Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry

The overall history and recent advances in surface enhanced laser desorption/ionization-time of flight-mass spectrometry (SELDI-TOF-MS) technology is reviewed herein. Fundamentals of SELDI-TOF analysis are presented while drawing comparisons with other laser-based mass spectrometry techniques. The application of SELDI-TOF-MS to functional genomics and biomarker discovery is discussed and exemplified by elucidating a biomarker candidate for prostatic carcinoma. Finally, a short discussion regarding future SELDI requirements and developments is supplied.     

Determination of IGF-I in horse plasma by LC electrospray ionisation mass spectrometry

The insulin-like-growth factor (IGF-I) peptide is considered to be the main indirect marker for growth hormone administration (GH) in a horse. Further to a previous investigation on measurement of IGF-I in plasma samples by mass spectrometry, this study focuses on quantitative and qualitative analysis of intact IGF-I in horse plasma. First, protein-transposing software has been developed for IGF-I to facilitate its quantification by HPLC–electrospray–ion-trap mass spectrometry. Second, product-ion scan experiments on IGF-I have been conducted on standard samples, non-fortified equine plasma samples, fortified plasma samples, and equine GH post-administration samples. This “top-down” approach method enables characterisation of fragment ions corresponding to the carboxy terminal end, which can be useful for the confirmation of the presence of IGF-I in plasma samples. Figure Structure of IGF-I and amino acid sequences of IGF-I and R3 IGF-I. Deconvolution mass spectra of the IGF-I and R3 IGF-I mixture     

Recent advances in computational analysis of mass spectrometry for proteomic profiling

The proteome, defined as an organism's proteins and their actions, is a highly complex end-effector of molecular and cellular events. Differing amounts of proteins in a sample can be indicators of an individual's health status; thus, it is valuable to identify key proteins that serve as 'biomarkers' for diseases. Since the proteome cannot be simply inferred from the genome due to pre- and posttranslational modifications, a direct approach toward mapping the proteome must be taken. The difficulty in evaluating a large number of individual proteins has been eased with the development of high-throughput methods based on mass spectrometry (MS) of peptide or protein mixtures, bypassing the time-consuming, laborious process of protein purification. However, proteomic profiling by MS requires extensive computational analysis. This article describes key issues and recent advances in computational analysis of mass spectra for biomarker identification.     

Liquid chromatography/mass spectrometry for metabonomics investigation of the biochemical effects induced by aristolochic acid in rats: the use of information-dependent acquisition for biomarker identification

The toxic effects of oral administrations of nephrotoxic and carcinogenic aristolochic acid (AA) to male Sprague-Dawley rats were investigated by using high-performance liquid chromatography coupled with a quadrupole time-of-flight mass spectrometer. Analysis of the urine and plasma samples revealed distinct changes in the biochemical patterns in the AA-dosed rats. After peak finding and alignment, principal component analysis (PCA) and partial least-squares discriminant analysis (PLS-DA) were used for multivariate data analysis. Potential biomarkers were studied by high-resolution mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses. The MS/MS spectra of all endogenous metabolites satisfying the pre-defined criteria were acquired in a single information-dependent acquisition (IDA) analysis, demonstrating that IDA was an efficient approach for structural elucidation in metabonomic studies. Citric acid and a glucuronide-containing metabolite were observed as potential biomarkers in rat urine. A significant increase in plasma creatinine concentration was also observed in the AA-dosed rats, which indicated that AA induced an adverse effect on the renal clearance function.     

