New lysine-acetylated proteins screened by immunoaffinity and liquid chromatography-mass spectrometry

The lack of selective extraction specific for lysine-acetylated proteins has been a major problem in the field of acetylation biology,though acetylation plays a key role in many biological processes.In this paper,we report for the first time the proteomic screening of lysine-acetylated proteins from a mouse liver tissue,by a new approach of immunoaffinity purification of lysine-acetylated peptides combined with nano-HPLC/MS/MS analysis.We have found 20 lysine-acetylated proteins with 21 lysine-acetylated si...     

Nano-high-performance liquid chromatography in combination with nano-electrospray ionization Fourier transform ion-cyclotron resonance mass spectrometry for proteome analysis

Fourier transform ion-cyclotron resonance (FTICR) mass spectrometry offers several advantages for the analysis of biological samples, including excellent mass resolution, ultra-high mass measurement accuracy, high sensitivity, and wide mass range. We report the application of a nano-HPLC system coupled to an FTICR mass spectrometer equipped with nanoelectrospray source (nano-HPLC/nano-ESI-FTICRMS) for proteome analysis. Protein identification in proteomics is usually conducted by accurately determining peptide masses resulting from enzymatic protein digests and comparing them with theoretically digested protein sequences from databases. A tryptic in-solution digest of bovine serum albumin was used to optimize experimental conditions and data processing. Spots from Coomassie Blue and silver-stained two-dimensional (2D) gels of human thyroid tissue were excised, in-gel digested with trypsin, and subsequently analyzed by nano-HPLC/nano-ESI-FTICRMS. Additionally, we analyzed 1D-gel bands of membrane preparations of COS-6 cells from African green monkey kidney as an example of more complex protein mixtures. Nano-HPLC was performed using 1-mm reverse-phase C-18 columns for pre-concentration of the samples and reverse-phase C-18 capillary columns for separation, applying water/acetonitrile gradient elution conditions at flow rates of 200 nL/min. Mass measurement accuracies smaller than 3 ppm were routinely obtained. Different methods for processing the raw data were compared in order to identify a maximum number of peptides with the highest possible degree of automation. Parallel identification of proteins from complex mixtures down to low-femtomole levels makes nano-HPLC/nano-ESI-FTICRMS an attractive approach for proteome analysis.     

Quantitation of human glutathione S-transferases in complex matrices by liquid chromatography/tandem mass spectrometry with signature peptides

Direct quantitation of glutathione S-transferase (GST) isoforms [alpha (GST-A) and micro (GST-M)] in human liver cytosol was achieved by liquid chromatography/tandem mass spectrometry (LC/ESI-MS/MS) analysis of signature peptides of GST-A and GST-M and their corresponding stable isotopic peptide internal standards via multiple reaction monitoring (MRM). The selection of signature peptides was performed via trypsin digestion of commercially available cDNA-expressed GST-A1 and GST-M1, followed by LC/ESI-MS/MS with an ion trap mass spectrometer and sequencing with the TurboSEQUEST application. Quantitative analysis of the selected signature peptides in the multi-reaction monitoring (MRM) mode was performed using a triple-quadruple mass spectrometer. A series of human cytosol samples was quantitatively analyzed for levels of GST-A and GST-M. The total level of GST-A and GST-M obtained from this LC/ESI-MS/MS method was well correlated with the total level of GST determined by the 1-chloro-2,4-dinitrobenzene (CDNB) method.     

