质谱在肽和蛋白质序列分析中的应用

了解肽和蛋白质的序列对理解其功能具有重要意义，测定其序列也是当前生命 科学研究中的重要内容之一，质谱作为高灵敏度的测定分子结构的仪器，其高灵敏 度、广泛的适用性及快速性等特性使它具有很大潜力发展成为辅助传统测序方法的 新方法，并得到了广泛的关注。从离子活化方法（包括碰撞诱导解离CID、源后裂 解PSD、源内裂解ISD等）、衍生化作用以及氨基酸残基消除方式（高能活化产生亚 稳离子、化学降解、酶降解）等多个角度介绍了利用质谱分析多肽和蛋白质序列的 方法，并对其发展前景作出展望。     

Qualitative and quantitative characterization of the arsenic‐binding behaviour of sulfur‐containing peptides and proteins by the coupling of reversed phase liquid chromatography to electrospray ionization mass spectrometry

Phenylarsenic‐substituted cysteine‐containing peptides and proteins were completely differentiated from their unbound original forms by the coupling of reversed phase liquid chromatography with electrospray ionization mass spectrometry. The analysis of biomolecules possessing structure‐stabilizing disulfide bridges after reduction provides new insights into requirements concerning the accessibility of cysteine residues for reducing agents as well as for arsenic compounds in a spatial protein structure. Complementary binding studies performed using direct ESI‐MS without chromatographic coupling in different solvent systems demonstrated that more than one binding site were activated for aprotinin and lysozyme in denaturing solvents because of a stronger defolding. From the intensities of the different charge states occurring in the mass spectra as well as from the LC elution behaviour, it can be deduced that the folding state of the arsenic‐bound protein species resembles the native, oxidized conformation. In contrast, although the milk protein α‐lactalbumin has several disulfide bridges, only one phenylarsenic moiety was bound under strongly denaturing conditions. Because of the charge state distribution in the ESI mass spectra, a conformational change to a molten globule structure is assumed. For the second considered milk protein ß‐lactoglobulin, a noncovalent interaction with phenylarsine oxide was detected. In general, smaller apparent binding constants for the condensation reactions of the biomolecules with phenylarsine oxide leading to covalent arsenic–sulfur bindings were determined from direct injection ESI‐MS measurements than from LC‐ESI‐MS coupling. The following order of binding affinities for one phenylarsenic group can be assumed from both ESI‐MS and LC‐ESI‐MS: nonapeptide vasopressin > nonapeptide vasotocin > lysozyme > aprotinin > α‐lactalbumin > thioredoxin. Kinetic investigations by LC‐ESI‐MS yielded a partial reaction order of 2 for vasopressin, Lys and α‐lactalbumin and corresponding half‐lives of 0.93, 2.56 and 123.5 min, respectively. Copyright © 2012 John Wiley & Sons, Ltd.     

Sequencing peptides by electrospray ion-trap mass spectrometry: A useful tool in synthesis of Axinastatin 3

Axinastatin 3 as a potential anticancer agent was synthesized by chemical methods. In an electrospray ion-trap mass spectrometer, using one stage of tandem mass spectrometry (MS/MS), the linear peptide intermediate was sequenced via the complementarities of y and b ions. Then, using multistep MS/MS (to MS⁶), the cyclic peptide was sequenced through sequentially removing one amino acid residue in each stage of MS/MS. The difference of the fragmentation mechanisms and the sequencing approaches between them is discussed.     

Liquid chromatographic/electrospray ionization tandem mass spectrometric study of the phenolic composition of cocoa (Theobroma cacao)

Liquid chromatography coupled with ionspray mass spectrometry in the tandem mode (LC/MS/MS) with negative ion detection was used for the identification of a variety of phenolic compounds in a cocoa sample. Gradient elution with water and acetonitrile, both containing 0.1% HCOOH, was used. Standard solutions of 31 phenolic compounds, including benzoic and cinnamic acids and flavonoid compounds, were studied in the negative ion mode using MS/MS product ion scans. At low collisional activation, the deprotonated molecule [M - H](-) was observed for all the compounds studied. For cinnamic and benzoic acids, losses of CO(2) or formation of [M - CH(3)](-*) in the case of methoxylated compounds were observed. However, for flavonol and flavone glycosides, the spectra present both the deprotonated molecule [M - H](-) of the glycoside and the ion corresponding to the deprotonated aglycone [A - H](-). The latter ion is formed by loss of the rhamnose, glucose, galactose or arabinose residue from the glycosides. Different fragmentation patterns were observed in MS/MS experiments for flavone-C-glycosides which showed fragmentation in the sugar part. Fragmentation of aglycones provided characteristic ions for each family of flavonoids. The optimum LC/MS/MS conditions were applied to the characterization of a cocoa sample that had been subjected to an extraction/clean-up procedure which involved chromatography on Sephadex LH20 and thin-layer chromatographic monitoring. In addition to compounds described in the literature, such as epicatechin and catechin, quercetin, isoquercitrin (quercetin-3-O-glucoside) and quercetin-3-O-arabinose, other compounds were identified for the first time in cocoa samples, such as hyperoside (quercetin-3-O-galactoside), naringenin, luteolin, apigenin and some O-glucosides and C-glucosides of these compounds.     

