Direct quantitation of peptide mixtures without standards using clusters formed by electrospray ionization mass spectrometry

Native mass spectrometry-based metabolomics identifies metal-binding compounds

Although metals are essential for the molecular machineries of life, systematic methods for discovering metal-small molecule complexes from biological samples are limited. Here, we describe a two-step native electrospray ionization-mass spectrometry method, in which post-column pH adjustment and metal infusion are combined with ion identity molecular networking, a rule-based data analysis workflow. This method enabled the identification of metal-binding compounds in complex samples based on defined mass (m/z) offsets of ion species with the same chromatographic profiles. As this native electrospray metabolomics approach is suited to the use of any liquid chromatography-mass spectrometry system to explore the binding of any metal, this method has the potential to become an essential strategy for elucidating metal-binding molecules in biology.

Optical and mass spectral characterization of the electrospray ionization/corona discharge ionization interface

The interchange between electrospray ionization (ESI) and corona discharge ionization (CDI) with respect to applied bias on the needle is customarily placed at the point where light production begins at the tip of the needle. If a liquid sample is flowing through a needle that is observed to produce light, the ionization process is assumed to be harsher and the term coronaspray ionization has been coined to describe this hybrid ionization mechanism. In this work, the transition between ESI and CDI is investigated with respect to applied bias through optical and mass spectrometric measurements. As a function of applied bias potential, the optical signal at the tip of the needle was recorded simultaneously with the resultant ionization products. In this effort, the production of ions from an electrospray ionization needle has been demonstrated to produce light regardless of bias if ions are also formed. With this understanding, an ESI/CDI needle was designed to allow the bias to be temporarily pulsed over the 'onset' voltage necessary for ionization and the rise and decay of the optical signal was measured. Positive mode CDI onset to a stable discharge state within 0.05 ms, while positive ESI required 1.9 ms to reach a stable condition. In the negative mode, the stability of the ionization process was highly variable in both ESI and CDI modes, though CDI was generally faster to reach the stable mode of operation. When the resultant ions were investigated, the effect of increased bias on an ESI needle was found to be species-dependent. Recognizing that the range of compounds probed was limited, for those examined, it appears that stable, non-labile species may be investigated via ESI under extremely high biases while labile species demonstrate a narrow range of stable biases before significant fragmentation occurs.

Dehydroascorbic acid S-Thiolation of peptides and proteins: Role of homocysteine and glutathione

Ascorbic acid (vitamin C) plays a significant role in the prevention of oxidative stress. In this process, ascorbate is oxidized to dehydroascorbate (DHA). We have investigated the impact of DHA on peptide/protein intramolecular disulfide formation as well as S-glutathionylation and S-homocysteinylation. S-glutathionylation of peptides/proteins is a reversible, potential regulatory mechanism in oxidative stress. Although the exact role of protein S-homocysteinylation is unknown, it has been proposed to be of importance in pathobiological processes such as onset of cardiovascular disease. Using an in vitro model system, we demonstrate that DHA causes disulfide bond formation within the active site of recombinant human glutaredoxin (Grx-1). DHA also facilities the formation of S-glutathionylation and S-homocysteinylation of a model peptide (AcFHACAAK) as well as Grx-1. We discuss the possible mechanisms of peptide/protein S-thiolation, which can occur either via thiol exchange or a thiohemiketal intermediate. A thiohemiketal DHA-peptide adduct was detected by mass spectrometry and its location on the peptide/protein cysteinyl thiol group was unambiguously confirmed by tandem mass spectrometry. This demonstrates that peptide/protein S-thiolation mediated by DHA is not limited to thiol exchange reactions but also takes place directly via the formation of a thiohemiketal peptide intermediate. Finally, we investigated a potential reducing role of glutathione (GSH) in the presence of S-homocysteinylated peptide/protein adducts. S-homocysteinylated AcFHACAAK, human hemoglobin α-chain and Grx-1 were incubated with GSH. Both peptide and proteins were reduced, and homocysteine replaced with GS-adducts by thiol exchange, as a function of time.

Trimethylation enhancement using diazomethane (TrEnDi): rapid on-column quaternization of peptide amino groups via reaction with diazomethane significantly enhances sensitivity in mass spectrometry analyses via a fixed, permanent positive charge

Defining cellular processes relies heavily on elucidating the temporal dynamics of proteins. To this end, mass spectrometry (MS) is an extremely valuable tool; different MS-based quantitative proteomics strategies have emerged to map protein dynamics over the course of stimuli. Herein, we disclose our novel MS-based quantitative proteomics strategy with unique analytical characteristics. By passing ethereal diazomethane over peptides on strong cation exchange resin within a microfluidic device, peptides react to contain fixed, permanent positive charges. Modified peptides display improved ionization characteristics and dissociate via tandem mass spectrometry (MS(2)) to form strong a2 fragment ion peaks. Process optimization and determination of reactive functional groups enabled a priori prediction of MS(2) fragmentation patterns for modified peptides. The strategy was tested on digested bovine serum albumin (BSA) and successfully quantified a peptide that was not observable prior to modification. Our method ionizes peptides regardless of proton affinity, thus decreasing ion suppression and permitting predictable multiple reaction monitoring (MRM)-based quantitation with improved sensitivity.

