Selective Detection of Peptide-Oligonucleotide Heteroconjugates Utilizing Capillary HPLC-ICPMS

A method for the selective detection and quantification of peptide:oligonucleotide heteroconjugates, such as those generated by protein:nucleic acid cross-links, using capillary reversed-phase high performance liquid chromatography (cap-RPHPLC) coupled with inductively coupled plasma mass spectrometry detection (ICPMS) is described. The selective detection of phosphorus as ³¹P⁺, the only natural isotope, in peptide-oligonucleotide heteroconjugates is enabled by the elemental detection capabilities of the ICPMS. Mobile phase conditions that allow separation of heteroconjugates while maintaining ICPMS compatibility were investigated. We found that trifluoroacetic acid (TFA) mobile phases, used in conventional peptide separations, and hexafluoroisopropanol/triethylamine (HFIP/TEA) mobile phases, used in conventional oligonucleotide separations, both are compatible with ICPMS and enable heteroconjugate separation. The TFA-based separations yielded limits of detection (LOD) of ~40 ppb phosphorus, which is nearly seven times lower than the LOD for HFIP/TEA-based separations. Using the TFA mobile phase, 1–2 pmol of a model heteroconjugate were routinely separated and detected by this optimized capLC-ICPMS method.     

Sequence analysis of peptide:oligonucleotide heteroconjugates by electron capture dissociation and electron transfer dissociation

Mass spectrometry analysis of protein-nucleic acid cross-links is challenging due to the dramatically different chemical properties of the two components. Identifying specific sites of attachment between proteins and nucleic acids requires methods that enable sequencing of both the peptide and oligonucleotide component of the heteroconjugate cross-link. While collision-induced dissociation (CID) has previously been used for sequencing such heteroconjugates, CID generates fragmentation along the phosphodiester backbone of the oligonucleotide preferentially. The result is a reduction in peptide fragmentation within the heteroconjugate. In this work, we have examined the effectiveness of electron capture dissociation (ECD) and electron-transfer dissociation (ETD) for sequencing heteroconjugates. Both methods were found to yield preferential fragmentation of the peptide component of a peptide:oligonucleotide heteroconjugate, with minimal differences in sequence coverage between these two electron-induced dissociation methods. Sequence coverage was found to increase with increasing charge state of the heteroconjugate, but decreases with increasing size of the oligonucleotide component. To overcome potential intermolecular interactions between the two components of the heteroconjugate, supplemental activation with ETD was explored. The addition of a supplemental activation step was found to increase peptide sequence coverage over ETD alone, suggesting that electrostatic interactions between the peptide and oligonucleotide components are one limiting factor in sequence coverage by these two approaches. These results show that ECD/ETD methods can be used for the tandem mass spectrometry sequencing of peptide:oligonucleotide heteroconjugates, and these methods are complementary to existing CID methods already used for sequencing of protein-nucleic acid cross-links.     

Automated deconvolution and deisotoping of electrospray mass spectra

Electrospray ionization (ESI) of peptides and proteins produces a series of multiply charged ions with a mass/charge (m/z) ratio between 500 and 2000. The resulting mass spectra are crowded by these multiple charge values for each molecular mass and an isotopic cluster for each nominal m/z value. Here, we report a new algorithm simultaneously to deconvolute and deisotope ESI mass spectra from complex peptide samples based on their mass-dependent isotopic mean pattern. All signals corresponding to one peptide in the sample were reduced to one singly charged monoisotopic peak, thereby significantly reducing the number of signals, increasing the signal intensity and improving the signal-to-noise ratio. The mass list produced could be used directly for database searching. The developed algorithm also simplified interpretation of fragment ion spectra of multiply charged parent ions.     

Accurate mass measurement of DNA oligonucleotide ions using high-resolution time-of-flight mass spectrometry

Matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) time-of-flight mass spectrometry (TOFMS) play an essential role in the analysis of biological molecules, not only peptides and proteins, but also DNA and RNA. Tandem mass spectrometry used for sequence analysis has been a major focus of technological developments in mass spectrometry, but accurate mass measurements by high-resolution TOFMS are equally important. This paper describes the role that high mass measurement accuracy can play in DNA composition assignment and discusses the influence of several parameters on mass measurement accuracy in both MALDI and ESI mass spectra. Five oligonucleotides (5-13mers) were used to test the resolving power and mass measurement accuracy obtained with MALDI and ESI instruments with reflectron TOF mass analyzers. The results from the experimental studies and additional theoretical calculations provide a basis to predict the practical utility of high-resolution TOFMS for the analysis of larger oligonucleotides.     

