Exploration of possible binding sites of nanoparticles on protein by cross-linking chemistry coupled with mass spectrometry

For the first time, the possible binding site of nanoparticles on protein was revealed by cross-linking chemistry coupled with mass spectrometry. The peptides located very close to the poly(acrylic acid) (PAA)-coated Fe(3)O(4) nanoparticles (NPs) during interaction with human serum albumin (HSA) were cross-linked to the surface of NPs. Following protease digestion, the attached peptides were cleaved off the particle surface and identified by matrix-assisted laser desorption/ionization-time-of-flight-mass spectrometry (MALDI-TOF-MS). The peptides were found to be part of the so-called drug binding site 2 of HSA; and the competitive binding to HSA between the corresponding drug, ibuprofen, and the NPs was observed. Our results demonstrated that cross-linking chemistry coupled with MS was a quick and simple method for locating the possible binding sites of NPs on protein. Information on NP-protein binding interface will benefit the study of how the interactions are governed by the physicochemical properties of NPs, for guiding the design of functional bionano constructs. It can also help to predict the biological consequence of protein adsorption on NPs, for obtaining more knowledge on nanotoxicity.     

Approach for determining protein ubiquitination sites by MALDI-TOF mass spectrometry

Protein ubiquitination plays an important role in the degradation and other functional regulation of cellular proteins in organisms ranging from yeasts to mammals. Trypsin digestion of ubiquitin conjugated proteins produces diglycine branched peptides in which the C-terminal Gly-Gly fragment of ubiquitin is attached to the epsilon-amino group of a modified lysine residue within the peptide. This provides a platform for mapping ubiquitination sites using mass spectrometry. Here we report the development of a novel strategy for determining posttraslational protein ubiquitination based on the N-terminal sulfonation of diglycine branched peptides. In contrast to conventional tandem MS spectra of native tryptic peptides, MALDI MS/MS analysis of a sulfonated tryptic peptide containing a diglycine branch generates a unique spectrum composed of a signature portion and a sequence portion. The signature portion of the spectrum consists of several intense ions resulting from the elimination of the tags, the N-terminal residues at the peptide and the branch, and their combination. This unique ion distribution pattern can distinguish ubiquitination modificatons from others and can identify the first N-terminal residues of the peptides as well. The sequence portion consists of an exclusive series of y-type ions and y' ions (differing by the loss of one glycine residue from the sulfonated diglycine branch) that can directly reveal the amino acid sequence of the peptide and the precise location of the ubiquitination site. The technique is demonstrated for a series of synthetic peptides and is validated by a model protein, tetraubiquitin. Our results show that the MALDI MS/MS analysis of sulfonated tryptic peptides can provide a highly effective method for the determination of ubiquitination substrates, ubiquitination sites on protein targets, and modification sites on ubiquitins themselves.     

Glycan analysis by reversible reaction to hydrazide beads and mass spectrometry

Investigation into glycoproteins and their associated glycans is the key to understanding the function of glycoproteins in biological pathways and disease development. Current methods for glycan analysis are generally based on multiple preparation processes to separate glycans from proteins and other molecules prior to analysis. During the multistep purification processes, glycans are continuously lost and the procedure increases the difficulty for accurate quantitative analysis of glycans. Here we describe the development of a novel technique, which uses hydrazide beads to capture glycans. It is based on the conjugation of glycans to hydrazide beads through the formation of reversible hydrazone, washing out unbound nonglycans, then releasing captured glycans by acids. The results showed that the glycans were able to be isolated from concatenate peptides by using hydrazide beads. This technique was also applied to the analysis of glycans from sera sample. The integrated capture-release on the solid-phase simplifies the procedure for glycan preparation from a complex mixture and can be a powerful tool for glycan analysis.     