Need for accurate and standardized determination of amino acids and bioactive peptides for evaluating protein quality and potential health effects of foods and dietary supplements

Accurate standardized methods for the determination of amino acid in foods are required to assess the nutritional safety and compositional adequacy of sole source foods such as infant formulas and enteral nutritionals, and protein and amino acid supplements and their hydrolysates, and to assess protein claims of foods. Protein digestibility-corrected amino acid score (PDCAAS), which requires information on amino acid composition, is the official method for assessing protein claims of foods and supplements sold in the United States. PDCAAS has also been adopted internationally as the most suitable method for routine evaluation of protein quality of foods by the Food and Agriculture Organization/World Health Organization. Standardized methods for analysis of amino acids by ion-exchange chromatography have been developed. However, there is a need to develop validated methods of amino acid analysis in foods using liquid chromatographic techniques, which have replaced ion-exchange methods for quantifying amino acids in most laboratories. Bioactive peptides from animal and plant proteins have been found to potentially impact human health. A wide range of physiological effects, including blood pressure-lowering effects, cholesterol-lowering ability, antithrombotic effects, enhancement of mineral absorption, and immunomodulatory effects have been described for bioactive peptides. There is considerable commercial interest in developing functional foods containing bioactive peptides. There is also a need to develop accurate standardized methods for the characterization (amino acid sequencing) and quantification of bioactive peptides and to carry out dose-response studies in animal models and clinical trials to assess safety, potential allergenicity, potential intolerance, and efficacy of bioactive peptides. Information from these studies is needed for determining the upper safe levels of bioactive peptides and as the basis for developing potential health claims for bioactive peptides. This information is, in turn, needed by regulatory agencies for developing appropriate policy and regulations on adding these substances to foods and for determining if health claims are scientifically substantiated.     

Peptide profile of human acquired enamel pellicle using MALDI tandem MS

The present study proposes a strategy for human in vivo acquired enamel pellicle (AEP) peptidome characterisation based on sequential extraction with guanidine and TFA followed by MALDI-TOF/TOF identification. Three different nanoscale analytical approaches were used: samples were subjected to tryptic digestion followed by nano-HPLC and mass spectrometry (MS and MS/MS) analysis. Undigested samples were analysed by LC-MS (both linear and reflector modes) and LC-MS/MS analysis, and samples were subjected to nano-HPLC followed by on-plate digestion and mass spectrometry (MS and MS/MS) analysis. The majority of the identifications corresponded to peptide/protein fragments of salivary protein, belonging to the classes: acidic PRPs, basic PRPs, statherin, cystatins S and SN and histatin 1 (all also identified in intact form). Overall, more than 90 peptides/proteins were identified. Results clearly show that peptides with acidic groups are enriched in the TFA fraction while peptides with no acidic or phosphate groups are prevalent on the guanidine extract. Also, phosphorylated peptides were observed mainly on the TFA fraction. Fragments present in the AEP show a predominance of cleavage points located at Arg, Tyr and Lys residues. Obtained data suggest that proteolytic activity could influence AEP formation and composition.     

Isocratic high-performance liquid chromatography-photodiode-array detection method for determination of lysine- and arginine-vasopressins and oxytocin in biological samples

A simple, isocratic, sensitive (1 ng), and specific high-performance liquid chromatographic (HPLC) method based on photodiode-array detection (PAD) is described for simultaneous quantitation of the bioactive peptides, lysine vasopressin (LVP), arginine vasopressin (AVP) and oxytocin (OXY). Acidified pig plasma and left ventricular (LV) tissue samples were first extracted with Sep-Pak C18 columns, and the bioactive peptides were eluted with methanol, then dried at 37 degrees C and reconstituted with HPLC mobile phase. The bioactive peptides were separated by HPLC on a Dynamax 3009-A C8 column with a mobile phase of 0.1% trichloroacetic acid-50 mM heptanesulfonic acid-30mM triethylamine-20% acetonitrile in water, pH 2.5 and identified with a Waters 990-PAD system (spectrum index plots in the range 200-400 nm). Standards of LVP, AVP and OXY and their mixtures showed a linear increase in the range 5 to 100 ng and were eluted at 6.1, 6.9 and 4.6 min, respectively. Spectrum analysis showed a distinct absorption peak at 280 nm, corresponding to peptide bonds. The reproducibility of the method coefficient of variation for standards is 6.9, 5.8 and 4.7% for LVP, AVP and OXY, respectively. In plasma and tissue it is much higher: 12.9% (LV tissue) and 18.6% (plasma) for LVP. Pig plasma contains negligible amounts of AVP and OXY; LVP is much higher (0.28 +/- 0.19 ng/ml). In pig tissue, LVP predominates (6.95 ng/g wet weight) compared to AVP (1.45) and OXY (1.50). Spectral analysis is necessary to identify the bioactive peptide peaks among interfering substances and to increase the sensitivity four-fold. The method described here is useful for the simultaneous determination of LVP, AVP and OXY in the nanogram range and can be extended to picogram levels by employing PAD spectral analysis techniques.     