Size exclusion chromatography coupled to electrospray ionization mass spectrometry for analysis and quantitative characterization of arsenic interactions with peptides and proteins

Arsenic‐binding proteins are of toxicological importance since enzymatic activities can be blocked by arsenic interactions. In the present work, a novel methodology based on size exclusion chromatography coupled to electrospray ionization mass spectrometry (SEC‐ESI‐MS) was developed with special emphasis to preserve the intact proteins and their arsenic bindings. The eluent composition of 25 mM Tris/HCl, pH 7.5, with the addition of 100‐mM NaCl optimized for SEC with UV detection provided the highest SEC separation efficiency, but was not compatible with the ESI‐MS because of the non‐volatility of the buffer substance and of the salt additive. In order to find the best compromise between chromatographic separation and ionization of the arsenic‐binding proteins, buffer type and concentration, pH value, portion of organic solvent in the SEC eluent as well as the flow rate were varied. In the optimized procedure five different arsenic‐binding peptides and proteins (glutathione, oxytocin, aprotinin, α‐lactalbumin, thioredoxin) covering a molar mass range of 0.3–14 kDa could be analyzed using 75% 10‐mM ammonium formate, pH 5.0/25% acetonitrile (v : v) as eluent and a turbo ion spray source operated at 300 °C and 5.5 kV. A complete differentiation of all peptides and proteins involved in the arsenic‐binding studies as well as of their arsenic‐bound forms has become feasible by means of the extracted ion chromatograms (XIC) of the mass spectrometric detection. The new method offered the possibility to estimate equilibrium constants for the reaction of phenylarsine oxide with different thiol‐containing biomolecules by means of the XIC peak areas of reactants and products. Limits of detection in the range of 2–10 µM were obtained by SEC‐ESI‐MS for the individual proteins. Copyright © 2009 John Wiley & Sons, Ltd.     

Binding sites of [Ru(bpy)2(H2O)2](BF4)2 with sulfur- and histidine-containing peptides studied by electrospray ionization mass spectrometry and tandem mass spectrometry

The composition and binding sites of cis-[Ru(II)(bpy)2]2+-bound sulfur-containing peptides of Met-Arg-Phe-Ala, glutathione and oxidized glutathione, and also histidine-containing peptide of oxidized insulin B chain, were investigated by electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). The composition of Ru(II)-containing peptides was precisely determined by ESI-MS, zoom scan and simulation of isotope distribution patterns. MS/MS analysis shows that, in sulfur-containing peptides, the Ru(II) complex prefers to anchor to a carboxyl group, although some other potential binding sites of thiol, thioether and N-terminal amino groups present in these peptides, and in oxidized insulin B chain, Ru(II) first anchors to His10, then either to the hydroxyl group of Thr27 or to the carboxyl group of Ala30. Its secondary structure and microenvironment surrounding the potential binding sites may affect the binding ability of cis-[Ru(II)(bpy)2]2+ to oxidized insulin B chain.     

Liquid chromatographic/electrospray ionization mass spectrometric identification of the oxidation end-products of metformin in aqueous solutions

Metformin is an antihyperglycemic drug that exhibits some antioxidant properties. HO*-induced oxidation of metformin was studied in aqueous solution, in both aerated and deaerated conditions. Gamma radiolysis of water was used to generate HO* free radicals, capable of initiating one-electron oxidation of metformin. Oxidation end-products were identified by direct infusion mass spectrometry (MS) and high-performance liquid chromatography/mass spectrometry (HPLC/MSn): for every product, structure elucidation was based on its mass (simple mass spectra confirmed by HPLC/MS). In addition, fragmentation spectra (MS2, MS3 and MS4) and the determination of deuterium-hydrogen exchange sites provided valuable information allowing the complete identification of some of the end-products. At low radiation dose, four products were identified as primary ones, since they result from the direct attack of HO* radicals on metformin. These primary oxidation end-products were identified respectively as hydroperoxide of metformin, covalent dimer of metformin, methylbiguanide and 2-amino-4-imino-5-methyl-1,3,5-triazine. At high radiation dose, seven other products were identified as secondary ones, resulting from the HO*-induced oxidation of the primary end-products. A reaction scheme was postulated for the interpretation of the results.     

