Proteome analysis using isoelectric focusing in immobilized pH gradient gels followed by mass spectrometry

Over the past several years, a large effort has been focused on improvements of two-dimensional (2-D) gel electrophoresis-based proteomics technology, and on development of novel approaches for proteome analysis. Here, we describe the application of an alternative strategy for the analysis of complex proteomes. The strategy combines isoelectric focusing in immobilized pH gradient strips (in-gel IEF), mass spectrometry (MS), and bioinformatics. A protein mixture is separated by in-gel IEF, and the entire strip is cut into a set of gel sections. Proteins in each gel section are digested with trypsin, and the tryptic peptides are subjected to liquid chromatography-nanoelectrospray-quadrupole ion-trap tandem mass spectrometry (LC-ESI-MS/MS). The LC-ESI-MS/MS data are used to identify the proteins through searches of a protein sequence database. Using this in-gel IEF-LC-MS/MS strategy, we have identified 127 proteins from a human pituitary. This study demonstrates the potential of the in-gel IEF-LC-MS/MS approach for analyses of complex mammalian proteomes.     

Proteome analysis in the bovine adrenal medulla using liquid chromatography with tandem mass spectrometry

Liquid chromatography/mass spectrometry (LC/MS)-based proteomics has been used to identify soluble proteins in the bovine adrenal medulla. This gland is a major source of hormones, opioids, neurotransmitters, and several vital proteins. The adrenal medulla proteins were first purified using ammonium sulfate precipitation. The resulting proteins were then pre-fractionated with a C-4 high-performance liquid chromatography (HPLC) column. Each 2-min HPLC fraction was digested with trypsin, and separated further and analyzed using capillary liquid chromatography/tandem mass spectrometry (capLC/nanospray-MS/MS) to map the proteome of the adrenal medulla. The parent mass and sequence ion information thus obtained for tryptic peptides was used to search the NCBInr database using the SEQUEST search engine. A total of 195 proteins were identified, of which 71 had good scores (delta correlation value greater than 0.1, preliminary score above 200, and cross-correlation value above 2.5). The prominent proteins thus identified are secretogranin I precursor, chromogranin A, proenkephalin A precursor, myosin X, hemoglobin beta chain, hemoglobin alpha chain, heat shock protein 10 kDa, and replicase.     

Strategies for shotgun identification of post-translational modifications by mass spectrometry

The global identification of post-translationally modified proteins is a difficult challenge that is currently being addressed by many researchers in the field of mass spectrometry (MS)-based proteomics. The ability to identify thousands of proteins by shotgun-based strategies has made the mere idea of a global analysis of a particular protein modification seem reasonable. There has been much progress in the development of methods that make use of shotgun-based protein identification in the analysis of a wide variety of protein modifications, some of which will be discussed here.     

Proteome analyses using accurate mass and elution time peptide tags with capillary LC time-of-flight mass spectrometry

We describe the application of capillary liquid chromatography (LC) time-of-flight (TOF) mass spectrometric instrumentation for the rapid characterization of microbial proteomes. Previously (Lipton et al., Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 11049) the peptides from a series of growth conditions of Deinococcus radiodurans have been characterized using capillary LC MS/MS and accurate mass measurements which are captured as an accurate mass and time (AMT) tag database. Using this AMT tag database, detected peptides can be assigned using measurements obtained on a TOF due to the additional use of elution time data as a constraint. When peptide matches are obtained using AMT tags (i.e., using both constraints) unique matches of a mass spectral peak occurs 88% of the time. Not only are AMT tag matches unique in most cases, the coverage of the proteome is high; approximately 3500 unique peptide AMT tags are found on average per capillary LC run. From the results of the AMT tag database search, approximately 900 ORFs detected using LC-TOFMS, with approximately 500 ORFs covered by at least two AMT tags. These results indicate that AMT database searches with modest mass and elution time criteria can provide proteomic information for approximately one thousand proteins in a single run of <3 h. The advantage of this method over using MS/MS based techniques is the large number of identifications that occur in a single experiment as well as the basis for improved quantitation. For MS/MS experiments, the number of peptide identifications is severely restricted because of the time required to dissociate the peptides individually. These results demonstrate the utility of the AMT tag approach using capillary LC-TOF MS instruments, and also show that AMT tags developed using other instrumentation can be effectively utilized.     