Bioanalytical chemistry of cytokines – A review

Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.     

Simple and sensitive quantification of bioactive peptides in biological matrices using liquid chromatography/selected reaction monitoring mass spectrometry coupled with trichloroacetic acid clean-up

A simple and sensitive liquid chromatography/electrospray ionization tandem mass spectrometric (LC/ESI-MS/MS) method has been developed for the quantification of bioactive peptides in biological fluids. The method employs protein precipitation with 4% trichloroacetic acid (TCA) and selected reaction monitoring (SRM) using an immonium ion as the product ion. This method was applied to determine the synthetic parathyroid hormone (PTH) analog (MW 1721) in rat plasma and human hepcidin-25 (MW 2789) in human serum. TCA clean-up showed a sufficient recovery for peptides with a MW of less than 3000, and would be useful as a simple and rapid method because of direct injection of the supernatant without evaporation or dilution. In addition, TCA clean-up allowed us not only to reduce sample preparation time, but also to select an immonium ion as a product ion of SRM, which led to detection more sensitive than SRM using other types of product ions. The lower limits of quantitation (LLOQs) of the PTH analog and the human hepcidin-25 were 0.2 ng/mL and 5 ng/mL, respectively. This method was fully validated with acceptable linearity, intra- and inter-assay precisions, and accuracy. Furthermore, this simple and rapid method is applicable to pharmacokinetic studies.     

Application of mass spectrometry to the characterization and quantification of food-derived bioactive peptides

Biologically active peptides are of particular interest in food science and nutrition because they have been shown to play different physiological roles, including antihypertensive, opioid, antimicrobial, and immunostimulating activities. Because these peptides are generated by protein hydrolysis or fermentation, they can represent only minor constituents in a highly complex matrix and therefore, identification of biologically active peptides in food matrixes is a challenging task in food technology. In this context, mass spectrometry (MS) has developed into a necessary tool to assess quality and safety of food and, more recently, to determine the presence and behavior of functional components such as these bioactive peptides. This review highlights the existing methods based on MS to identify, characterize, and quantify food-derived biologically active peptides, taking into account the different ionization sources used for the analysis of these high-value food components. The quantitative determination of bioactive peptides in food products or biological fluids is also discussed.     

LC–MS bioanalysis of intact proteins and peptides

Bioanalysis assays that reliably quantify biotherapeutics and biomarkers in biological samples play pivotal roles in drug discovery and development. Liquid chromatography coupled with mass spectrometry (LC–MS), owing to its superior specificity, faster method development and multiplex capability, has evolved as one of the most important platforms for bioanalysis of biotherapeutics, particularly new scaffolds such as half-life extension platforms for proteins and peptides, as well as antibody drug conjugates. Intact LC–MS analysis is orthogonal to bottom-up surrogate peptide approach by providing whole molecule quantitation and high-level sequence and structure information. Here we review the latest development in LC–MS bioanalysis of intact proteins and peptides by summarizing recent publications and discussing the important topics such as the comparison between top-down intact analysis and bottom-up surrogate peptide approach, as well as simultaneous quantitation and catabolite identification. Key bioanalytical issues around intact protein bioanalysis such as sensitivity, data processing strategies, specificity, sample preparation and LC condition are elaborated. For peptides, topics including quantitation of intact peptide vs. digested surrogate peptide, metabolites, sensitivity, LC condition, assay performance, internal standard and sample preparation are discussed.     