Degradation of poly(butyl methacrylate) model compounds studied via high‐resolution electrospray ionization mass spectrometry

This study investigates the degradation behavior of poly(n‐butyl methacrylate) ( p(nBMA) ), poly(tert‐butyl methacrylate) ( p(tBMA) ), and poly(hexafluoro butyl methacrylate) ( p(HFBMA) ) on a molecular level under extreme environmental conditions. The polymers chosen are readily applicable in the formulation of surface coatings and were degraded under conditions which replicated the harsh Australian climate, in which surface coatings may reach temperatures of up to 95 °C and are exposed to broad‐spectrum UV radiation of up to 1 kW m^?2. The degradation profiles were mapped with high‐resolution electrospray ionization mass spectrometry (ESI‐MS) with a LCQ quadrupole ion trap mass analyzer, with the peak assignments confirmed to within 3 ppm using ESI‐MS with a LTQ‐Orbitrap mass detector. It was found that in all the butyl ester polymers analyzed herein—regardless of their tertiary side‐chain structure—the loss of the butyl ester group and subsequent formation of acid side groups are a component of the overall degradation pathway of poly(butyl methacrylate)s under these harsh conditions. However, it is also demonstrated that the magnitude of this pathway is intimately linked to the side‐chain structure with the propensity for degradation decreasing in the order p(tBMA) > p(nBMA) > p(HFBMA) . The degradation mechanisms identified in this study, in combination with the previous end‐group degradation studies of poly(methyl methacrylate) and poly(n‐butyl acrylate), have allowed a much deeper understanding of the molecular degradation behavior of poly(acrylate)s and poly(methacrylate)s in an extreme natural environment. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Induction based fluidics (IBF) for droplet‐based mass spectrometric analysis of oligonucleotides

Here, we report the utility of induction‐based fluidics (IBF) for the introduction of oligonucleotides to a mass spectrometer via charged droplets. The device produces nanoliter‐sized droplets, which are field transported with minimal concerns related to source plugging or sampling loss. The IBF source enabled detection of oligonucleotides at the nanomolar concentration level. Importantly, analysis of individual droplets revealed that oligonucleotide mixtures could be detected with ion abundance ratios that closely match the initial concentration ratios within the sample. Copyright © 2015 John Wiley & Sons, Ltd.     

Analysis of lipids with desorption atmospheric pressure photoionization‐mass spectrometry (DAPPI‐MS) and desorption electrospray ionization‐mass spectrometry (DESI‐MS)

In this article, the effect of spray solvent on the analysis of selected lipids including fatty acids, fat‐soluble vitamins, triacylglycerols, steroids, phospholipids, and sphingolipids has been studied by two different ambient mass spectrometry (MS) methods, desorption electrospray ionization‐MS (DESI‐MS) and desorption atmospheric pressure photoionization‐MS (DAPPI‐MS). The ionization of the lipids with DESI and DAPPI was strongly dependent on the spray solvent. In most cases, the lipids were detected as protonated or deprotonated molecules; however, other ions were also formed, such as adduct ions (in DESI), [M‐H]⁺ ions (in DESI and DAPPI), radical ions (in DAPPI), and abundant oxidation products (in DESI and DAPPI). DAPPI provided efficient desorption and ionization for neutral and less polar as well as for ionic lipids but caused extensive fragmentation for larger and more labile compounds because of a thermal desorption process. DESI was more suitable for the analysis of the large and labile lipids, but the ionization efficiency for less polar lipids was poor. Both methods were successfully applied to the direct analysis of lipids from pharmaceutical and food products. Although DESI and DAPPI provide efficient analysis of lipids, the multiple and largely unpredictable ionization reactions may set challenges for routine lipid analysis with these methods. Copyright © 2012 John Wiley & Sons, Ltd.     

