullinated proteins relies on antibody staining after specific derivatization of citrulline residues by 2,3‐butanedione and antipyrine. We have recently reported on the details of this reaction. Here, we show that this chemical modification can be utilized to specifically detect and identify citrullinated peptides and their citrullination sites by liquid chromatography/tandem mass spectrometry (LC/MS/MS) analysis. Using model compounds, we demonstrate that in collision‐induced dissociation (CID) a specific, modification‐derived fragment ion appears as the dominating signal at m/z 201.1 in the MS/MS spectra. When applying electron transfer dissociation (ETD), however, the chemical modification of citrulline remained intact and extensive sequence coverage allowed identification of peptides and their citrullination sites. Therefore, LC/MS/MS analysis with alternating CID and ETD has been performed, using CID for specific, signature ion‐based detection of derivatized citrullinated peptides and ETD for sequence determination. The usefulness of this targeted analysis was demonstrated by identifying citrullination sites in myelin basic protein deiminated in vitro. Combining antibody‐based enrichment of chemically modified citrulline‐containing peptides with specific mass spectrometric detection will increase the potential of such a targeted analysis of protein citrullination in the future. Copyright © 2009 John Wiley & Sons, Ltd.     

A new approach to phosphoserine and phosphothreonine analysis in peptides and proteins: chemical modification,enrichment via solid-phase reversible binding,and analysis by mass spectrometry

beta-Elimination of the phosphate group on phosphoserine and phosphothreonine residues and addition of an alkyldithiol is a useful tool for analysis of the phosphorylation states of proteins and peptides. We have explored the influence of several conditions on the efficiency of this PO(4)(3-) elimination reaction upon addition of propanedithiol. In addition to the described influence of different bases, the solvent composition was also found to have a major effect on the yield of the reaction. In particular, an increase in the percentage of DMSO enhances the conversion rate, whereas a higher amount of protic polar solvents, such as water or isopropanol, induces the opposite effect. We have also developed a protocol for enrichment of the modified peptides, which is based on solid-phase covalent capture/release with a dithiopyridino-resin. The procedure for beta-elimination and isolation of phosphorylated peptides by solid-phase capture/release was developed with commercially available alpha-casein. Enriched peptide fragments were characterized by MALDI-TOF mass spectrometric analysis before and after alkylation with iodoacetamide, which allowed rapid confirmation of the purposely introduced thiol moiety. Sensitivity studies, carried out in order to determine the detection limit, demonstrated that samples could be detected even in the low picomolar range by mass spectrometry. The developed solid-phase enrichment procedure based on reversible covalent binding of the modified peptides is more effective and significantly simpler than methods based on the interaction between biotin and avidin, which require additional steps such as tagging the modified peptides and work-up of the samples prior to the affinity capture step.     

Selective detection of phosphopeptides in complex mixtures by electrospray liquid chromatography/mass spectrometry

A mass spectrometry-based method that does not involve the use of radiolabeling was developed for selective detection of phosphopeptides in complex mixtures. Mixtures of phosphorylated and nonphosphorylated peptides at the low picomole level are analyzed by negative ion electrospray liquid chromatography/mass spectrometry using C-18 packed fused-silica columns (≤320-μm i.d.). Peptides and phosphopeptides in the chromatographic eluant undergo collision-induced dissociation in the free-jet expansion region prior to the mass analyzing quadrupole. Using relatively high collisional excitation potentials, phospho|peptides containing phosphoserine, phosphothreonine, and phosphotyrosine fragment to yield diagnostic ions at m/z 63 and 79 corresponding to PO₂ ^?; and PO₃ ^?, respectively. Chromatographic peaks containing phosphopeptides are indicated where these diagnostic ions maximize. The highest sensitivity for phosphopeptide detection is obtained using selected-ion monitoring for m/z 63 and 79. Full-scan mass spectra that exhibit the diagnostic phosphopeptide fragment ions, together with pseudomolecular ions, may be obtained by stepping the collisional excitation potential from a high value during the portion of each scan in which the low-mass-to-charge ratio diagnostic marker ions are being detected to a lower value while the upper mass-to-charge ratio range is being scanned. Good sensitivity for phosphopeptide detection was achieved using standard trifluoroacetic acid containing mobile phases for reversed-phase high-performance liquid chromatography. Data illustrating the selectivity and sensitivity of the approach are presented for mixtures of peptides and phosphopeptides containing the three commonly phosphorylated amino acids.     

Location of double-bond position in tetradecenols without chemical modification by mass spectrometry

Twelve positional isomers of tetradecenol were analysed by conventional combined gas chromatography/mass Spectrometry without any chemical derivatization for the elucidation of the double-bond position. The spectra were interpreted in terms of similarity of mass spectral patterns based on a fuzzy reasoning method, in which the relative abundances of selected predominant fragment ions were chosen as standard parameters and similarity indices were devised. The method was tested with pure alcohols and enabled the double-bond position to be located with acceptable accuracy.     

