Direct profiling and imaging of plant metabolites in intact tissues by using colloidal graphite-assisted laser desorption ionization mass spectrometry

Laser desorption/ionization (LDI)-based imaging mass spectrometry (MS) has been applied to several biological systems to obtain information about both the identities of the major chemical species and their localization. Colloidal graphite-assisted LDI (GALDI) MS imaging was introduced for the imaging of small molecules such as phospholipids, cerebrosides, oligosaccharides, flavonoids, and other secondary metabolites with high spatial homogeneity due to finely dispersed particles. Mass profiles and images of Arabidopsis thaliana have been recorded directly from various plant surfaces and cross sections. The main targeted metabolites were flavonoids and cuticular waxes, both of which are important in many aspects of functional genomics, proteomics, and metabolomics. The mass spectral profiles revealed tissue-specific accumulation of flavonoids in flowers and petals. In addition, many other location-specific ions were observed. The location and the degree of light-induced accumulation of flavonoids in stem sections were successfully probed by GALDI MS.     

Sweet Substitute: a software tool for in silico fragmentation of peptide-linked N-glycans

A software tool, Sweet Substitute, is described, which assists tandem mass spectrometry (MS/MS)-based glycosylation characterization from within a tryptic digest. The algorithm creates a virtual nanoelectrospray-quadrupole time-of-flight style-MS/MS spectrum of any user-defined N-linked glycan structure. An empirical peak height modeling routine is implemented in the program. By comparing the theoretical MS/MS data with the deconvoluted and deisotoped experimental MS/MS data, the user is able to quickly assess whether a proposed candidate oligosaccharide structure is a plausible one.     

电热蒸发-催化热解-原子吸收法直接测定茶叶中镉

重金属镉（Cd）一直是茶叶产品质量安全关注的重点。本研究基于电热蒸发-催化热解-原子吸收光谱仪（SS-ETV-AAS）,使用镍材质样品舟,在300 mL/min空气条件下,350 ℃干燥20 s,350~725 ℃灰化55 s;引入300 mL/min氢气与空气反应形成氮氢混合气氛,在725~800 ℃（50 s）下完成Cd的蒸发;之后,在高岭土填料催化热解炉800 ℃和准直管700 ℃条件下,氮氢火焰原子吸收测定镉的含量。方法检出限（LOD）为0.3 ng/g、定量限（LOQ）为1.0 ng/g,R2>0.998,多次测定的相对标准偏差（RSD）为1.8%~8.6%,多种茶叶样品中Cd的测定值与微波消解石墨炉原子吸收光谱法（GFAAS）无显著性差异（P>0.05）,Cd的回收率在92%~107%之间。试验结果表明,该方法灵敏度高、稳定性好、简单高效,且无需消解处理,样品分析时间仅为3min,适用于茶叶中Cd的快速检测。     

Mass spectrometry imaging for drug distribution studies

Since its introduction mass spectrometry imaging (MSI) has proven to be a powerful tool for the localization of molecules in biological tissues. In drug discovery and development, understanding the distribution of both drug and its metabolites is of critical importance. Traditional methods suffer from a lack of spatial information (tissue extraction followed by LCMS) or lack of specificity resulting in the inability to resolve parent drug from its metabolites (whole body autoradiography). MSI is a sensitive and label-free approach for imaging drugs and metabolites in tissues. In this article we review the different MSI technologies that have been applied to the imaging of pharmaceuticals. Recent technical advances, applications and current analytical limitations are discussed.     

High-throughput characterization of lipopolysaccharide-binding proteins using mass spectrometry

Lipopolysaccharide (LPS)-binding proteins interact with LPS in human serum and mediate various immune responses. We describe a high-throughput LPS-binding protein profiling platform for discovering unknown LPS-binding proteins and potential inflammatory mediators. As a pull-down method, the LPS molecules were immobilized onto epoxy beads and then directly incubated with human serum to screen LPS-binding proteins. Through the "untargeted" mass spectrometric approach, potential LPS-binding proteins which elicit various immune responses in human serum were identified by a highly sensitive LTQ Orbitrap Hybrid Fourier Transform Mass Spectrometer (LTQ Orbitrap FT MS). Therefore, this mass spectrometry (MS)-based profiling method is straightforward for screening unknown LPS-binding proteins and provides physiologically relevant binding partners in human serum.     