An on-line protein digestion device for rapid peptide mapping by electrospray mass spectrometry

A simple laboratory-constructed device has been developed for fast on-line protein digestion followed by peptide mapping by use of electrospray mass spectrometry. Taking advantage of its nonsolubility properties at near-neutral pH values, pepsin could be nonpermanently attached to the PEEK tube commonly employed as transfer capillary between the syringe and the electrospray ion source. After optimization of experimental conditions such as pH, solvent, and exposure time, efficient digestion of several model proteins of molecular weights between 14,000 and 66,000, some having disulfide bridges, was successfully carried out. This technique provided reliable and reproducible sequence information by means of C-terminal-specific cleavages of aromatic and hydrophobic residues. As an application, protein identification could be achieved using a protein database search software.     

Identification and quantitative studies of protein immobilization sites by stable isotope labeling and mass spectrometry

A method was developed for characterizing immobilization sites on a protein based on stable isotope labeling and MALDI-TOF mass spectrometry. The model for this work was human serum albumin (HSA) immobilized onto silica by the Schiff base method. The immobilized HSA was digested by various proteolytic enzymes in the presence of normal water, while soluble HSA was digested in (18)O-enriched water for use as an internal standard. These two digests were mixed and analyzed, with the (18)O/(16)O ratio for each detected peptide then being measured. Several peptides in the tryptic, Lys-C, and Glu-C digests gave significantly higher (18)O/(16)O ratios than other peptides in the same digests, implying their involvement in immobilization. Analysis of these results led to identification of the N-terminus and several lysines as likely immobilization sites for HSA (e.g., K4, K41, K190, K225, K313, and K317). It was also possible from these results to quantitatively rank these sites in terms of the relative degree to which each might take part in immobilization. This method is not limited to HSA and silica but can be used with other proteins and supports.     

Fiber introduction mass spectrometry: fully direct coupling of solid-phase microextraction with mass spectrometry

This work describes the first fully direct coupling of solid-phase microextraction (SPME) with mass spectrometry. An inlet system using a septum as the only interface between the ambient and the high-vacuum mass spectrometer was constructed to allow the introduction of the SPME needle directly into the ionization region of a mass spectrometer. The PDMS-coated fiber was then placed and exposed exactly between the two ionization filaments. Uniform heating of the fiber, efficient thermal desorption, and electron ionization of the analytes were achieved. Using this new analytical technique, here termed fiber introduction mass spectrometry (FIMS), we have been able to detect and quantitate several volatile (VOC) and semivolatile (SVOC) organic chemicals (carbon tetrachloride, benzene, toluene, xylenes, gamma-terpinene, diisoamyl ether, chlorobenzene, and many PAHs) and two herbicides (Sylvex and its methyl ether) from aqueous solutions at low-ppb to ppt levels using either SPME headspace or solution extraction. FIMS shows high sensitivity (ng/L), good reproducibility, and accuracy, providing therefore a simple and effective approach to rapid analysis of VOC and SVOC in various matrixes.     

Nanosecond laser-induced photochemical oxidation method for protein surface mapping with mass spectrometry

We have developed an ultrafast pulse method for protein surface footprinting by laser-induced protein surface oxidations. This method makes use of a pulse UV laser that produces, in nanoseconds, a high concentration of hydroxyl (OH) free radicals by photodissociation of a hydrogen peroxide (H2O2) solution. The OH radicals oxidize amino acid residues located on the protein surface to produce stable covalent modifications. The oxidized protein is then analyzed by mass spectrometry to map the oxidized amino acid residues. Ubiquitin and apomyoglobin were used as model proteins in this study. Our results show that a single laser pulse can produce extensive protein surface oxidations. We found that monooxidized ubiquitins were more susceptible to further oxidations by subsequent laser irradiation, as compared to nonoxidized ones. This is due to the conformational changes of proteins by oxidation that increases the solvent-accessible surface area. Therefore, it is crucial to perform this experiment with a single pulse of laser so as to avoid oxidation of proteins after conformation of the protein changes. Subsequently, to obtain a high frequency and coverage of the oxidation sites while keeping the number of laser shots to one, we further optimized the laser power and concentration of hydrogen peroxide as well as the concentration of protein. This ultrafast OH radical generation method allows for rapid and accurate detection of surface residues, enabling mapping of the solvent-accessible regions of a protein in its native state.     

