Proteome profile of cytosolic component of zebrafish liver generated by LC-ESI MS/MS combined with trypsin digestion and microwave-assisted acid hydrolysis

The zebrafish genome has recently been sequenced and annotated allowing for high-throughput proteomic analysis. Here, we report for the first time a proteomic subset of zebrafish liver, an important organ for metabolizing toxins. Using a newly developed analytical procedure, we have identified 1204 proteins from the cytosolic component of a zebrafish liver tissue sample. Our methods involve cell-compartment fractionation of liver tissue samples, four levels of protein digestion, and off-line two-dimensional liquid chromatography (2-D LC) separations of resultant peptides. Proteins are identified using an electrospray ionization quadrupole time-of-flight tandem mass spectrometer (ESI-QTOF MS/MS), which provides high-resolution and high-accuracy mass measurement of peptide ions and their fragment ions. We demonstrate that greater proteome coverage can be achieved by combining the results obtained from four methods of protein digestion: three tryptic digests (one in buffer, one in methanol, and another in SDS), and a microwave-assisted acid hydrolysate of the protein extracts. Identified proteins--which included several groups of established protein biomarkers--were functionally classified. We discuss the functions and implications of these biomarkers within the context of zebrafish toxicology.     

Rapid protein identification using monolithic enzymatic microreactor and LC-ESI-MS/MS

A monolithic enzymatic microreactor was prepared in a fused-silica capillary by in situ polymerization of acrylamide, glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) in the presence of a binary porogenic mixture of dodecanol and cyclohexanol, followed by ammonia solution treatment, glutaraldehyde activation and trypsin modification. The choice of acrylamide as co-monomer was found useful to improve the efficiency of trypsin modification, thus, to increase the enzyme activity. The optimized microreactor offered very low back pressure, enabling the fast digestion of proteins flowing through the reactor. The performance of the monolithic microreactor was demonstrated with the digestion of cytochrome c at high flow rate. The digests were then characterized by CE and HPLC-MS/MS with the sequence coverage of 57.7%. The digestion efficiency was found over 230 times as high as that of the conventional method. In addition, for the first time, protein digestion carried out in a mixture of water and ACN was compared with the conventional aqueous reaction using MS/MS detection, and the former solution was found more compatible and more efficient for protein digestion.     

Identification of protein components in in vivo human acquired enamel pellicle using LC-ESI-MS/MS

The acquired enamel pellicle is a thin protein film forming upon exposure of tooth enamel surfaces to saliva. The structural analysis of this integument relies on efficient pellicle harvesting and protein identification procedures. Material from three individual subjects and two pooled samples yielded the identification by LC-ESI-MS/MS of 130 pellicle proteins of which 89 were found in three or more experiments. A high intersubject consistency in pellicle composition was observed.     

Proteome profile of functional mitochondria from human skeletal muscle using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS

Mitochondria can be isolated from skeletal muscle in a manner that preserves tightly coupled bioenergetic function in vitro. The purpose of this study was to characterize the composition of such preparations using a proteomics approach. Mitochondria isolated from human vastus lateralis biopsies were functional as evidenced by their response to carbohydrate and fat-derived fuels. Using one-dimensional gel electrophoresis and HPLC-ESI-MS/MS, 823 unique proteins were detected, and 487 of these were assigned to the mitochondrion, including the newly characterized SIRT5, MitoNEET and RDH13. Proteins detected included 9 of the 13 mitochondrial DNA-encoded proteins and 86 of 104 electron transport chain (ETC) and ETC-related proteins. In addition, 59 of 78 proteins of the 55S mitoribosome, several TIM and TOM proteins and cell death proteins were present. This study presents an efficient method for future qualitative assessments of proteins from functional isolated mitochondria from small samples of healthy and diseased skeletal muscle.     

Identification and tissue mapping of APGWamide-related peptides in Sepia officinalis using LC-ESI-MS/MS

This paper demonstrates for the first time the occurrence of tetrapeptides related to APGWamide in the mollusk cephalopod Sepia officinalis. LC-ESI-MS/MS analysis allowed the identification of the APGWamide-related peptides predicted by the two genes cloned previously in Lymnaea stagnalis and in Mytilus edulis, as well as the dipeptide GWamide released from the processing of the tetrapeptides by a dipeptidyl aminopeptidase (DPAP). TPGWamide and GWamide appeared to be exclusively located in the CNS, and the APGWamide in both the CNS and the nerve endings. The RPGWamide and the KPGWamide were not detected by LC-ESI-MS/MS suggesting they could be totally processed into GWamide. The in vitro processing of the tetrapeptides into GWamide by optic lobe extract revealed a differential processing for each, with APGWamide (44.7%)>RPGWamide(24.3%)>KPGWamide(19.3%)>TPGWamide (11.7%). The tissue mapping results, together with the processing efficiency data suggest that the GWamide is mainly produced from the M. edulis gene products RPGWamide and KPGWamide.     