Liquid extraction surface analysis (LESA) of food surfaces employing chip‐based nano‐electrospray mass spectrometry

An automated surface‐sampling technique called liquid extraction surface analysis (LESA), coupled with infusion nano‐electrospray high‐resolution mass spectrometry and tandem mass spectrometry (MS/MS), is described and applied to the qualitative determination of surface chemical residues resulting from the artificial spraying of selected fresh fruits and vegetables with representative pesticides. Each of the targeted pesticides was readily detected with both high‐resolution and full‐scan collision‐induced dissociation (CID) mass spectra. In the case of simazine and sevin, a mass resolution of 100 000 was insufficient to distinguish the isobaric protonated molecules for these compounds. When the surface of a spinach leaf was analyzed by LESA, trace levels of diazinon were readily detected on the spinach purchased directly from a supermarket before they were sprayed with the five‐pesticide mixture. A 30 s rinse under hot running tap water appeared to quantitatively remove all remaining residues of this pesticide. Diazinon was readily detected by LESA analysis on the skin of the artificially sprayed spinach. Finally, incurred pyrimethanil at a level of 169 ppb in a batch slurry of homogenized apples was analyzed by LESA and this pesticide was readily detected by both high‐resolution mass spectrometry and full‐scan CID mass spectrometry, thus showing that pesticides may also be detected in whole fruit homogenized samples. This report shows that representative pesticides on fruit and vegetable surfaces present at levels 20‐fold below generally allowed EPA tolerance levels are readily detected and confirmed by the title technologies making LESA‐MS as interesting screening method for food safety purposes. Copyright © 2011 John Wiley & Sons, Ltd.     

Purification and identification of corn peptides that facilitate alcohol metabolism by semi‐preparative high‐performance liquid chromatography and nano liquid chromatography with electrospray ionization tandem mass spectrometry

In this study, peptides that facilitate alcohol metabolism were purified and identified from corn protein hydrolysates. The ultra‐filtered fraction with a molecular weight < 3 kDa (F3) potential activity was separated into six fractions (F3‐H1–F3‐H6) by semi‐preparative high‐performance liquid chromatography. Among the resultant six fractions, F3‐H4 and F3‐H5 exhibited the highest ability to eliminate alcohol in vivo. A total of 16 peptides with strong signal values were identified from F3‐H4 and F3‐H5 fractions by nano liquid chromatography coupled with electrospray ionization tandem mass spectrometry. Several identified peptides were then selected and synthesized to determine their potential to facilitate alcohol metabolism. We found that Leu‐Leu and Pro‐Phe were the key structure units in Gln‐Leu‐Leu‐Pro‐Phe responsible for this peptide's ability to facilitate alcohol metabolism. However, the role of Leu‐Leu and Pro‐Phe may be affected by peptide chain length and hydrophobic properties. Our results have thus provided some insight into the study of the structure–activity relationships of corn peptides.     

Proteomics analysis of human breast milk by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) coupled with mass spectrometry to assess breast cancer risk

Breast cancer (BC) is one of the most common cancers and one of the most common causes for cancer-related mortality. Discovery of protein biomarkers associated with cancer is considered important for early diagnosis and prediction of the cancer risk. Protein biomarkers could be investigated by large-scale protein investigation or proteomics, using mass spectrometry (MS)-based techniques. Our group applies MS-based proteomics to study the protein pattern in human breast milk from women with BC and controls and investigates the alterations and dysregulations of breast milk proteins in comparison pairs of BC versus control. These dysregulated proteins might be considered potential future biomarkers of BC. Identification of potential biomarkers in breast milk may benefit young women without BC, but who could collect the milk for future assessment of BC risk. Previously we identified several dysregulated proteins in different sets of human breast milk samples from BC patients and controls using gel-based protein separation coupled with MS. Here, we performed 2D-PAGE coupled with nano-liquid chromatography–tandem MS (nanoLC-MS/MS) in a small-scale study on a set of six human breast milk pairs (three BC samples vs. three controls) and we identified several dysregulated proteins that have potential roles in cancer progression and might be considered potential BC biomarkers in the future.     

Characterization of superoxide dismutase 1 (SOD‐1) by electrospray ionization‐ion mobility mass spectrometry

In this paper, we report nano‐electrospray ionization‐ion mobility mass spectrometry (nano‐ESI‐IM‐MS) characterization of bovine superoxide dismutase (SOD‐1) and human SOD‐1 purified from erythrocytes. SOD‐1 aggregates are characteristic of amyotrophic lateral sclerosis (ALS), a fatal neurodegenerative disease in humans that could be triggered by dissociation of the native dimeric enzyme (Cu₂,Zn₂‐dimer SOD‐1). In contrast to ESI‐MS, nano‐ESI‐IM‐MS allowed an extra dimension for ion separation, yielding three‐way mass spectra (drift time, mass‐to‐charge ratio and intensity). Drift time provided valuable structural information related to ion size, which proved useful to differentiate between the dimeric and monomeric forms of SOD‐1 under non denaturing conditions. In order to obtain detailed structural information, including the most relevant post‐translational modifications, we evaluated several parameters of the IM method, such as sample composition (10 mM ammonium acetate, pH 7) and activation voltages (trap collision energy and cone voltage). Neutral pH and a careful selection of the most appropriate activation voltages were necessary to minimize dimer dissociation, although human enzyme resulted less prone to dissociation. Under optimum conditions, a comparison between monomer‐to‐dimer abundance ratios of two small sets of blood samples from healthy control and ALS patients demonstrated the presence of a higher relative abundance of Cu,Zn‐monomer SOD‐1 in patient samples. Copyright © 2013 John Wiley & Sons, Ltd.     