Two birds with one stone: Doing metabolomics with your proteomics kit

Proteomic research facilities and laboratories are facing increasing demands for the integration of biological data from multiple ‘‐OMICS’ approaches. The aim to fully understand biological processes requires the integrated study of genomes, proteomes and metabolomes. While genomic and proteomic workflows are different, the study of the metabolome overlaps significantly with the latter, both in instrumentation and methodology. However, chemical diversity complicates an easy and direct access to the metabolome by mass spectrometry (MS). The present review provides an introduction into metabolomics workflows from the viewpoint of proteomic researchers. We compare the physicochemical properties of proteins and peptides with metabolites/small molecules to establish principle differences between these analyte classes based on human data. We highlight the implications this may have on sample preparation, separation, ionisation, detection and data analysis. We argue that a typical proteomic workflow (nLC‐MS) can be exploited for the detection of a number of aliphatic and aromatic metabolites, including fatty acids, lipids, prostaglandins, di/tripeptides, steroids and vitamins, thereby providing a straightforward entry point for metabolomics‐based studies. Limitations and requirements are discussed as well as extensions to the LC‐MS workflow to expand the range of detectable molecular classes without investing in dedicated instrumentation such as GC‐MS, CE‐MS or NMR.     

Improved detection of botulinum neurotoxin type A in stool by mass spectrometry

Botulinum neurotoxins (BoNTs) are the most toxic substances known to humankind. Rapid and sensitive detection of BoNTs is necessary for timely clinical confirmation of the disease state in botulism. BoNTs cleave proteins and peptide mimics at specific sites. A mass spectrometry (MS)-based method, Endopep–MS, can detect these cleavages and has detection limits of 0.05–0.5 mouse LD₅₀ (U) in serum, depending on the BoNT serotypes. In this method, the products generated from cleavage of peptide substrates using antibody affinity-purified toxins are detected by MS. Nonspecific bound endogenous proteases or peptidases in stool can coextract with the toxin, cleaving the peptide substrates and reducing the sensitivity of the method. Here we report a method to reduce nonspecific substrate cleavage by reducing stool protease coextraction in the Endopep–MS assay.     

Mass spectrometry-based analysis of glycoproteins and its clinical applications in cancer biomarker discovery

Glycosylation is one of the most important posttranslational modifications of proteins and plays essential roles in various biological processes. Aberration in the glycan moieties of glycoproteins is associated with many diseases. It is especially critical to develop the rapid and sensitive methods for analysis of aberrant glycoproteins associated with diseases. Mass spectrometry (MS) has become a powerful tool for glycoprotein analysis. Especially, tandem mass spectrometry can provide highly informative fragments for structural identification of glycoproteins. This review provides an overview of the development of MS technologies and their applications in identification of abnormal glycoproteins and glycans in human serum to screen cancer biomarkers in recent years.     

A mass spectrometry-based approach to host cell protein identification and its application in a comparability exercise

Host cell proteins (HCPs) are process-related impurities present in biopharmaceuticals and are generally considered to be critical quality attributes. Changes in a biopharmaceutical production process may result in qualitative shifts in the HCP population. These shifts are not necessarily detectable when overall HCP levels are measured with traditional approaches such as enzyme-linked immunosorbent assays (ELISAs). Thus, the development of techniques that complement the ELISA’s functionality is desirable. Here, a mass spectrometry (MS)-based approach for the analysis of HCP populations in biopharmaceuticals is presented. It consists of (i) the generation of exclusion lists that represent the masses of the active pharmaceutical ingredient (API), (ii) the compilation of inclusion lists based on an HCP catalog derived from the analysis of protein A-purified samples, and (iii) the analysis of purified biopharmaceuticals using the generated exclusion and inclusion lists. With this approach, it was possible to increase sensitivity for HCP detection compared with a standard liquid chromatography tandem MS (LC–MS/MS) run. The workflow was successfully implemented in a comparability exercise assessing HCP populations in drug substance samples before and after a process change. Furthermore, the results suggest that size can be an important factor in the copurification of HCPs and API.     

Analysis of stereoisomers of chiral drug by mass spectrometry

Chiral molecules are of great importance in the life science since individual enantiomers may differ in biological activity, mechanism, and toxicity, making it necessary to explore efficient chiral analysis methods. Chromatography approaches are often used to differentiate enantiomers while mass spectrometry (MS) was thought to be blind in chiral analysis. With the development of MS technique, it began to play a more and more crucial part in chiral observation. In this review, we will give a detailed introduction of the analysis methods related to MS for chiral drugs, including its mechanism, applications, and future development.     