Mixed-Isotope Labeling with LC-IMS-MS for Characterization of Protein–Protein Interactions by Chemical Cross-Linking

Chemical cross-linking of proteins followed by proteolysis and mass spectrometric analysis of the resulting cross-linked peptides provides powerful insight into the quaternary structure of protein complexes. Mixed-isotope cross-linking (a method for distinguishing intermolecular cross-links) was coupled with liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS) to provide an additional separation dimension to the traditional cross-linking approach. This method produced multiplet m/z peaks that are aligned in the IMS drift time dimension and serve as signatures of intermolecular cross-linked peptides. We developed an informatics tool to use the amino acid sequence information inherent in the multiplet spacing for accurate identification of the cross-linked peptides. Because of the separation of cross-linked and non-cross-linked peptides in drift time, our LC-IMS-MS approach was able to confidently detect more intermolecular cross-linked peptides than LC-MS alone.      

High-throughput biopolymer desalting by solid-phase extraction prior to mass spectrometric analysis.

In the last 10 years mass spectrometry (MS) has become an important method for analysis of peptides, proteins and DNA. It was recently utilized for accurate high-throughput protein identification, sequencing and DNA genotyping. The presence of non-volatile buffers compromises sensitivity and accuracy of MS biopolymer analysis; it is essential to remove sample contaminants prior to analysis. We have developed a fast and efficient method for desalting of DNA oligonucleotides and peptides using 96-well solid-phase extraction plates packed with 5 mg of Waters Oasis HLB sorbent (Waters, Milford, MA, USA). This reversed-phase sorbent retains the biopolymer analytes, while non-retained inorganic ions are washed out with pure deionized water. DNA oligonucleotides or peptides are eluted using a small amount (20-100 microl) of acetonitrile-water (70:30, v/v) solution. The SPE desalting performance meets the requirements for MS applications such as protein digest analysis and DNA genotyping.     

The use of mass defect in modern mass spectrometry

Mass defect is defined as the difference between a compound's exact mass and its nominal mass. This concept has been increasingly used in mass spectrometry over the years, mainly due to the growing use of high resolution mass spectrometers capable of exact mass measurements in many application areas in analytical and bioanalytical chemistry. This article is meant as an introduction to the different uses of mass defect in applications using modern MS instrumentation. Visualizing complex mass spectra may be simplified with the concept of Kendrick mass by plotting nominal mass as a function of Kendrick mass defect, based on hydrocarbons subunits, as well as slight variations on this theme. Mass defect filtering of complex MS data has been used for selectively detecting compounds of interest, including drugs and their metabolites or endogenous compounds such as peptides and small molecule metabolites. Several strategies have been applied for labeling analytes with reagents containing unique mass defect features, thus shifting molecules into a less noisy area in the mass spectrum, thus increasing their detectability, especially in the area of proteomics. All these concepts will be covered to introduce the interested reader to the plethora of possibilities of mass defect analysis of high resolution mass spectra. Copyright © 2012 John Wiley & Sons, Ltd.     

Improved peptide mass fingerprinting matches via optimized sample preparation in MALDI mass spectrometry

Peptide mass fingerprinting (PMF) is a powerful technique in which experimentally measured m/z values of peptides resulting from a protein digest form the basis for a characteristic fingerprint of the intact protein. Due to its propensity to generate singly charged ions, along with its relative insensitivity to salts and buffers, matrix-assisted laser desorption and ionization (MALDI)-time-of-flight mass spectrometry (TOFMS) is the MS method of choice for PMF. The qualitative features of the mass spectrum can be selectively tuned by employing different methods to prepare the protein digest and matrix for MALDI-TOFMS. The selective tuning of MALDI mass spectra in order to optimize PMF is addressed here. Bovine serum albumin, carbonic anhydrase, cytochrome c, hemoglobin alpha- and beta-chain, and myoglobin were digested with trypsin and then analyzed by MALDI-TOFMS. 2,5-dihydroxybenzoic acid (DHB) and alpha-cyano-4-hydroxycinnamic acid (CHCA) were prepared using six different sample preparation methods: dried droplet, application of protein digest on MALDI plate followed by addition of matrix, dried droplet with vacuum drying, overlayer, sandwich, and dried droplet with heating. Improved results were obtained for the matrix alpha-cyano-4-hydroxycinnamic acid using a modification of the died droplet method in which the MALDI plate was heated to 80 °C prior to matrix application, which is supported by observations from scanning electron microscopy. Although each protein was found to have a different optimum sample preparation method for PMF, in general higher sequence coverage for PMF was obtained using DHB. The best PMF results were obtained when all of the mass spectral data for a particular protein digest was convolved together.     