Complete characterization of posttranslational modification sites in the bovine milk protein PP3 by tandem mass spectrometry with electron capture dissociation as the last stage

A comprehensive approach to protein identification and determination of sites of posttranslational modifications (PTMs) in heavily modified proteins was tested. In this approach, termed "reconstructed molecular mass analysis" (REMMA), the molecular mass distribution of the intact protein is measured first, which reveals the extent and heterogeneity of modifications. Then the protein is digested with one or several enzymes, with peptides separated by reversed-phase HPLC, and analyzed by Fourier transform mass spectrometry (FTMS). Vibrational excitation (collisional or infrared) or electron capture dissociation (ECD) of peptide ions provides protein identification. When a measured peptide molecular mass indicates the possibility of a PTM, vibrational excitation is applied to determine via characteristic losses the type and eventually the structure of the modification, while ECD determines the PTM site. Chromatographic peak analysis continues until full sequence coverage is obtained, after which the molecular mass is reconstructed and compared with the measured value. An agreement indicates that the PTM characterization was complete. This procedure applied to the bovine milk PP3 protein containing 25% modifications by weight yielded all known modifications (five phosphorylations, two O- and one N-glycosylation) as well as the previously unreported NeuNAc-Hex-[NeuNAc]HexNAc group O-linked to Ser60. With the FTMS performance improved, REMMA can serve as the basis for high-throughput, high-sensitivity PTM characterization of biological important proteins, which should speed up the proteomics research.     

Phosphopeptide/phosphoprotein mapping by electron capture dissociation mass spectrometry

Of methods for dissociation of multiply charged peptide and protein ions, electron capture dissociation (ECD) has the advantages of cleaving between a high proportion of amino acids, without loss of such posttranslational modifications as glycosylation and carboxylation. Here this capability is successfully extended to phosphorylation, for which collisionally activated dissociation (CAD) can cause extensive loss of H3PO4 and HPO3. As shown here, these losses are minimal in ECD spectra, an advantage for measuring the degree of phosphorylation. For phosphorylated peptides, ECD and CAD spectra give complementary backbone cleavages for identifying modification sites. For a 24-kDa heterogeneous phosphoprotein, bovine beta-casein, activated ion ECD cleaved 87 of 208 backbone bonds that identified a phosphorylation site at Ser-15, and localized three more among Ser-17,-18, -19, and -22 and Thr-24, and the last among four other sites. This is the first direct site-specific characterization of this key post-translational modification on a protein without its prior degradation, such as proteolysis.     

Detection of in vitro kinase generated protein phosphorylation sites using gamma[18O4]-ATP and mass spectrometry

A novel stable-isotope labeling approach for identification of phosphopeptides that utilizes adenosine triphosphate, in which four oxygen-16 atoms attached to the terminal phosphate group are substituted with oxygen-18 [gamma((18)O4)-ATP], has been developed. The ability to use gamma((18)O4)-ATP to monitor phosphorylation modification within various proteins was conducted by performing in vitro kinase reactions in the presence of a 1:1 mixture of gamma((18)O4)-ATP and normal isotopic abundance ATP (ATP). After tryptic digestion, the peptides were analyzed using mass spectrometry (MS). Phosphorylated peptides are easily recognized within the MS spectrum owing to the presence of doublets separated by 6.01 Da; representing versions of the peptide modified by ATP and gamma((18)O4)-ATP. Standard peptides phosphorylated using gamma((18)O4)-ATP via in vitro kinase reactions showed no exchange loss of (18)O with (16)O. The identity of these doublets as phosphorylated peptides could be readily confirmed using tandem MS. The method described here provides the first direct stable-isotope labeling method to definitely detect phosphorylation sites within proteins.     