Proteome analysis of rat polymorphonuclear leukocytes: a two-dimensional electrophoresis/mass spectrometry approach

The development of a two-dimensional (2-D) map of rat polymorphonuclear (PMN) leukocytes is here reported for the first time. The map is built up by utilizing a wide immobilized pH gradient (IPG), pH 3-10, in the first dimension and also a narrower IPG pH 4.5-8.5 gradient. In addition, the map is constructed by adopting the most recent protocols in 2-D mapping, which call for reduction and alkylation of the sample prior to the start of any electrophoretic step, including the IPG dimension. Fifty-two major protein spots have been so far identified by utilizing both matrix assisted laser desorption/ionization-time of flight (MALDI-TOF) and electrospray quadrupole (Q)-TOF mass spectrometry. A large number of house-keeping and cytoskeleton proteins were detected, together with proteins which are specific to PMN organelles or related to PMN functions such as phagocytosis and chemotaxis. The results obtained demonstrate the possibility of obtaining a single 2-D gel based proteomic map of PMN with representative proteins from different cellular compartments, also including membrane components, allowing the study of PMN protein expression on a proteome-wide scale. The aim of this project is to build an extensive database of such proteins, to be utilized for future studies where the expression of PMN proteins is used as a disease- or drug treatment marker.     

High-throughput analysis using gated multi-inlet mass spectrometry

Gated multi-inlet mass spectrometry is introduced for high-throughput chemical analysis. In this design, multiple high-pressure liquid chromatography (HPLC) columns or capillary electrophoresis (CE) capillaries are attached to multiple electrosprayers (one for each column or capillary) that spray toward a gated multi-inlet time-of-flight mass spectrometer (TOF-MS). Although all of the sprayers are spraying continuously, only one inlet is exposed at any given time for a specific duration set by the MS data system. The gated multi-sprayer, multi-inlet design significantly enhances the performance of the multi-ESI, multi-inlet TOF-MS with minimal cost and reduces analysis time. The gated multi-sprayer, multi-inlet design was applied to the investigation of column-to-column reproducibility of multiple HPLCs using a peptide mixture and to the simultaneous analysis of four protein digests. In addition, it was applied to the analysis of peptide mixtures using eight CE capillaries. The gated multi-inlet MS has several advantages compared to our previous non-gated multi-inlet MS. For example, because only one inlet is open at one time, the original manufacturer's inlet inner diameter and pumping system can be used, which enhances the sensitivity of detection for each inlet and minimizes the manufacturing cost. In addition, the number of inlets can be increased as desired. The maximum number of liquid streams that can be concurrently analyzed is limited by: (1) the number of inlets, (2) the chromatographic (electrophoretic) peak width, and (3) how fast the gate can move from one position to the next.     

Trace analysis of tetracycline antibiotics in human urine using UPLC–QToF mass spectrometry

A rapid, sensitive and specific ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry (UPLC–QToF-MS) method has been developed and validated for simultaneous determination of three tetracyclines (TCs) including oxytetracycline, tetracycline, and chlortetracycline in human urine. Human urine sample preparation involves pH adjustment to 4 with hydrochloric acid, pre-concentration, and cleanup by solid phase extraction (SPE) process. The chromatographic separation of all TCs was achieved in less than 5 min using UPLC and ESI-QToF-MS was successfully employed for the identification and quantification. The accurate masses of the product ions were calculated using lock mass correction, and were deviated from the theoretical masses by 0.5–1.9 mDa and 1.1–4.5 ppm, respectively. The developed method was validated in terms of linearity, sensitivity, selectivity, decision limit, detection capability, accuracy, and precision. Limit of detection and limit of quantitation for all TCs were estimated in the range of 0.089–0.138 ng mL^{− 1} and 0.294–0.455 ng mL^{− 1}, respectively. High overall recoveries of greater than 90% were achieved with linear responses over the 0.5–2 ng mL^{− 1} range for all TCs in urine samples.     