Relative quantitation of proteins fractionated by the ProteomeLab™ PF 2D system using isobaric tags for relative and absolute quantitation (iTRAQ)

We describe an optimised protocol for application of isobaric tags for relative and absolute quantitation (iTRAQ) and tandem mass spectrometry to obtain relative quantitative data from peptides derived from tryptic digestions of proteins fractionated by using the 2D liquid-phase ProteomeLab™ PF 2D technique. This methodology is suitable for the quantitation of proteins from a pool of co-eluting proteins which are often difficult to identify for the purpose of candidate protein selection for biologically relevant qualitative/quantitative changes under experimental conditions or in disease states. iTRAQ quantitation also facilitates the possibility of result to result comparison using other methodologies such as UV protein quantitation via the ProteomeLab™ PF 2D technique. The optimised protocol outlined here allows relative quantitation by MALDI-TOF/TOF mass spectrometry with high sensitivity and without the need to perform 2D HPLC separation of labelled peptides. The overall outcome is the simplification in the data complexity and the ease of use of the labelling protocol. This study is dedicated to Dr. Josef Chmelik in memory of his contribution and constant inspiration.     

具有双活性序列的新型抗菌肽的设计及性质

设计合成了具有2个活性序列的线性和环状多肽及具有单个活性序列的短链多肽, 研究了它们的杀菌活性、 细胞毒性及溶血性. 结果表明, 线性肽和环状肽的杀菌活性高于短链肽. 利用计算模拟的方法计算了多肽与细菌细胞膜中一种重要的成分磷脂酰甘油(DMPG)的结合能. 结果表明, 多肽-DMPG的结合能与多肽的杀菌活性具有较高的相关性, 线性和环状多肽与DMPG的结合能大于短链肽. 线性和环状多肽均含有2个活性序列, 可提供多个荷正电氨基酸与荷负电的磷脂结合, 结合能较大, 杀菌活性较强. 采用模拟生物膜对其中几条多肽的作用机理进行了初步研究. 结果表明, 该类多肽有可能使正常哺乳动物细胞的细胞膜产生孔洞; 而对于细菌细胞膜, 多肽并未在膜上产生明显孔洞, 而是引起了细菌细胞膜的聚集.     

生物膜层干涉技术在生物分子分析和检测中应用的研究进展

生物膜层干涉技术是基于光干涉信号实现对生物分子动力学分析或快速检测的非标记分析检测技术。因具有实时提供分析物信息、分析速度快和样品耗量少等优点,该技术已被应用于蛋白质、核酸、脂质、糖类及其他生物分子之间相互作用的分析;所需样品量少、特异性强等优点也为该技术应用于快速检测奠定了基础。该文介绍了生物膜层干涉技术的基本原理,综述了其在动力学分析和快速检测领域的相关应用研究,并对其发展趋势和应用前景进行了展望。     

Sample preparation and direct electrospray ionization on a tip column for rapid mass spectrometry analysis of complex samples

A handheld pipette tip column electrospray ionization source (PTC-ESI source) was developed for rapid mass spectrometry analysis at ambient pressure. The PTC-ESI source was made up of three main component parts including a micro DC high voltage (HV) power supply, a micropipette and a disposable micropipette tip filled with a plug of adsorbent. A DC high voltage was applied to the sharp point of the micropipette tip column to induce electrospray ionization. The PTC-ESI source was successfully used for direct analysis of basic organic compounds, organic acids and peptides in a simple matrix. In the case of complex samples, micro-extraction based on the adsorbent phase filled in the pipette tip was used to remove impurities and concentrate target analytes prior to ionization. The eluting solution was not pipetted out, but directly dispersed in the form of electrospray from the pipette tip for ionization. The effectiveness of the PTC-ESI source has been further demonstrated by fast analysis of therapeutic compounds and endogenous bioactive chemicals in complex biological samples.     