Identification of free phosphopeptides in different biological fluids by a mass spectrometry approach

Human body fluids have been rediscovered in the post-genomic era as a great source of biological markers and perhaps as source of potential biomarkers of disease. Recently, it has been found that not only proteins but also peptides and their modifications can be indicators of early pathogenic processes. This paper reports the identification of free phosphopeptides in human fluids using an improved IMAC strategy coupled to iterative mass spectrometry-based scanning techniques (neutral loss, precursor ion, multiple reaction monitoring). Many peptides were detected in the enriched extract samples when submitted to the MS-integrated strategy, whereas they were not detected in the initial extract samples. The combination of the IMAC-modified protocol with selective "precursor ion" and constant "neutral loss" triple quadrupole scan modes confers a high sensitivity on the analysis, allowing rapid phosphopeptide identification and characterization, even at low concentrations. To the best of our knowledge this work represents the first report exclusively focused on the detection of free phosphorylated peptides in biological fluids.     

Sensitive determination of inosine RNA modification in single cell by chemical derivatization coupled with mass spectrometry analysis

Inosine is a vital RNA modification across three kingdoms of life. It has been demonstrated that inosine plays important roles in modulation of the fate of RNAs. In the current study, we developed a highly sensitive method to determine inosine in a single cell by N-cyclohexyl-N’-β-(4-methylmorpholinium)ethylcarbodiimide p-toluenesulfonate(CMCT) derivatization in combination with mass spectrometry analysis. The results showed that the detection sensitivity of inosine was increased by 556-fold aft...     

Characterization of phosphopeptides from protein digests using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanoelectrospray quadrupole time-of-flight mass spectrometry

A two-step mass spectrometric method for characterization of phosphopeptides from peptide mixtures is presented. In the first step, phosphopeptide candidates were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) based on their higher relative intensities in negative ion MALDI spectra than in positive ion MALDI spectra. The detection limit for this step was found to be 18 femtomoles or lower in the case of unfractionated in-solution digests of a model phosphoprotein, beta-casein. In the second step, nanoelectrospray tandem mass (nES-MS/MS) spectra of doubly or triply charged precursor ions of these candidate phosphopeptides were obtained using a quadrupole time-of-flight (Q-TOF) mass spectrometer. This step provided information about the phosphorylated residues, and ruled out nonphosphorylated candidates, for these peptides. After [(32)P] labeling and reverse-phase high-performance liquid chromatography (RP-HPLC) to simplify the mixtures and to monitor the efficiency of phosphopeptide identification, we used this method to identify multiple autophosphorylation sites on the PKR-like endoplasmic reticulum kinase (PERK), a recently discovered mammalian stress-response protein.     

Preparative separation of a multicomponent peptide mixture by mass spectrometry

We report on the first multiplex preparative separation by mass spectrometry of bio-organic molecules in the 200-350 Da mass range that is typical for synthetic drugs. A five-component mixture consisting of two di- and three tripeptides has been separated by mass using a specially designed mass spectrometer. The instrument for preparative separations consists of an electrospray ionization (ESI) source, ion transfer optics, an electrostatic sector, and an inhomogeneous-field magnetic mass analyzer that achieves linear mass dispersion of ion beams. Protonated peptides produced by electrospray were separated, nondestructively landed on a 16-channel array of dry collector plates, and reconstituted in solution. The preparation procedures and the instrumental conditions have been optimized to maximize the ion currents. The significant features of the special mass spectrometer are high ion currents and simultaneous separation and collection of mixture components.     

Determination of the double-bond position in hexadecenols by mass spectrometry without prior chemical modification

Fourteen isomers of chemically unmodified hexadecenol were analysed by two types of quadrupole mass spectrometer, coupled with a gas chromatograph, for the location of the double-bond position. A series of spectra were interpreted in terms of mass spectral patterns on a fuzzy classification, in which the intensity ratios of six diagnostic pairs of the predominant ions were preferred in devising similarity indices. The accuracy of the method in the location of double-bond position was confirmed by testing with other series of spectra.     

Selective detection of sulfur-containing compounds by gas chromatography/chemical reaction interface mass spectrometry

Addition of a reactant gas to a low pressure microwave-induced plasma creates a reaction interface in which complex molecules are converted into small polyatomic neutral species. For a given reactant gas the array of these small molecules reflect s the elemental composition of the original analyte. In this study HCI has been found highly effective as a reactant gas for selective detection of sulfur-eontaining compounds using capillary gas chromatography/ chernical reaction interface mass spectrometry. Detection limits as low as 30 pg of a sulfur-containing compound and a dynamic range of two orders of magnitude were achieved.     