Use of top-down and bottom-up Fourier transform ion cyclotron resonance mass spectrometry for mapping calmodulin sites modified by platinum anticancer drugs

Calmodulin (CaM) is a highly conserved, ubiquitous, calcium-binding protein; it binds to and regulates many different protein targets, thereby functioning as a calcium sensor and signal transducer. CaM contains 9 methionine (Met), 1 histidine (His), 17 aspartic acid (Asp), and 23 glutamine acid (Glu) residues, all of which can potentially react with platinum compounds; thus, one-third of the CaM sequence is a possible binding target of platinum anticancer drugs, which represents a major challenge for identification of specific platinum modification sites. Here, top-down electron capture dissociation (ECD) was used to elucidate the transition metal-platinum(II) modification sites. By using a combination of top-down and bottom-up mass spectrometric (MS) approaches, 10 specific binding sites for mononuclear complexes, cisplatin and [Pt(dien)Cl]Cl, and dinuclear complex [{cis-PtCl(2)(NH(3))}(2)(μ-NH(2)(CH(2))(4)NH(2))] on CaM were identified. High resolution MS of cisplatin-modified CaM revealed that cisplatin mainly targets Met residues in solution at low molar ratios of cisplatin-CaM (2:1), by cross-linking Met residues. At a high molar ratio of cisplatin:CaM (8:1), up to 10 platinum(II) bind to Met, Asp, and Glu residues. [{cis-PtCl(2)(NH(3))}(2)(μ-NH(2)(CH(2))(4)NH(2))] forms mononuclear adducts with CaM. The alkanediamine linker between the two platinum centers dissociates due to a trans-labilization effect. [Pt(dien)Cl]Cl forms {Pt(dien)}(2+) adducts with CaM, and the preferential binding sites were identified as Met51, Met71, Met72, His107, Met109, Met124, Met144, Met145, Glu45 or Glu47, and Asp122 or Glu123. The binding of these complexes to CaM, particularly when binding involves loss of all four original ligands, is largely irreversible which could result in their failure to reach the target DNA or be responsible for unwanted side-effects during chemotherapy. Additionally, the cross-linking of cisplatin to CaM might lead to the loss of the biological function of CaM or CaM-Ca(2+) due to limiting the flexibility of the CaM or CaM-Ca(2+) complex to recognize target proteins or blocking the binding region of target proteins to CaM.     

Bacterial identification by protein mass mapping combined with an experimentally derived protein mass database

A protein mass mapping approach using mass spectrometry (MS) combined with an experimentally derived protein mass database is presented for rapid and effective identification of bacterial species. A prototype mass database from the protein extracts of nine bacterial species has been created by off-line high-performance liquid chromatography (HPLC) matrix-assisted laser desorption/ionization (MALDI) MS, in which the microbiological parameter of bacterial growth time is considered. A numerical method using a statistical weight factor algorithm is devised for matching the protein masses of an unknown bacterial sample against the database. The sum of these weight factors produces a corresponding summed weight factor score for each bacterial species listed in the database, and the database species producing the highest score represents the identity of the respective unknown bacterium. The applicability and reliability of this protein mass mapping approach has been tested with seven bacterial species in a single-blind study by both direct MALDI MS and HPLC electrospray ionization MS methods, and identification results with 100% accuracy are obtained. Our studies have demonstrated that the protein mass database can be rapidly established and readily adopted with relatively less dependency on experimental factors. Furthermore, it is shown that a number of proteins can be detected using a protein sample amount equivalent to an extract of less than 1000 cells, demonstrating that this protein mass mapping approach can potentially be highly sensitive for rapid bacterial identification.     

Millisecond radiolytic modification of peptides by synchrotron X-rays identified by mass spectrometry.