Options for veterinary drug analysis using mass spectrometry

Several classes of chemical compounds, exhibiting many different chemical properties, are classified under the generic term of “veterinary drugs”, among which are the antimicrobial medicines such as antibiotics or dyes, and drugs exhibiting growth promoting properties like steroids, β-agonist compounds, thyrostats or growth hormones. For food safety purposes, the resort to these substances in animal breeding has been submitted to strict regulation within the European Union for more than 15 years. Systems of control have therefore been set up within the same period of time to ensure compliance with the regulation. The current strategy relies on targeted analytical approaches focusing on the detection of residues of the administered compounds or their metabolites in different kinds of feed, food or biological matrices. If screening methods, which provide rapid discrimination between compliant and suspect samples, may be based on several techniques such as immunoassays or mass spectrometry, confirmatory methods mainly rely on the latter, which provides adequate specificity and sensitivity for unambiguous identification of the target analytes in biological matrices at trace level. The present article reviews the main mass spectrometric strategies, from the very first, nonetheless still efficient, single MS and multidimensional and high-resolution MS through to advanced isotope ratio MS. Several applications in the field of residue analysis illustrate each of these approaches and focus on the balance between issues related to the compounds of interest (chemistry, matrix, concentration, …) and the large offer of mass spectrometric-related technical possibilities, from the choice of the ionization conditions (EI, NCI, PCI, reagent gases, ESI+, ESI?), to the mass analyzers (single quadrupole, triple quadrupole, ion traps, time-of-flight, magnetic sectors, isotope ratio mass spectrometer) and corresponding acquisition modes (full scan, LR–SIM, HR–SIM, SRM, precursor scan, …). All the displayed strategies, from the importance of sample preparation to MS analysis to potential derivatization steps and chromatographic separation parameters are discussed in that context. Besides the advantages of each strategy, main issues associated to such MS approaches are commented with an emphasis not only on such critical points as ion suppression and resolution, but also on the adequacy of the current regulation regarding the evolution of the technology. Finally, future trends which may lead to strong and positive impacts in the field of residue analysis are presented, including latest developments and improvements in chromatography or software dedicated to signal acquisition and data analysis.     

Proteome analysis of human stomach tissue: separation of soluble proteins by two-dimensional polyacrylamide gel electrophoresis and identification by mass spectrometry

Two-dimensional gel electrophoresis (2-DE) maps for human stomach tissue proteins have been prepared by displaying the protein components of the tissue by 2-DE and identifying them using mass spectrometry. This will enable us to present an overview of the proteins expressed in human stomach tissues and lays the basis for subsequent comparative proteome analysis studies with gastric diseases such as gastric cancer. In this study, 2-DE maps of soluble fraction proteins were prepared on two gel images with partially overlapping pH ranges of 4-7 and 6-9. On the gels covering pH 4-7 and pH 6-9, about 900 and 600 protein spots were detected by silver staining, respectively. For protein identification, proteins spots on micropreparative gels stained with colloidal Coomassie Brilliant Blue G-250 were excised, digested in-gel with trypsin, and analyzed by peptide mass fingerprinting with delayed extraction-matrix assisted laser desorption/ionization-mass spectrometry (DE-MALDI-MS). In all, 243 protein spots (168 spots in acidic map and 75 spots in basic map) corresponding to 136 different proteins were identified. Besides these principal maps, overview maps (displayed on pH 3-10 gels) for total homogenate and soluble fraction, are also presented with some identifications mapped on them. Based on the 2-DE maps presented in this study, a 2-DE database for human stomach tissue proteome has been constructed and is available at http://proteome.gsnu.ac.kr/DB/2DPAGE/Stomach/. The 2-DE maps and the database resulting from this study will serve important resources for subsequent proteomic studies for analyzing the normal protein variability in healthy tissues and specific protein variations in diseased tissues.     

A shotgun tandem mass spectrometric analysis of phospholipids with normal-phase and/or reverse-phase liquid chromatography/electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry is used in lipidomics studies. The present research established a top-down liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI-MS/MS) shotgun analysis method for phospholipids (PLs) using a normal-phase column or a C30 reverse-phase column with the data-dependent MS/MS scanning mode. A normal-phase column can separate most of the major different classes of PLs. By using LC/ESI-MS/MS with a normal-phase column, approximately 50 molecular species were identified in a PL mixture from rat liver. When the reverse-phase column was used, the PLs could be separated depending on their hydrophobicity, essentially the length of their fatty acyl chains and the number of unsaturated bonds in them. The LC/ESI-MS/MS method using a C30 reverse-phase column was applied to phosphatidylcholine (PC) and phosphatidylethanolamine (PE) mixtures as test samples. Molecular species with the same molecular mass but with different pairs of fatty acyl chains were separately identified. As a result, about 60 PC and 50 PE species were identified. PLs from rat liver were subjected to LC/ESI-MS/MS using the C30 reverse-phase column and about 110 molecular species were identified. Off-line two-dimensional LC/ESI-MS/MS with the normal-phase and C30 reverse-phase columns allowed more accurate identification of molecular species by using one-dimensional C30 reverse-phase LC/ESI-MS/MS analysis of the collected fractions.     