Highly sensitive and specific detection of histamine via the formation of a self-assembled magic number cluster with thymine by mass spectrometry

The self-assembled magic number cluster of thymine (T) significantly enhanced the MS signal of histamine with high specificity.

DNA oligonucleotides: a model system with tunable binding strength to study monomer-dimer equilibria with electrospray ionization-mass spectrometry

Electrospray ionization (ESI) is increasingly used to measure binding strengths, but it is not always clear whether the ESI process introduces artifacts. Here we propose a model monomer-dimer equilibrium system based on DNA oligonucleotides to systematically explore biomolecular self-association with the ESI-mass spectrometry (MS) titration method. The oligonucleotides are designed to be self-complementary and have the same chemical composition and mass, allowing for equal ionization probability, ion transmission, and detection efficiency in ESI-MS. The only difference is the binding strength, which is determined by the nucleotide sequence and can be tuned to cover a range of dissociation constant values. This experimental design allows one to focus on the impact of ESI on the chemical equilibrium and to avoid the other typical sources of variation in ESI-MS signal responses, which yields a direct comparison of samples with different binding strengths. For a set of seven model DNA oligonucleotides, the monomer-dimer binding equilibrium was probed with the ESI-MS titration method in both positive and negative ion modes. A mathematical model describing the dependence of the monomer-to-dimer peak intensity ratio on the DNA concentration was proposed and used to extract apparent Kd values and the fraction of DNA duplex that irreversibly dissociates in the gas phase. The Kd values determined via ESI-MS titration were compared to those determined in solution with isothermal titration calorimetry and equilibrium thermal denaturation methods and were found to be significantly lower. The observed discrepancy was attributed to a greater electrospray response of dimers relative to that of monomers.

Simultaneous quantitation of amino acid mixtures using clustering agents

A method that uses the abundances of large clusters formed in electrospray ionization to determine the solution-phase molar fractions of amino acids in multi-component mixtures is demonstrated. For solutions containing either four or 10 amino acids, the relative abundances of protonated molecules differed from their solution-phase molar fractions by up to 30-fold and 100-fold, respectively. For the four-component mixtures, the molar fractions determined from the abundances of larger clusters consisting of 19 or more molecules were within 25% of the solution-phase molar fractions, indicating that the abundances and compositions of these clusters reflect the relative concentrations of these amino acids in solution, and that ionization and detection biases are significantly reduced. Lower accuracy was obtained for the 10-component mixtures where values determined from the cluster abundances were typically within a factor of three of their solution molar fractions. The lower accuracy of this method with the more complex mixtures may be due to specific clustering effects owing to the heterogeneity as a result of significantly different physical properties of the components, or it may be the result of lower S/N for the more heterogeneous clusters and not including the low-abundance more highly heterogeneous clusters in this analysis. Although not as accurate as using traditional standards, this clustering method may find applications when suitable standards are not readily available.

Direct standard-free quantitation of Tamiflu and other pharmaceutical tablets using clustering agents with electrospray ionization mass spectrometry

Accurate and rapid quantitation is advantageous to identify counterfeit and substandard pharmaceutical drugs. A standard-free electrospray ionization mass spectrometry method is used to directly determine the dosage in the prescription and over-the-counter drugs Tamiflu, Sudafed, and Dramamine. A tablet of each drug was dissolved in aqueous solution, filtered, and introduced into solutions containing a known concentration of l-tryptophan, l-phenylalanine, or prednisone as a clustering agent. The active ingredient(s) incorporates statistically into large clusters of the clustering agent where effects of differential ionization/detection are substantially reduced. From the abundances of large clusters, the dosages of the active ingredients in each of the tablets were determined to typically better than 20% accuracy even when the ionization/detection efficiency of the individual components differed by over 100x. Although this unorthodox method for quantitation is not as accurate as using conventional standards, it has the advantages that it is fast, it can be applied to mixtures where the identities of the analytes are unknown, and it can be used when suitable standards may not be readily available, such as schedule I or II controlled substances or new designer drugs that have not previously been identified.

Standard-free quantitation of mixtures using clusters formed by electrospray mass spectrometry

Ion abundances in electrospray ionization mass spectra depend on many factors, including molecular hydrophobicity, basicity, solution composition, and instrumental parameters. A recently introduced method that uses nonspecific cluster ion abundances to obtain solution-phase molar fractions of analytes directly from ESI mass spectra without using standards was evaluated using solutions containing 0.03-24% L-threonine, D-threonine, L-leucine, L-lysine, L-glutamic acid, or diglycine with L-serine as a major component. Because of the propensity of serine clusters to exhibit "magic" numbers, which can be chirally selective, these experiments provide a rigorous test of this standard-free cluster quantitation method, which requires that clusters form statistically from analytes in solution. For each of these solutions, the compositions of clusters containing > or = 32 molecules reflect the solution molar fractions of each component. From the abundances of these larger clusters, the solution molar fraction can be determined to better than 10% accuracy over nearly 3 orders of magnitude in concentration. In contrast, the ionization/detection efficiency of the individual amino acids differs by as much as a factor of 460 in these experiments. The protonated octamer incorporates some molecules statistically but efficiently excludes other molecules that have significantly different properties or chirality. This standard-free quantitation method may be most advantageous for rapidly characterizing mixtures, such as products of chemical synthesis, which contain unknown products or molecules for which suitable standards are not readily available.