两种微波等离子体炬质谱测定水中铅的对比研究

建立了一种新型的能够灵敏分析水中痕量铅的质谱方法,以微波等离子体炬(MPT)为离子源,可无需样品预处理而直接分析水样。样品经雾化和去溶后由MPT的中心管道引入等离子体,离子由国产的四极杆质谱仪(Q-MS)检测,得到铅的MPT特征质谱。定量结果表明,该方法的检出限为20 ng/L,线性范围为200~1 000 ng/L,相对标准偏差(RSD)为5.3%;所得定量指标优于相同条件下商用的线性离子阱质谱(LTQ-MS)测试结果,且四极杆质谱仪上所得的铅离子特征质谱信号更简单、易归属,无需复杂的多级串联质谱加以确认。这种MPT可与国产质谱仪器相结合发展成为一种低成本的现场检测铅的质谱仪器,在环境监控、饮用水检验等方面具有一定的应用价值。     

A metallomics approach discovers selenium-containing proteins in selenium-enriched soybean

Our previous study found that high-molecular-weight selenium (Se) species make up 82% of the total Se in the bean of Se-enriched soybean plants (Chan et al. 2010, Metallomics, 2(2): p. 147–153). The Se species have been commonly seen in other plants in addition to soybean, but their identities remain unresolved. The present study employs a multi-technique metallomics approach to characterize the proteins containing Se in the beans of Se-enriched soybean plants. Two main categories of proteins, maturation proteins and protease inhibitors, were found in Se-containing high-performance liquid chromatography (HPLC) fractions. The proteins were screened by two-dimensional HPLC-inductively coupled plasma mass spectrometry, size-exclusion chromatography, and anion-exchange chromatography, and the Se-containing fractions were then identified by peptide mapping using HPLC-Chip-electrospray ion trap mass spectrometry. Based on the belief that Se goes into proteins through non-specific incorporation, a new method was designed and applied for the Se-containing peptide identification. The Se-containing peptide KSDQSSSYDDDEYSKPCCDLCMCTRS, part of the sequence of protein Bowman–Birk proteinase isoinhibitor (Glycine max), was found in one of the Se-containing fractions. The nutritional value of the Se-containing proteins in Se-enriched soybeans will be an interesting topic for the future studies.     

Quantitative analysis of a proteome by N-terminal stable-isotope labelling of tryptic peptides

Covalent modification of peptides and proteins with compounds containing stable isotopes (isotope tagging) has become an essential tool to detect dynamic changes in the proteome following external or internal influence; however, using terminal amino groups for global isotope labelling of tryptic peptides is challenged by the similar reactivity of the amino groups of lysine residues. We describe a new quantitative method based on selective tagging of the terminal amino groups of tryptic peptides with pentafluorophenyl esters containing stable isotopes. The labelled peptides were resolved by two-dimensional nanoflow liquid chromatography on weak anion-exchange and reversed-phase columns and then identified and quantified by tandem mass spectrometry. The method was applied to compare the proteomes of plasma membranes from proliferating and differentiated human colorectal adenocarcinoma (Caco-2) cells and endosomes purified from the livers of rats stimulated with insulin and epidermal growth factor. The comparison of the results obtained by isotope tagging and biochemical assays demonstrate that global isotope tagging with pentafluorophenyl esters allows accurate quantification of complex protein samples.     

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.     

Biomarker discovery in rat plasma for estrogen receptor-alpha action

To support in vivo screening efforts for estrogen receptor (ER) subtype selective therapeutic agents, we initiated work to discover surrogate markers (biomarkers) in blood plasma that would change in response to ER subtype-specific action. We used a proteomic approach employing strong anion exchange chromatography (SAX), PAGE, and MS to identify potential plasma markers for selective ER-alpha action. The methodology was used to compare blood from vehicle-treated rats to blood from rats treated with either 17beta-estradiol (an ER-alpha/ER-beta agonist) or compound 1 (17alpha-ethynyl-[3,2-c]pyrazolo-19-nor-4-androstene-17beta-ol, an ER-alpha-selective agonist). Blood samples were first fractionated by SAX to separate fractions containing dominant common plasma proteins from fractions enriched for less-abundant plasma proteins. 1-D PAGE analysis of fractions depleted of dominant plasma proteins revealed treatment-specific changes in protein profiles. Protein bands that changed reproducibly in response to ER-alpha action were excised from the gel, separated by capillary LC, and identified by microspray ESI-MS. Using this method, the plasma levels of two proteins, transthyretin and apolipoprotein E, were shown to decrease in response to ER-alpha agonism. The method lacked the sensitivity to identify the known, 1000-fold less-abundant, estrogenic marker prolactin (PRL). However, using a commercial RIA and immunoblots, we showed that PRL levels increase significantly in response to treatment with the ER-alpha selective agonist, compound 1.     