Targeted proteome investigation via selected reaction monitoring mass spectrometry

Due to the enormous complexity of proteomes which constitute the entirety of protein species expressed by a certain cell or tissue, proteome-wide studies performed in discovery mode are still limited in their ability to reproducibly identify and quantify all proteins present in complex biological samples. Therefore, the targeted analysis of informative subsets of the proteome has been beneficial to generate reproducible data sets across multiple samples. Here we review the repertoire of antibody- and mass spectrometry (MS) -based analytical tools which is currently available for the directed analysis of predefined sets of proteins. The topics of emphasis for this review are Selected Reaction Monitoring (SRM) mass spectrometry, emerging tools to control error rates in targeted proteomic experiments, and some representative examples of applications. The ability to cost- and time-efficiently generate specific and quantitative assays for large numbers of proteins and posttranslational modifications has the potential to greatly expand the range of targeted proteomic coverage in biological studies. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.     

Osteogenic differentiation of adipose derived stem cells promoted by overexpression of osterix

Secreted proteins, which may be involved in the regulation of various biological processes, are the potential targets for diagnosis and treatment of diverse diseases. In this study, to identify the human hepatoma HepG2 cells-derived secreted proteins more extensively, we applied the protein sample preparations using the combinations of denaturation methods and molecular-mass cutoff via ultrafiltration to the two-dimensional liquid chromatography coupled with tandem mass spectrometry (2D LC–MS/MS) analysis. We were able to identify a total of 86 proteins containing widely known secreted proteins of HepG2 such as alpha-fetoprotein, of which 73 proteins including 27 signal peptide-containing proteins have never been reported to be secreted from HepG2 cells in other proteomic studies. Among the identified signal peptide-containing proteins, ten proteins such as growth differentiation factor 15, osteopontin and stanniocalcin 2 were discovered as new secreted proteins of HepG2 cells. These observations suggest that the combinations of different sample preparation methods and 2D LC–MS/MS analysis are useful for identifying a wider range of low-abundance proteins and that the secreted proteins from HepG2 identified in this study may be useful as liver-specific biomarkers for diagnosis and treatment.     

An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology

Selected reaction monitoring (SRM) is an accurate quantitative technique, typically used for small-molecule mass spectrometry (MS). SRM has emerged as an important technique for targeted and hypothesis-driven proteomic research, and is becoming the reference method for protein quantification in complex biological samples. SRM offers high selectivity, a lower limit of detection and improved reproducibility, compared to conventional shot-gun-based tandem MS (LC-MS/MS) methods. Unlike LC-MS/MS, which requires computationally intensive informatic postanalysis, SRM requires preacquisition bioinformatic analysis to determine proteotypic peptides and optimal transitions to uniquely identify and to accurately quantitate proteins of interest. Extensive arrays of bioinformatics software tools, both web-based and stand-alone, have been published to assist researchers to determine optimal peptides and transition sets. The transitions are oftentimes selected based on preferred precursor charge state, peptide molecular weight, hydrophobicity, fragmentation pattern at a given collision energy (CE), and instrumentation chosen. Validation of the selected transitions for each peptide is critical since peptide performance varies depending on the mass spectrometer used. In this review, we provide an overview of open source and commercial bioinformatic tools for analyzing LC-MS data acquired by SRM.     

Imaging mass spectrometry of thin tissue sections: a decade of collective efforts

Imaging mass spectrometry (MS) allows to monitor the spatial distribution and abundance of endogenous and administered compounds present within tissue specimens. Several different but complementary imaging MS technologies have been developed allowing the analysis of a wide variety of compounds including inorganic elementals, metabolites, lipids, peptides, proteins and xenobiotics with spatial resolutions from micrometer to nanometer scales. In the past decade, an enormous collective body of work has been done to develop and improve the imaging MS technology. This article gives a historical perspective, an overview of the principle and status of the technology and lists the main fields of applications. It also enumerates some of the critical challenges we need to collectively address for imaging MS to be considered a mainstream analytical method.     

质谱和核磁共振成为研究生物大分子的重要方法 ———简介2002年诺贝尔化学奖得主的贡献

2002年诺贝尔化学奖授予了在质谱和核磁共振领域有杰出贡献的三位科学家。Jonh B. Fenn和Koichi Tanaka发展了质谱鉴定生物大分子质量的方法,Kurt Wuethrich建立了核磁共振测定蛋白质分子溶液三维结构的方法。他们的研究成果是质谱和核磁共振方法发展的里程碑,极大地推动了这两种研究方法的进一步发展。如今,质谱和核磁共振已发展成为认识生物大分子的强劲的研究手段。     

Miniaturized proteomics and peptidomics using capillary liquid separation and high resolution mass spectrometry