Visualization of cancer‐related chemical components in mouse pancreas tissue by tapping‐mode scanning probe electrospray ionization mass spectrometry

Mass spectrometry imaging is an informative approach for the comprehensive analysis of multiple components inside biological specimens. We used novel tapping‐mode scanning probe electrospray ionization mass spectrometry method to visualize cancer‐related chemical components in the mouse pancreas tissue section at a sampling pitch of 100 µm. Positive ion mode measurements from m/z 100 to 1500 resulted in the visualization of multiple components that are tentatively assigned as polyamines, lipids and proteins. Their signal intensities inside the cancerous and the non‐cancerous regions were found to be significantly different by the two‐sample t‐test. Copyright © 2015 John Wiley & Sons, Ltd.     

MALDI‐TOF mass spectrometry of hordeins: rapid approach for identification of malting barley varieties

A procedure for identification of malting barley varieties using matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) of ethanol‐soluble barley proteins (hordeins) is described. The hordeins were first extracted from milled barley grains by several extraction protocols (using different extraction agents and conditions). Hordein extracts were then analyzed directly via MALDI‐TOF MS without any preliminary purification or separation step, and the protein profiles of analyzed hordein extracts were compared in order to find out the most suitable extraction procedure for mass spectrometric analysis. The optimized procedure was successfully applied to identification of 13 malting barley varieties. Our results revealed that the proposed mass spectrometry‐based approach provides characteristic mass patterns of extracted hordeins, which can be advantageously used for barley variety identification. Copyright © 2009 John Wiley & Sons, Ltd.     

Recommended criteria for the mass spectrometric identification of target peptides and proteins (<8 kDa) in sports drug testing

Mass spectrometry has become an invaluable tool for the identification of prohibited peptide hormones and proteins in doping control analysis. Regulatory authorities have established criteria for identifying banned drugs in doping control specimens, but these criteria do not address the specific issues for high molecular weight protein drugs such as molecular weight determination of multiply charged molecules, analysis of chemically or enzymatically derived degradation products, identification of amino acid sequence tags, etc. Technical considerations such as sample preparation methods (e.g. immunoaffinity purification), resulting analytes (e.g. intact compounds vs. chemically or enzymatically derived peptides), ionization modes, analyzer resolution, and the information provided by respective techniques are discussed in light of sports drug testing requirements using typical application examples.     

The characterization of column heating effect in nanoflow liquid chromatography mass spectrometry (nanoLC‐MS)–based proteomics

Column heating strategy is often applied in nano–high‐performance liquid chromatography–mass spectrometer (nanoHPLC‐MS) platform for enhancing the analytical efficiency of peptides or proteins. Nonetheless, the influence effects of column heating in peptides or proteins identification still lack of deep understanding. In this study, a systematic comparison of room temperature (RT) and column heating of nanoHPLC was done. Based on the data, under column heating condition, the backpressure of nanoHPLC can be decreased. Due to the increase of resolution, the peak widths of precursor ion were narrowed. As a result, in MS/MS data acquisition part, more time was spared for MS1 detecting and MS2 fragmenting, which eventually resulted in increased identification of peptides and proteins. Moreover, we also proposed the application scope of column heating by evaluating its influence on sample detection. On one hand, column heating significantly increased the identification of membrane proteins due to more efficient elution of highly hydrophobic peptides compared with RT. On the other hand, heating was not suitable for analyzing short or/and hydrophilic peptides with low retention time, which would be eluted out during sample loading process under high temperature and missed by mass spectrometric detection. In conclusion, our study provides a reference for rational application of column heating in proteomics research.     

Non‐covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study

Study of the non‐covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI‐MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI‐MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non‐covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε‐NH₂ of lysine and C‐terminal amide (? CONH₂) facilitate the dimerization through intermolecular hydrogen bonding network. Copyright © 2010 John Wiley & Sons, Ltd.