Characterization of N-glycans of recombinant human thyrotropin using mass spectrometry

Thyroid-stimulating hormone is a vital component of the regulatory mechanism that maintains the structure and function of the thyroid gland and governs thyroid hormone release. In this paper we report the first detailed structural characterization of the N-linked oligosaccharides of recombinant human thyroid-stimulating hormone (rhTSH). Using a strategy combining mass spectrometric analysis and sequential exoglycosidase digestion, we have defined the structures of the N-glycans released from recombinant human thyrotropin by peptide N-glycosidase F. All glycans are complex-type glycans and are mainly of the bi- and triantennary type with variable degrees of fucosylation and sialylation. The major non-reducing epitope in the complex-type glycans is: NeuAcalpha2-3Galbeta1-4GlcNAc (sialylated LacNAc). The carbohydrate microheterogeneity at the three glycosylation sites was studied using reversed-phase high-performance liquid chromatography (RP-HPLC), concanavalin A affinity chromatography and mass spectrometric techniques, including both matrix-assisted laser desorption/ionization (MALDI) and electrospray. rhTSH was reduced, carboxymethylated and then digested with trypsin. The mixture of peptides and glycopeptides was subjected to RP-HPLC and the structures of the glycopeptides were determined by MALDI in conjunction with on-target exoglycosidase digestions. After PNGase F digestion, the peptide moiety of the glycopeptide was determined by the presence of the b- and y-series ions derived from its amino acid sequence in the quadrupole time-of-flight tandem mass (QTOF-MS/MS) spectrum. Glycosylation sites Asn-alpha52 and Asn-alpha78 contain mainly bi- and triantennary complex-type glycans. Only glycosylation site Asn-alpha52 bears fucosylated N-glycans. Minor tetraantennary complex structures were also observed on both glycosylation sites. Profiling of the carbohydrate moieties of Asn-beta23 indicates a large heterogeneity. Bi-, tri-, and tetraantennary N-glycans were present at this site. These data demonstrate site-specificity of glycosylation in the alpha subunit but not in the beta subunit of rhTSH with Asn-alpha52 bearing essentially di- and triantennary glycans with or without core fucosylation and bi- and triantennary glycans with no core fucosylation being attached to Asn-alpha78.     

Quantitative analysis of docetaxel in human plasma using liquid chromatography coupled with tandem mass spectrometry

An assay for the quantitative determination of docetaxel in human plasma is described. Docetaxel was extracted from the matrix using liquid-liquid extraction with ter-butylmethylether, followed by high-performance liquid chromatographic analysis using an alkaline eluent. Paclitaxel was used as internal standard. Positive ionization electrospray tandem mass spectrometry was performed for selective and sensitive detection. The method was validated according to the FDA guidelines on bioanalytical method validation. The validated range for docetaxel was from 0.25--1000 ng/mL using 200 microL plasma aliquots. The method requires only a limited volume (200 microL) of human plasma and the method can be applied in studies requiring a low lower limit of quantitation of 0.25 ng/mL. The assay was applied successfully in several clinical and pharmacological studies with docetaxel.     

Multidimensional mass spectrometry-based shotgun lipidomics analysis of vinyl ether diglycerides

Diglycerides play a central role in lipid metabolism and signaling in mammalian cells. Although diacylglycerol molecular species comprise the majority of cellular diglycerides that are commonly measured using a variety of approaches, identification of extremely low abundance vinyl ether diglycerides has remained challenging. In this work, representative molecular species from the three diglyceride subclasses (diacyl, vinyl ether, and alkyl ether diglycerides; hereafter referred to as diradylglycerols) were interrogated by mass spectrometric analysis. Product ion mass spectra of the synthesized diradylglycerols with varied chain lengths and degrees of unsaturation demonstrated diagnostic fragmentation patterns indicative of each subclass. Multidimensional mass spectrometry-based shotgun lipidomics (MDMS-SL) analysis of mouse brain and heart lipid extracts were performed using the identified informative signature product ions. Through an array of tandem mass spectrometric analyses utilizing the orthogonal characteristics of neutral loss scanning and precursor ion scanning, the differential fragmentation of each subclass was exploited for high-yield structural analyses. Although molecular ion mass spectra readily identified diacylglycerol molecular species directly from the hexane fractions of tissue extracts enriched in nonpolar lipids, molecular ion peaks corresponding to ether-linked diglycerides were not observable. The power of MDMS-SL utilizing the tandem mass spectrometric array analysis was demonstrated by identification and profiling of individual molecular species of vinyl ether diglycerides in mouse brain and heart from their undetectable molecular ion peaks during MS¹ analysis. Collectively, this technology enabled the identification and profiling of previously inaccessible vinyl ether diglyceride molecular species in mammalian tissues directly from extracts of biologic tissues.