Protein Profiles of Human Serum by SELDI-TOF-MS with Multiwalled Carbon Nanotubes as Absorbent

The present paper describes a biomarker capturing strategy based on the enrichment efficiency of multiwalled carbon nanotubes (MWCNTs) for peptides and proteins from human serum. The method is shown to enrich proteins/peptides, and the captured molecules were profiled using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF-MS). Mass spectra of the MWCNTs-treated human serum samples showed a significant enrichment of proteins by MWCNTs. Preliminary results indicated a good level of reproducibility in serum profiles with coefficients of variation (CVs) on signal intensity ranging from 8.9% to 25.2%. The developed method holds promise for improving the discovery of low-abundance serum biomarkers.     

Metabolite profiling of l‐isocorypalmine in rat urine,plasma, and feces after oral administration using high performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry

l ‐Isocorypalmine, an active alkaloid compound isolated from Rhizoma Corydalis yanhusuo, has been reported to possess biological activity for treating cocaine use disorder. A high‐performance liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry method was established for identification of the metabolites of l ‐isocorypalmine in urine, plasma and feces samples of rats after a single intragastric gavage of l ‐isocorypalmine at a dose of 15 mg/kg. As a result, a total of 21 metabolites (six phase ? metabolites and fifteen phase II metabolites) were detected and tentatively identified by mass spectrometry and fragment ions from tandem mass spectrometry spectra. All metabolites were present in the urine samples, nine metabolites were found in the plasma samples and three metabolites were found in the feces samples. Results indicated that metabolic pathways of l ‐isocorypalmine included oxidation, dehydrogenation, demethylation, sulfate conjugation, and glucuronide conjugation. In addition, glucuronidation was the major metabolic reaction. Results of this investigation could provide significant experimental basis for efficacy, safety and action mechanism of l ‐isocorypalmine, which will be advantageous to new drug development for treating cocaine addiction.     

多壁碳纳米管对质谱分析中的血清蛋白富集作用研究

通过多壁碳纳米管(MWCNTs)对临床血清蛋白提取物进行富集处理,经表面增强激光解析离子化飞行时间质谱(SELDI-TOF-MS)检测,发现MWCNTs对血清中小分子量蛋白(<20 kDa)具有很好的富集效果。同时还考察了内径、长度等参数对血清蛋白富集效果的影响。该方法可用于临床血清样本中低丰度的小分子量蛋白的检测。     

Polarization induced electrospray ionization mass spectrometry for the analysis of liquid,viscous and solid samples

In this study, a polarization‐induced electrospray ionization mass spectrometry (ESI‐MS) was developed. A micro‐sized sample droplet was deposited on a naturally available dielectric substrate such as a fruit or a stone, and then placed close to (~2 mm) the orifice of a mass spectrometer applied with a high voltage. Taylor cone was observed from the sample droplet, and a spray emitted from the cone apex was generated. The analyte ion signals derived from the droplet were obtained by the mass spectrometer. The ionization process is similar to that in ESI although no direct electric contact was applied on the sample site. The sample droplet polarized by the high electric field provided by the mass spectrometer initiated the ionization process. The dielectric sample loading substrate facilitated further the polarization process, resulting in the formation of Taylor cone. The mass spectral profiles obtained via this approach resembled those obtained using ESI‐MS. Multiply charged ions dominated the mass spectra of peptides and proteins, whereas singly charged ions dominated the mass spectra of small molecules such as amino acids and small organic molecules. In addition to liquid samples, this approach can be used for the analysis of solid and viscous samples. A small droplet containing suitable solvent (5–10 µl) was directly deposited on the surface of the solid (or viscous) sample, placed close the orifice of mass spectrometer applied with a high voltage. Taylor cone derived from the droplet was immediately formed followed by electrospray processes to generate gas‐phase ions for MS analysis. Analyte ions derived from the main ingredients of pharmaceutical tablets and viscous ointment can be extracted into the solvent droplet in situ and observed using a mass spectrometer. Copyright © 2015 John Wiley & Sons, Ltd.     