Study of non-covalent complexation between catechin derivatives and peptides by electrospray ionization mass spectrometry

The recent development of electrospray ionization mass spectrometry (ESI-MS) has allowed its use to study molecular interactions driven by non-covalent forces. ESI-MS has been used to detect non-covalent complexes between proteins and metals, ligands and peptides and interactions involving DNA, RNA, oligonucleotides and drugs. Surprisingly, the study of the interaction between polyphenolic molecules and peptides/proteins is still an area where ESI-MS has not benefited. With regard to the important influence of these interactions in the biological and food domains, ESI-MS was applied to the detection and the characterization of soluble polyphenol-peptide complexes formed in model solution. The ability to observe and monitor the weak interactions involved in such macromolecular complexation phenomena was demonstrated for monomeric and dimeric flavonoid molecules (catechin-derived compounds) largely encountered in plants and plant derived products. Intact non-covalent polyphenol-peptide complexes were observed by ESI-MS using different experimental conditions. Utilizing mild ESI interface conditions allowed the detection of 1 : 1 polyphenol-peptide complexes in all tested solutions and 2 : 1 complexes for the dimers and galloylated polyphenols (flavanols). These results show that there is a preferential interaction between polymerized and/or galloylated polyphenols and peptide compared with that between monomeric polyphenols and peptides. Thus, ESI-MS shows potential for the study of small polyphenolic molecule-peptide interactions and determination of stoichiometry.     

A novel method for identification and relative quantification of N-terminal peptides using metal-element-chelated tags coupled with mass spectrometry

By means of the reaction between a DOTA-NHS-ester bifunctional reagent and N-terminal peptides of proteins,and then chelation of lanthanide metal ions as tags,we established a novel method for the identification of N-terminal peptides of proteins and their relative quantification using metal-element-chelated tags coupled with mass spectrometry.The experimental results indicate that metal elements are able to completely label N-terminal peptides at the protein level.The N-terminal peptides are enriched as the peptides digested with trypsin are selectively eliminated by isothiocyanate-coupled silica beads.We successfully identified the N-terminal peptides of 158 proteins of Thermoanaerobacter tengcongensis incubated at 55 and 75°C,among which N-terminal peptides of 24 proteins are partially acetylated.Moreover,metal-element tags with high molecule weights make it convenient for N-terminal peptides consisting of less than 6 amino acids to be identified;these make up 55percent of the identified proteins.Finally,we developed a general approach for the relative quantification of proteins based on N-terminal peptides.We adopted lysozyme and ribonuclease B as model proteins;the correlation coefficients(R2)of the standard curves for the quantitative method were 0.9994 and 0.9997,respectively,with each concentration ratio ranging from0.1 to 10 and both relative standard derivations(RSD)measured at less than 5%.In T.tengcongensis at two incubation temperatures,80 proteins possess quantitative information.In addition,compared with the proteins of T.tengcongensis incubated at 55°C,in T.tengcongensis incubated at 75°C,7 proteins upregulate whereas 16 proteins downregulate,and most differential proteins are related to protein synthesis.     

Confirmatory analysis of Trenbolone using accurate mass measurement with LC/TOF-MS

The use of accurate mass measurement as a confirmation tool is examined on a TOF-MS and compared with confirmation using a triple quadrupole mass spectrometer (QqQ-MS). Confirmation of the identity of a substance using mass-spectrometric detection has been described. However, the use of accurate mass measurement for confirmatory analysis has not been taken into account. In this study, criteria for confirmation with accurate mass are proposed and feasibility is demonstrated. Mass accuracy better than 3 ppm of the quasi-molecular ion and a fragment and their relative ratios determined with LC/TOF-MS are compared to the criteria of two transition ions and their ratio of LC/QqQ-MS. The results show that these criteria can be met for Trenbolone in samples of bovine urine and that single MS accurate mass measurement is comparable to nominal mass MS/MS for confirmation. The increase in popularity and availability of LC/TOF-MS instruments and the ease, of which exact masses can be measured, make it important to formulate criteria for this type of instrumentation. It is shown in this study that accurate mass measurement can be used for confirmatory analysis. However, more experiments need to be conducted to demonstrate the applicability of accurate mass measurement in general for residue analysis.     