Radiolysis of peptide and protein solutions with high-energy X-ray beams induces stable, covalent modifications of amino acid residues that are useful for synchrotron protein footprinting. A series of 5-14 amino acid residue peptides of varied sequences were selected to study their synchrotron radiolysis chemistry. Radiolyzed peptide products were detected within 10 ms of exposure to a white light synchrotron X-ray beam. Mass spectrometry techniques were used to characterize radiolytic modification to amino acids cysteine (Cys), methionine (Met), phenylalanine (Phe), tyrosine (Tyr), tryptophan (Trp), proline (Pro), histidine (His), and leucine (Leu). A reactivity order of Cys, Met > Phe, Tyr, > Trp > Pro > His, Leu was determined under aerobic reaction conditions from MS/MS analysis of the radiolyzed peptide products. Radiolysis of peptides in 18O-labeled water under aerobic conditions revealed that oxygenated radical species from air and water both contribute to the modification of amino acid side chains. Cysteine and methionine side chains reacted with hydroxyl radicals generated from radiolysis of water as well as molecular oxygen. Phenylalanine and tyrosine residues were modified predominantly by hydroxyl radicals, and the source of modification of proline was exclusively through molecular oxygen.     

Individualization of gasoline samples by covariance mapping and gas chromatography/mass spectrometry

A set of 10 fresh (unevaporated) gasoline samples from a single metropolitan area were differentiated based on a covariance mapping method combined with a t-test statistic. The covariance matrix for each sample was calculated from the retention time-ion abundance data set obtained by gas chromatography/mass spectrometry analysis. Distance metrics were calculated between the covariance matrices from replicate analyses of the same sample and between the replicate analyses of different samples. The distance metric for the same-sample comparisons were shown to constitute a population significantly different from the distance metric for the different-sample comparisons. A power analysis was performed to estimate the number of analyses needed to discriminate between two samples while maintaining a probability of type II error, beta, below 1%, e.g., a test power greater than 99%. Triplicate analyses of two gasoline samples was shown to be sufficient to discriminate between the two using a t-test, while keeping beta<0.01 at a significance level, alpha, of 0.05. Analysis of the 45 possible pairwise comparisons between samples found that 100% of the samples were statistically distinguishable, and no type II errors occurred. Blind tests were conducted wherein 2 of the 10 gasoline samples where presented as unknowns. One of the unknowns was found to be indistinguishable from the original source, and one unknown was determined to be statistically different from the original source, constituting a type I error. The effects of evaporation on sample comparison are not addressed in this paper. The results from this study demonstrate a statistically acceptable method of physical evidence comparison in forensic casework.     

Proteomic profiling of intact mycobacteria by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Current methods for the identification of mycobacteria in culture are time-consuming, requiring as long as 12 weeks for positive identification. One potential approach to rapid mycobacterial identification is to utilize proteomic profiling of cultures by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). In this report, we have applied MALDI-TOF MS to proteomic profiling of cultured microorganisms representing six species of the genus Mycobacterium. We find that analysis of acetonitrile/trifluoroacetic acid cellular extracts produces data similar to that of the analysis of deposited whole cells, while minimizing human contact with the microorganisms and rendering them nonviable. A matrix composition of alpha-cyano-4-hydroxycinnamic acid with fructose yields highly reproducible MALDI-TOF spectra. Statistical analysis of MALDI-TOF MS data allows differentiation of each individual mycobacterial species on the basis of unique mass fingerprints. The methodology allows identification of a number of unique (potentially diagnostic) biomarkers as targets for protein identification by MS/MS experiments. In addition, we observe a number of signals common to all mycobacterial species studied by MALDI-TOF MS, which may be genus-specific biomarkers. The potentially genus-specific biomarkers occur at low mass (<2 kDa) and are likely to be lipids and cell wall components such as mycolic acids. This study demonstrates the potential for mass spectrometry-based identification/classification of mycobacteria.     