Fluorescence-based Western blotting for quantitation of protein biomarkers in clinical samples

Since most high throughput techniques used in biomarker discovery are very time and cost intensive, highly specific and quantitative analytical alternative application methods are needed for the routine analysis. Conventional Western blotting allows detection of specific proteins to the level of single isotypes while its quantitative accuracy is rather limited. We report a novel and improved quantitative Western blotting method. The use of fluorescently labelled secondary antibodies strongly extends the dynamic range of the quantitation and improves the correlation with the protein amount (r=0.997). By an additional fluorescent staining of all proteins immediately after their transfer to the blot membrane, it is possible to visualise simultaneously the antibody binding and the total protein profile. This allows for an accurate correction for protein load. Applying this normalisation it could be demonstrated that fluorescence-based Western blotting is able to reproduce a quantitative analysis of two specific proteins in blood platelet samples from 44 subjects with different diseases as initially conducted by 2D-DIGE. These results show that the proposed fluorescence-based Western blotting is an adequate application technique for biomarker quantitation and suggest possibilities of employment that go far beyond.     

Simultaneous determination by GC-MS-SIM of o-, m-, p-hydroxyphenylacetic acid, 3:4-dihydroxyphenylacetic acid and homovanillic acid in biological samples using a common selected ion

A GC-MS-SIM method is described for the simultaneous determination of five acid metabolites, o-, m-, and p-hydroxyphenylacetic acid, 3:4-dihydroxyphenylacetic acid and homovanillic acid in biological samples using a common selected ion for all the acids. The TMS ethers of methyl or ethyl esters of these compounds have a common ion at m/e 179 which is used for their quantitation by selected ion monitoring. The molecular ion at m/e 238 of the three monohydroxy phenylacetic acids, which is also the M-30 ion for homovanillic acid, is also used for their quantitation. The GC conditions for their separation, the relative sensitivities and some advantages of TMS ethers over other derivatives are described. The application of this method to biological samples is illustrated by data on human urine and plasma.     

Electrospray ionization detection of inherently nonresponsive epoxides by peptide binding

A small organic molecule that is inherently nonresponsive to electrospray analysis, 1,3-butadiene diepoxide, was analyzed via electrospray ionization (ESI) by binding it to various peptides and observing the product at the characteristic mass shift. The epoxide reacted only with peptides with arginines in their sequence, most likely through a base-catalyzed ring opening to form a covalently bound product. A calibration curve linear over 3 orders of magnitude was generated for the butadiene diepoxide/peptide adduct. Several other epoxides were also reacted with the peptide of choice (angiotensin II), and adducts of these epoxides with the peptide were observed as well, demonstrating the versatility of this method for the analysis of small epoxides. This study demonstrates the possibility of assaying epoxides bound to peptides or proteins in biological samples. Furthermore, it demonstrates an important concept that could be applied to other analytical problems in electrospray: the ability to react an analyte that is nonresponsive to electrospray analysis with an analyte well suited for the technique, and accomplish quantitation based on the adduct formed between the two.     

Evaluation of sample fractionation using micro-scale liquid-phase isoelectric focusing on mass spectrometric identification and quantitation of proteins in a SILAC experiment

Mass spectrometric methods based on stable isotopes have shown great promise for identification and quantitation of complex mixtures. Stable isotope labelling by amino acids in cell culture (SILAC) is a straightforward and accurate procedure for quantitation of proteins from cell lines, that are cultured in media containing the natural amino acid or its isotopically labelled analogue, giving rise to either 'light' or 'heavy' proteins. The two cell populations are pooled and treated as a single sample, which allows the use of various protein purification methods without introducing errors into the quantitative analysis. The quantitation of the proteins is based on the intensities of the light and heavy peptides. The increased number of peptides in a quantitative experiment arising from peptide pairs implies that prefractionation is critical prior to liquid chromatography/mass spectrometric (LC/MS) analysis to minimise signal suppression effects and errors in measurements of the intensity ratios. In this study, the effect of a prefractionation step on identification and quantitation of proteins in a SILAC experiment was evaluated. We show that micro-scale liquid-phase isoelectric focusing in the Micro Rotofor separates proteins into well-defined fractions and reduces the sample complexity. Furthermore, the fractionation enhanced the number of identified proteins and improved their quantitation.