Chromatographic and physical studies of tropomyosin in aqueous-organic media at low pH

Non-cross-linked and disulfide-cross-linked two-chain molecules comprising the alpha and/or beta chains of rabbit skeletal tropomyosin were studied by electrophoretic, chromatographic and physical methods. Elution order on C4 reversed-phase high-performance liquid chromatography depends markedly on the number and position of the cross-links. In the C4 reversed-phase elution medium, cross-linked and non-cross-linked species are greater than 85% helical by circular dichroism, but the non-cross-linked elute later from high-performance size-exclusion chromatography (G4000) and have molecular mass of 31,000-41,000 dalton by equilibrium ultracentrifugation. The data suggest that in the C4 reversed-phase high-performance liquid chromatography elution medium non-cross-linked tropomyosin exists as amphipathic single-chain alpha-helices.     

The carbon versus mass diagram to visualize and exploit FTICR‐MS data of natural organic matter

A two‐dimensional diagram is proposed, in which the carbon number of each formula is plotted against its nominal mass, to visualize large sets of molecular formula data that can be derived from data generated by ultrahigh‐resolution Fourier transform ion cyclotron resonance‐MS. In such a carbon versus mass (CvM) diagram, each formula (C_cH_hO_o) is unambiguously described by c, its (nominal) mass and the parameter i = c + o. Calculations of chemically allowable formulas illustrate that organic molecules occupy only certain spaces in such a diagram. The extension of these spaces increases with molecular mass in x‐direction (hydrogenation) and y‐direction (oxygenation). The data sets of molecules determined in natural organic matter(NOM) occupy only a certain range of the allowable space. The intensity of the mass spectrometric signals can be included as the third dimension into a CvM diagram. Separate CvM diagrams can be plotted for NOM molecules that include different heteroatoms. The benefits of the CvM diagram are illustrated by application onto data sets of fulvic acids from riverine and marine origin, of secondary organic aerosol, including organosulfates and organonitrates, as well as of ozonation of fulvic acids. The CvM diagram is a useful tool to visualize the elemental regularities in NOM isolates as well as the differences between isolates. It may also be applicable to large sets of molecular formula data generated in other disciplines such as petroleum biogeochemistry or metabolomics. Copyright © 2010 John Wiley & Sons, Ltd.     

Detailed molecular characterization of castor oil ethoxylates by liquid chromatography multistage mass spectrometry

The molecular characterization of castor oil ethoxylates (CASEOs) was studied by reverse-phase liquid chromatography (RPLC) mass spectrometry (MS) and multistage mass spectrometry (MS(n)). The developed RPLC method allowed the separation of the various CASEO components, and especially, the baseline separation of multiple nominal isobars (same nominal mass) and isomers (same exact mass). MS and MS(n) were used for the determination and structure elucidation of various structures and for the discrimination of the isobars and isomers. Different ionization techniques and adduct ions were also tested for optimization of the MS detection and the MS(n) fragmentation. A unique fragmentation pathway of ricinoleic acid is proposed, which can be used as a marker of the polymerization process and the topology of ethoxylation in the CASEO. In addition, characteristic neutral losses of ricinoleic acid reveal its (terminal or internal) position in the molecule.     

Synthesis of DNA conjugates by solid-phase fragment condensation via aldehyde-nucleophile coupling

Oligodeoxyribonucleotides were synthesized that contain a novel nucleoside, 2′-O-(2,3-dihydroxypropyl)cytidine. Its 2′-diol group was blocked by an allyloxycarbonyl protecting group. Selective deprotection of diol group(s) of the support-immobilized blocked oligodeoxyribonucleotide by Pd(0) followed by periodate oxidation resulted in generation of the 2′-aldehyde group(s) on solid-phase. The modified oligonucleotides were used to prepare a number of conjugates with acridine, biotin and N-modified laminin peptides by oxime, hydrazone and hydrazine formation. The method may be applicable to the synthesis of oligonucleotide-peptide conjugates.     