Computational modeling of the human serum proteome response to colon resection surgery

Principal component analysis (PCA) is much used in exploring time-course biological data sets, but does not distinguish variation between time and subjects. This study proposes a new integrated approach by combining analysis of variance (ANOVA) and three component modeling methods. The former was used to separate the between- and within-subject variation, and the latter represent modeling strategies on a scale moving from commonality to individuality. The proposed approach was applied to a surface-enhanced laser desorption and ionization time of flight mass spectrometry (SELDI-TOF-MS) data set of a serum protein expression time course before and after colon resection. Two common biological processes are identified and individual differences among patients were also detected, and the biological relevance of both is discussed.     

Proteomic Evaluation of Biomarkers to Determine the Postmortem Interval

Proteomics separates and analyzes proteins for investigation at the cellular level in regard to disease processing by analyzing the proteins’ expression, function, structure, post-translational modification, and protein–protein interaction. In general forensic investigations, the postmortem interval was evaluated by measuring changes in body temperature after death, along with forensic entomological knowledge. These investigations may be restrictive and subjective because of external factors. The objectives of this study are to sort biomarker candidates and develop a direct postmortem-interval characterization method using proteomics through analyzing and tracking down proteins in the deceased that change in accordance with the postmortem interval. The liver and heart tissues of rats were collected for protein extraction in the 24-h interval following death, and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis was conducted based on the isoelectric point and the molecular weight for separation. To validate protein spot changes on the gel, the stained electrophoresis gels were scanned and converted to digital images. Through image analysis, 14 liver proteins and 12 heart proteins were sorted and classified into four groups based on pattern changes. These proteins containing spots were extracted from the gel and analyzed by high-performance liquid chromatography with tandem mass spectrometry. Finally, 26 protein postmortem-interval relevant biomarker candidates were identified using software. Some of the proteins were muscle proteins while others were oxidation-related proteins. This study presents a new approach to the postmortem-interval research using proteomics and could be substituted for postmortem-interval evaluation.     

微波等离子体常压解吸电离质谱法快速检测化学药剂中的活性成分

构建了一种新型电离源--微波等离子体常压解吸电离源, 等离子体由微波等离子体炬产生, 工作气体为Ar气, 微波频率为2450 MHz, 该离子源可在大气压下产生稳定的等离子体. 将该电离源与具有大气压接口的Corsair API-TOF型飞行时间质谱仪结合, 实现了化学药剂中单一或多种主要活性成分的快速分析, 在手动进样条件下, 检测速度可达每小时360次. 在微波等离子体环境下, 活性物质成盐时母体化合物上结合的酸性物质可被直接除掉, 谱图中主要离子为母体化合物的准分子离子[M+H]⁺, 便于识别. 微波等离子体常压解吸电离质谱法无需化学试剂, 具有实时、 快速及无污染等特点, 为药剂研发及化学工业提供了一种新的检测技术.     

Proteomic identification of technologically modified proteins in malt by combination of protein fractionation using convective interaction media and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

A method for the fast separation of proteins and identification of their modifications based on the use of monolithic chromatographic media and mass spectrometric techniques is described. This method has been developed and applied to the analysis of malt proteins and its posttranslational modifications (glycation). Glycation, one of the most common forms of posttranslational modifications (PTM), can be detected in both biological and industrial samples. Our attention was focused on the investigations of possible chemical modifications of water-soluble barley proteins during malting process by combination of anion-exchange chromatography with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The malt extract was directly fractioned by anion-exchange chromatography using short monolithic columns and a linear gradient from 0 to 700 mM NaCl. Sufficient fractionation was obtained for malt sample, which demonstrates the potential of anion-exchange chromatography on this type of column. Proteins in separated fractions were identified by MALDI-TOF/TOF MS. Our proteomic analysis provided the identification of the major proteins present in the malt that were found to be heterogeneously glycated after malting. One of these proteins: nonspecific lipid transfer protein 1 (LTP1) can be used as a marker for characterization of glycation during malting. This protein and its modifications can be easily determined by the developed method.     