Analysis of protein phosphorylation by hypothesis-driven multiple-stage mass spectrometry

We describe a strategy, which we term hypothesis-driven multiple-stage mass spectrometry (HMS-MS), for the sensitive detection and identification of phosphopeptides derived from enzymatic digests of phosphoproteins. In this strategy, we postulate that any or all of the potential sites of phosphorylation in a given protein may be phosphorylated. Using this assumption, we calculate the m/z values of all the corresponding singly charged phosphopeptide ions that could, in theory, be produced by the enzyme employed for proteolysis. We test ions at these m/z values for the presence of phosphoserine or phosphothreonine residues using tandem mass spectrometry (MS(2)) in a vacuum MALDI ion trap mass spectrometer, where the neutral loss of the elements of H(3)PO(4) (98 Da) provides a sensitive assay for the presence of phosphopeptides. Subsequent MS(3) analysis of the (M + H - 98)(+) peaks allows us to confirm or reject the hypotheses that the putative phosphopeptides are present in the sample. HMS-MS was successfully applied to the detection and identification of phosphopeptides from substrates of the Saccharomyces cerevisiae cyclin-dependent kinase (Cdk) Cdc28, phosphorylated in vitro (Ipl1) and in vivo (Orc6), basing hypothesis formation on the minimal Cdk consensus phosphorylation motif Ser/Thr-Pro. The method was also used to find in vitro phosphopeptides from a domain of the Drosophila melanogaster protein PERIOD, hypothesizing possible phosphorylations of all Ser/Thr residues without assuming a consensus motif. Our results demonstrate that HMS-MS is a sensitive, highly specific tool for systematically surveying proteins for Ser/Thr phosphorylation, and represents a significant step toward our goal of comprehensive phosphorylation mapping.     

Stable-isotope labeled hydrophobic hydrazide reagents for the relative quantification of N-linked glycans by electrospray ionization mass spectrometry

This study presents the development of stable-isotope labeled hydrophobic, hydrazide reagents for the relative quantification of N-linked glycans. The P2GPN "light" ((12)C) and "heavy" ((13)C(6)) pair are used to differentially label two N-linked glycan samples. The samples are combined 1:1, separated using HILIC, and then mass differentiated and quantified using mass spectrometry. These reagents have several benefits: (1) impart hydrophobic character to the glycans affording an increase in electrospray ionization efficiency and MS detection; (2) indistinguishable chromatographic, MS, and MS/MS performance of the "light" and "heavy" reagents affording relative quantification; and (3) analytical variability is significantly reduced due to the two samples being mixed together after sample preparation. Obtaining these analytical benefits only requires ~4 h of sample preparation time. It is shown that these reagents are capable of quantifying changes in glycosylation in simple mixtures, and the analytical variability of the reagents in pooled plasma samples is shown to be less than ±30%. Additionally, the incorporation of an internal standard allows one to account for the difference in systematic error between the two samples due to the samples being processed in parallel and not mixed until after derivatization.     

Microorganism identification by mass spectrometry and protein database searches.

A method for rapid identification of microorganisms is presented, which exploits the wealth of information contained in prokaryotic genome and protein sequence databases. The method is based on determining the masses of a set of ions by MALDI TOF mass spectrometry of intact or treated cells. Subsequent correlation of each ion in the set to a protein, along with the organismic source of the protein, is performed by searching an Internet-accessible protein database. Convoluting the lists for all ions and ranking the organisms corresponding to matched ions results in the identification of the microorganism. The method has been successfully demonstrated on B. subtilis and E. coli, two organisms with completely sequenced genomes. The method has been also tested for identification from mass spectra of mixtures of microorganisms, from spectra of an organism at different growth stages, and from spectra originating at other laboratories. Experimental factors such as MALDI matrix preparation, spectral reproducibility, contaminants, mass range, and measurement accuracy on the database search procedure are addressed too. The proposed method has several advantages over other MS methods for microorganism identification.