The analysis of salen complexes by fast atom bombardment mass spectrometry and atmospheric pressure chemical ionization mass spectrometry

Fast atom bombardment (FAB) mass spectrometry provides useful structural information about salen complexes and salen-based oxo transfer catalysts that are not appreciably soluble in organic solvents. It was discovered that initial dissolution of these complexes in trifluoroacetic acid was crucial for producing good FAB mass spectra. Trifluoroacetic acid helps dissolve the salen-based catalysts, concentrates the analyte molecules at the matrix surface, and most importantly, suppresses the reduction process, which is a well-known phenomenon when protic matrices are used. The best FAB matrices for these catalysts were found to be thioglycerol and “magic bullet.” However, dechlorination occurred under the acid conditions for complexes containing iron chloride and manganese chloride. Demetalation also occurred for nickel-containing oxo transfer salen-based complexes. When the salen-based complexes are soluble in LC solvents, they can be analyzed easily by atmospheric pressure chemical ionization (APCI) mass spectrometry without the employment of relatively nonvolatile matrices. In addition, APCI/MS provides much more sensitive detection for manganese-salen complexes when compared with FAB results. No dechlorination or demetalation were observed when a negative ion mode APCI was employed. To our knowledge, this is the first time that an intact molecule of this type of complex has been observed by mass spectrometry.     

Characterization of chlorins within a natural chlorin mixture using electrospray/ion trap mass spectrometry

Chlorins in a sedimentary mixture were characterized, without prior isolation of individual components, using electrospray ionization combined with ion trap mass spectrometry. Collision-induced dissociation in the atmospheric sampling interface and multi-step mass spectrometry (i.e. MSⁿ where n ? 2) were used in order to obtain structural information about the macrocycle. Fragmentation pathways are proposed for different macrocycle types based on data from model chlorins. Three unknown chlorins (RMM = 888, 844 and 790) are assigned as having bacteriochlorophyll macrocycle types esterifled to unusual side-chains (i.e. dihydrophytol for the unknown with a bacteriopheophorbide a structure, phytol and an alcohol with a molecular mass of 242 u for the two unknowns with a proposed bacteriopyropheophorbide d structure).     

Identifying sites of protein modification by using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry and on-line membrane preconcentration-capillary electrophoresis-tandem mass spectrometry

A strategy for rapidly identifying the number and sites of chemical or posttranslational modification of proteins is described. The use of matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry to determine the molecular weight of the adducted protein as well as map the proteolytic digest of peptides offers a rapid method to screen for the possible site of adduction. To unequivocally determine the amino acid sequence of the peptide bearing the adduct as well as structurally characteize the covalent modification, the peptide mixture is subjected to membrane preconcentration-capillary electrophoresis-mass spectrometry and tandem mass spectrometry (mPC-CE-MS/MS). The high resolving separation capability of capillary electrophoresis (CE) afford a chromatograhic step that lends itself to separation of complex mixtures of peptides with minimal sample loss. The membrane preconcentration-CE cartridge allows sample loading volumes 10,000-fold greater than conventional CE. In this work the binding site of the fluorescent label acrylodan to the intestinal fatty binding protein is characterized and shown to be covalently bound at lysine-27, by using mPC-CE-MS/MS.     

Evaluation of protein modification during anti-viral heat bioprocessing by electrospray ionization mass spectrometry

During the preparation of therapeutic plasma and recombinant protein biopharmaceuticals heat-treatment is routinely applied as a means of viral inactivation. However, as most proteins denature and aggregate under heat stress, it is necessary to add thermostabilizing excipients to protein formulations destined for anti-viral heat-treatment in order to prevent protein damage. Anti-viral heat-treatment bioprocessing therefore requires that a balance be found between the bioprocessing conditions, virus kill and protein integrity. In this study we have utilized a simple model protein, beta-lactoglobulin, to investigate the relationship between virucidal heat-treatment conditions (protein formulation and temperature) and the type and extent of protein modification in the liquid state. A variety of industrially relevant heat-treatments were undertaken, using formulations that included sucrose as a thermostabilizing excipient. Using liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) we show here that protein modifications do occur with increasingly harsh heat-treatment. The predominant modification under these conditions was protein glycation by either glucose or fructose derived from hydrolyzed sucrose. Advanced glycation end products and additional unidentified products were also present in beta-lactoglobulin protein samples subjected to extended heat-treatment. These findings have implications for the improvement of anti-viral heat-treatment bioprocesses to ensure the safety and efficacy of protein biopharmaceuticals. CopyrightCopyright 2001 John Wiley & Sons, Ltd.     

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

An investigation of phosphate loss from phosphopeptide ions was conducted, using both atmospheric pressure matrix-assisted laser desorption/ionization (AP MALDI) and electrospray ionization (ESI) coupled to an ion trap mass spectrometer (ITMS). These experiments were carried out on a number of phosphorylated peptides in order to investigate gas phase dephosphorylation patterns associated with phosphoserine, phosphothreonine, and phosphotyrosine residues. In particular, we explored the fragmentation patterns of phosphotyrosine containing peptides, which experience a loss of 98 Da under collision induced dissociation (CID) conditions in the ITMS. The loss of 98 Da is unexpected for phosphotyrosine, given the structure of its side chain. The fragmentation of phosphoserine and phosphothreonine containing peptides was also investigated. While phosphoserine and phosphothreonine residues undergo a loss of 98 Da under CID conditions regardless of peptide amino acid composition, phosphate loss from phosphotyrosine residues seems to be dependent on the presence of arginine or lysine residues in the peptide sequence.