Divide and conquer: rat liver tissue proteomics based on the analysis of purified constituents

Comparative proteome data of normal and diseased tissue samples are difficult to interpret. Proteins detected in tissues are derived from different cell types and blood constituents. Pathologic or toxicant-induced aberrations may affect the proteome profile of tissues in several ways since different cell types may respond in very different and highly specific manners. The aim of this study was to analyze the proteome profiles of purified rat liver primary cells and of blood plasma in comparison to liver whole tissue. Moreover, we investigated alterations of these profiles induced by the liver toxicant N-nitrosomorpholine (NNM) used as a model compound. Whole liver samples, pure hepatocytes and Kupffer cells as well as blood plasma were obtained from saline- or NNM-treated rats. Proteins were separated by 2-D PAGE and their amounts were estimated by fluorography. Selected proteins were identified by MS analysis of tryptic digests. Among them we identified proteins exclusively expressed in the analysed constituents. Several of these proteins were assigned in the proteome profile of whole-tissue homogenates. Furthermore, we identified several proteins that were modified, up-regulated or down-regulated due to NNM treatment in total liver homogenates. Some of these protein alterations were specifically detected in primary cells isolated from NNM-treated rats. Thus, we demonstrated the successful assignment of NNM-induced proteome alterations in rat liver to the cell type of origin. The currently applied approach may help to better understand pathologic processes at a whole-tissue level.     

Serum Protein Profiling of Cervical Cancer Patients Using Surface-Enhanced Laser Desorption/Ionization Time-of-Flight Mass Spectrometry

Using surface-enhanced laser desorption/ionization time of flight mass spectrometry (SELDI-TOF-MS) technology, serum protein profiling was screened for the discovery of differentially expressed proteins between cervical cancer patients and control samples. Proteins and peptides in serum were captured by a CM10 proteinchip, and then detected by a proteinchip reader. The resulting profiling of all collected samples was analyzed with proteinchip software. Seven protein peaks were significantly regulated between the cancer group and the control group (p < 0.05). Fifty-three peaks in the m/z range from 2 kDa to 20 kDa were selected for partial least squares discriminant analysis (PLS-DA). The diagnostic model can distinguish cervical cancer in the blind test set from health controls with an accuracy of 90%. The combination of SELDI-TOF-MS and PLS-DA model can be used to screen significant proteins of differential expression in the serum of cervical cancer and may play a potential role in the diagnostics of cervical cancer.     

Use of ProteinChip array surface enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS) to identify thymosin beta-4, a differentially secreted protein from lymphoblastoid cell lines

The identification of proteins differentially expressed between cancer and normal cells is vital for the development of cancer diagnostics, therapeutics and vaccines. Using a ProteinChip Biomarker System (Ciphergen Biosystems, Fremont, CA) which combines ProteinChip technology with time-of-flight mass spectrometry, we have developed a simple method to screen and identify differentially secreted proteins from tumor cell lines. Mass spectra of the range of proteins secreted from normal B-cells were generated along with those secreted from Epstein-Barr virus transformed B-cells. A mass peak at m/z = 4972.1 that was highly over-represented in the transformed B-cell line was chosen for identification and purified by reversed phase chromatography with concomitant monitoring of fractions by SELDI-TOF MS. The resulting purified protein was digested with trypsin and the peptide masses derived from the SELDI-TOF spectrum were used to search the public databases for protein identification. Fragment matching of the resulting peptides identified the protein as thymosin beta-4. Using LC-electrospray ionization MS/MS, the identity of this protein was confirmed. Thymosin beta-4 is a known marker in LCLs establishing the utility of this method to discover and identify proteins differentially expressed between cancers and their matched normal counterparts.