Knowledge of the protein and peptide content in a tissue or a body fluid is vital in many areas of medical and biomedical sciences. Information from proteomic and peptidomic studies may reveal alterations in expression due to, e.g., a disease and facilitate the understanding of the pathophysiology and the identification of biological markers. In this minireview, we discuss miniaturized proteomic and peptidomic approaches that have been applied in our laboratory in order to investigate the protein and peptide contents of body fluids (such as plasma, cerebrospinal and amniotic fluid), as well as extracted tissues. The methods involve miniaturized liquid separation, i.e., capillary liquid chromatography and capillary electrophoresis, combined with high resolution mass spectrometry (MS), i.e., Fourier transform ion cyclotron resonance MS. These approaches provide the opportunity to analyze samples of small volumes with high throughput, high sensitivity, good dynamic range and minimal sample handling. Also, the experiments are relatively easy to automate.     

iTRAQ技术及其在蛋白质组学中的应用

近年来随着蛋白质组学的迅速发展,其相应的方法学研究也取得了巨大的进步, 一系列新技术融入了蛋白质组学研究中,极大地促进了这门学科的发展.相对和绝对定量同位素标记(iTRAQ)技术与高度敏感性和准确性的串联质谱及多维液相色谱联用技术已成为蛋白质定性和定量研究的主要工具之一. 该技术可对复杂样本、细胞器、细 胞裂解液等样本进行相对和绝对定量研究,具有较好的定量效果、较高的重复性.由于其能够同时对多达8种样品进行标记分析,故在生命科学的各个领域得到了广泛的应用.本文对iTRAQ的原理、实验流程、优缺点及近几年的应用进展进行综述.     

Determination of the structure of lipid vesicle-bound angiotensin II and angiotensin I

A mass spectrometry (MS)-based strategy was developed to determine the structure of lipid vesicle-bound angiotensin II (AII) and angiotensin I (AI). It involves hydrogen-deuterium exchange (HDX), chemical modifications (e.g., nitration of tyrosine, acetylation of free amino group), and ladder sequencing. HDX is also combined with tandem mass spectrometry (MS/MS) to provide structural details at individual amino acid residues. It was observed that a major portion of both of these peptide hormones interacts with the phospholipid head groups on the surface of the vesicles and that Tyr residue is embedded in the vesicles. Both peptides have a U-shaped structure in the lipid environment.     

Development of a coupled-column liquid chromatographic–tandem mass spectrometric method for the direct determination of betamethasone in urine

Different hyphenated liquid chromatographic (LC) and mass spectrometric (MS) techniques were investigated in order to set-up a method for the fast, direct analysis of betamethasone in hydrolysed and non-hydrolysed urine using large-volume sample injection. After the optimisation of the LC parameters using a traditional UV detector and of the thermospray and mass spectrometric parameters by flow injection, urine samples (0.5 ml) were submitted to analysis by either LC combined with tandem mass spectrometry (MS–MS), coupled-column LC (LC–LC) combined with single quadrupole MS, and LC–LC–MS–MS. Both the three-step configurations (LC–MS–MS and LC–LC–MS) did not provide satisfactory results: loss of sensitivity was noted in the case of LC–MS–MS (likely due to reduced efficiency in the ionisation of betamethasone in the thermospray owing to the presence of large amounts of matrix interference), while in the case of LC–LC–MS a high chemical noise resulting in insufficient selectivity of detection was observed. On the contrary, LC–LC–MS–MS analysis proved to meet the demand of high speed of analysis (sample throughput, 4.5 h⁻¹), selectivity, and sensitivity (LOQ, 1 ng/ml; LOD, 0.2 ng/ml). Notwithstanding the complex analytical system adopted, the developed procedure was manageable and very robust, provided that at the beginning of each analytical session the performance of the system was controlled by checking the retention time of the analytes on the first analytical column with UV detection and by optimising vaporiser temperature of the thermospray by flow injection.     

A fluorescence polarization assay using an engineered human respiratory syncytial virus F protein as a direct screening platform

Probe electrospray ionization (PESI) is one of the most promising methods in biochemical analysis because it enables us to analyze biological samples very quickly without any special pretreatment. Moreover, due to the small size of the needle tip, this method has advantages such as low invasiveness to the samples, making it possible to analyze the biological profiles of organs or tissues in living animal in situ. In this study, we performed a real-time analysis of living mice that delineates the differences in lipid composition of hepatocytes between normal and steatotic mice. In steatotic mice, the number of peaks and the ion abundance for triacylglycerols were much higher compared with those of control mice. All mice used in this study tolerated the procedure well and survived for more than a month until sacrificed for further analysis. To test a potential for medical diagnosis, human tumor tissues were also measured and we obtained discriminative results judged as useful for diagnostics. These results pave the way into the application of PESI to the in vivo analysis of biological molecules.