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Doping control analysis of methoxyphenamine using liquid chromatography-tandem mass spectrometry

Methoxyphenamine (o-methoxy-N,alpha-dimethylphenethylamine, Orthoxine) used in earlier times as a bronchodilator is prohibited in sports according to the regulations of the World Anti-Doping Agency (WADA). The drug and several of its metabolites are commonly analysed in doping control screening assays using gas chromatography-mass spectrometry requiring extraction from urine specimens. A complementary method employing liquid chromatography-atmospheric pressure chemical ionisation-tandem mass spectrometry and direct injection of urine aliquots was developed, which provided a fast and sensitive alternative to confirm the presence of the prohibited compound and degradation products in sports drug testing samples. In particular, the chromatographic separation of the active drug from isomeric compounds such as the designer drug p-methoxymetamphetamine (PMMA) was of particular interest to unambiguously identify the applied substance and was accomplished using a C6-phenyl reverse-phase column with isocratic elution. The established procedure was validated for methoxyphenamine with regard to specificity, limit of detection (0.7 ng mL(-1)), intraday- and interday precision (2.5-5.8% and 10.8-16.2%, respectively) and its applicability was demonstrated with an authentic doping control sample which tested positive for the prohibited compound early in 2008.     

Simultaneous analysis of butene isomer mixtures using process mass spectrometry

The feasibility of simultaneous analysis of mixtures containing two to four butene isomers and up to six total components using process mass spectrometry is assessed. As for typical (nonisomeric) applications of process mass spectrometry, simultaneous analysis is based on the assumption that the electron ionization mass spectra of mixtures are linear combinations of the spectra of the individual constituents. Limits of detection for binary isomer mixtures are on the order of 0.1% to 10%, limited by the ability to distinguish small differences between similar spectra. As spectral and mixture complexity increase, both accuracy and precision decrease. Not surprisingly the similarity of the spectra of stereoisomers cis- and trans-2-butene is greater than that of the other (nonstereoisomeric) isomer pairs, and mixtures containing both cis- and trans-2-butene are the most difficult to quantitate. However, even for mixtures of all four butenes, accuracy (root-mean-square ERROR = 2.43%), precision (average coefficient of VARIATION = 6.72%), and linearity (correlation coefficient of a plot of measured versus actual concentration r² = 0.985 ± 0.002) are reasonably good.     

样品制备方法对高效液相色谱-串联质谱分析人乳内源肽的影响

人乳内源肽是乳蛋白在乳腺中被降解形成的具有生理功能的肽,是人乳的重要组成部分,研究人乳内源肽对于婴儿健康具有重要的意义.高效液相色谱-串联质谱(LC-MS/MS)联用技术的应用,促使人乳内源肽的研究取得了突破性的进展.人乳中内源肽含量低、干扰组分多,样品制备方法是影响分析结果的关键步骤.为了研究样品制备方法对分析结果的...     

Quantitative analysis of estrogens in human urine using gas chromatography/negative chemical ionisation mass spectrometry

A sensitive procedure for the determination of estrogens in urine has been developed, using enzymatic hydrolysis and ether extraction followed by capillary gas chromatography with negative chemical ionisation mass spectrometry (GC/NCI-MS) of the pentafluorobenzoyl derivatives. These derivatives were superior for GC/NCI-MS to trifluoroacetyl, heptafluorobutyl, pentadecafluorooctanoyl and perfluorotolyl derivatives, giving characteristic negative molecular ions as the base peak for each of the naturally occurring estrogens estrone, estradiol and estriol, and for the synthetic estrogen ethynylestradiol used in contraceptive pills. The method was also suitable for determination of some metabolites of estrone and estradiol. The specificity and sensitivity of the GC/NCI-MS method simplifies sample preparation. Recovery of spiked samples was in the range 84-101% for the natural estrogens based on additions to increase the concentration by 5 and 1 microg L(-1). The repeatability of the method was 1-8% for all estrogens.