Enhanced mass detection of oligonucleotides using reverse-phase high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry

A new method providing enhanced sensitivity for the analysis of oligonucleotides using an on-line coupled system of reversed-phase high-performance liquid chromatography (RP-HPLC) and electrospray ionization ion-trap mass spectrometry (ESI-MS) has been developed. The presented method allows the use of the standard gradient elution of 0.1 M triethylammonium acetate (TEAA) buffer (adjusted to pH 7.0 with acetic acid) and acetonitrile that is typically used for the separation of oligonucleotides in RP-HPLC. An added feature of this method is the ability to combine and mix additional 0.1 M imidazole in acetonitrile after the separation column for improved ESI-MS performance. This is similar to the post-column reaction method in liquid chromatography (LC) and the liquid sheath flow method in LC/ESI-MS, both of which offer the advantage of not compromising the chromatographic separation conditions. The application of this new method is demonstrated to afford improved sensitivity for the analysis of oligonucleotides (20-50 mer) via on-line coupled HPLC/ESI-MS analysis and purification systems.     

Peptide sequencing through N-terminal phosphonylation and electrospray ionization mass spectrometry

Peptides were phosphonylated at their N-termini by reacting with ethoxyphenylphosphinate in the presence of triethylamine and tetrachloromethane under mild conditions. The phosphonylated peptides were analyzed by tandem electrospray ionization mass spectrometry. N-Terminal phosphonylation selectively increased the intensities of b(n)-type ions relative to other ion types. The resulting simplified mass spectra clearly show the sequential loss of amino acid residues from the C-termini of peptides, providing a convenient and rapid method for peptide sequencing.     

MALDI post-source decay and LIFT-TOF/TOF investigation of α-cyano-4-hydroxycinnamic acid cluster interferences

Large signals from alpha-cyano-4-hydroxycinnamic acid (CHCA) matrix complexes with sodium and potassium ions were found to interfere with sensitive matrix-assisted laser desorption/ionization (MALDI) analysis of a hydrochloric acid digest of gelatine preparations. The nature of some selected matrix clusters was investigated by conventional post-source decay and LIFT-TOF/TOF experiments. The matrix clusters fragmented readily by neutral evaporation to give smaller sized matrix cluster species without matrix disintegration. Their characterization distinguished them from peptide signals, in particular from those that had the same nominal mass and differed only in the fractional part of the mass as encountered for gelatine-derived peptides. Knowledge of the molecular composition of these cluster species allowed using them for internal calibration of the MALDI mass spectra. The hydrolytic peptides could be analyzed with increased sensitivity when using 2,5-dihydroxy benzoic acid (DHB) as the MALDI matrix.     

Probing of arginine residues in peptides and proteins using selective tagging and electrospray ionization mass spectrometry

A general labelling method is presented which allows the determination of the number of guanidine groups (related to arginine and homoarginine in peptides and proteins) by means of mass spectrometry. It implies a guanidine-selective derivatization step with 2,3-butanedione and an arylboronic acid under aqueous, alkaline conditions (pH 8-10). The reaction mixture is then directly analysed by electrospray ionization mass spectrometry without further sample pretreatment. Other amino acids are not affected by this reaction although it is demonstrated that lysine side-chains may be unambiguously identified when they are converted to homoarginine prior to derivatization. Guanidine functionalities, as e.g. in the amino acid arginine, are easily identified by the characteristic mass shift between underivatized and derivatized analyte. The tagging procedure is straightforward and selective for guanidine groups. The influence of several experimental parameters, especially the pH of the solution and the choice of reagents, is examined and the method is applied to various arginine-containing peptides and to lysozyme as a representative protein. Possible applications of this technique and its limitations are discussed.     

氨基酸-稳定同位素稀释质谱法用于合成肽段准确含量分析

建立了氨基酸同位素稀释液相色谱-串联质谱法准确测定合成肽段绝对含量的方法。实验中对合成肽段的纯度进行了表征,色谱纯度表征结果为99%以上,质谱纯度为90%以上。在肽段溶液中加入13C标记的氨基酸后进行酸溶液水解时间的优化,水解后的氨基酸直接经液相色谱分离和质谱检测,结果表明肽段中的被测氨基酸在150 ℃、6 mol/L HCl溶液水解4～6 h就可以达到水解平衡。每个肽段选择两个或两个以上的被测氨基酸,测得随机选择的5种合成肽段的绝对含量为62.07%～88.18%,测定结果的相对标准偏差小于8%,相对误差小于5%,均满足定量要求。除常用的被测氨基酸苯丙氨酸、缬氨酸、异亮氨酸外,还考察了选择赖氨酸和精氨酸作为被测氨基酸的可行性,实验结果表明增加精氨酸为被测氨基酸是可行的,从而进一步增加了方法的普适性。该方法的建立避免了色谱法定量时氨基酸衍生化处理带来的副反应影响及操作繁琐等问题,提高了肽段含量测定的准确度和精密度,为肽段含量的准确测定提供了一种新的方法。