Determination of the major mercapturic acids of acrylamide and glycidamide in human urine by LC-ESI-MS/MS

We developed a LC-MS/MS method for the quantitative determination of the mercapturic acid (MA) metabolites of acrylamide (AA) AAMA and of its oxidative metabolite glycidamide (GA) GAMA in urine samples from the general population. The method requires 4 mL of urine which is solid phase extracted prior to LC-MS/MS analysis. The metabolites are detected by ESI-tandem mass spectrometry in negative ionisation mode and quantified by isotope dilution. Detection limits ranged down to 1.5 microg/L urine for both AAMA and GAMA. The imprecision expressed as R.S.D. lay between 2% and 6% for both analytes (intra- and inter-assay). First results on a small group of 29 persons out of the general population ranged from 5 to 338 microg/L AAMA and 相似文献   

Proteome profile of human urine with two-dimensional liquid phase fractionation

Two-dimensional liquid chromatography separation (2-DL), based on chromatofocusing for first dimension and hydrophobicity for second, can be used as a complementary method to two-dimensional gel electrophoresis (2-DE). A platform now available, ProteomeLab PF 2D provided by Beckman Coulter, (Fullerton, CA, USA), assembles these methods in automation. This system was applied to resolve large numbers of urine proteins. Reproducibility and sensitivity in protein resolution were evaluated in this study using urines collected from male blood donors. About 1000 peaks were detected at a pH range of 4.0-8.5 by applying 1 mg of proteins. Furthermore, the same fractions showing peaks with high absorbance intensities in second dimension were collected and subjected to matrix-assisted laser desorption/ionization-time of flight/mass spectrometry analysis for identification. The results showed that the 2-DL provides high reproducibility of two-dimensional protein map, and lends fractions to subsequent mass spectrometry analysis without the further need for extraction or solubilization of samples as required for spots excised from 2-DE gels. In addition, this system also allows to separate particularly proteins with 40-9 kDa molecular weight.     

Quantification of trans-4-hydroxy-2-nonenal enantiomers and metabolites by LC-ESI-MS/MS

Lipid peroxidation is a causal factor in multiple diseases including Alzheimer's disease, atherosclerosis, and alcoholic liver disease. One of the most studied products of lipid peroxidation, trans-4-hydroxy-2-nonenal (HNE), has multiple cell signaling and cytotoxic effects. In this work, we developed an LC-MS/MS method for the quantitation of HNE enantiomers, the metabolite trans-4-hydroxy-2-nonenoic acid, and HNE-glutathione adducts in a single chromatographic run. In this method, (R)-HNE and (S)-HNE are derivatized by (S)-carbidopa to form diastereomers that are separated by a reversed-phase column. This method was successfully validated and tested using respiring rat brain mitochondria that enantioselectively metabolize HNE. Metabolic profiles of HNE biotransformation, including the enantiomeric disposition of HNE, will provide useful biomarker data regarding lipid peroxidation in disease states.     

Identification of lignans and related compounds in Anthriscus sylvestris by LC-ESI-MS/MS and LC-SPE-NMR

The aryltetralin lignan deoxypodophyllotoxin is much more widespread in the plant kingdom than podophyllotoxin. The latter serves as a starting compound for the production of cytostatic drugs like etoposide. A better insight into the occurrence of deoxypodophyllotoxin combined with detailed knowledge of its biosynthestic pathway(s) may help to develop alternative sources for podophyllotoxin. Using HPLC combined with electrospray tandem mass spectrometry and NMR spectroscopy techniques, we found nine lignans and five related structures in roots of Anthriscus sylvestris (L.) Hoffm. (Apiaceae), a common wild plant in temperate regions of the world. Podophyllotoxone, deoxypodophyllotoxin, yatein, anhydropodorhizol, 1-(3′-methoxy-4′,5′-methylenedioxyphenyl)1-ξ-methoxy-2-propene, and 2-butenoic acid, 2-methyl-4-[[(2Z)-2-methyl-1-oxo-2-buten-1-yl]oxy]-, (2E)-3-(7-methoxy-1,3-benzodioxol-5-yl)-2-propen-1-yl ester, (2Z)- were the major compounds. α-Peltatin, podophyllotoxin, β-peltatin, isopicropodophyllone, β-peltatin-a-methylether, (Z)-2-angeloyloxymethyl-2-butenoic acid, anthriscinol methylether, and anthriscrusin were present in lower concentrations. α-Peltatin, β-peltatin, isopicropodophyllone, podophyllotoxone, and β-peltatin-a-methylether have not been previously reported to be present in A. sylvestris. Based on our findings we propose a hypothetical biosynthetic pathway of aryltetralin lignans in A. sylvestris.     

Optimization of protein solubilization for the analysis of the CD14 human monocyte membrane proteome using LC-MS/MS

Proteomic profiling of membrane proteins is of vital importance in the search for disease biomarkers and drug development. However, the slow pace in this field has resulted mainly from the difficulty to analyze membrane proteins by mass spectrometry (MS). The objective of this investigation was to explore and optimize solubilization of membrane proteins for shotgun membrane proteomics of the CD14 human monocytes by examining different systems that rely on: i) an organic solvent (methanol) ii) an acid-labile detergent 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate (PPS), iii) a combination of both agents (methanol + PPS). Solubilization efficiency of different buffers was first compared using bacteriorhodopsin as a model membrane protein. Selected approaches were then applied on a membrane subproteome isolated from a highly enriched human monocyte population that was ~ 98% positive for CD14 expression as determined by FACS analysis. A methanol-based buffer yielded 194 proteins of which 93 (48%) were mapped as integral membrane proteins. The combination of methanol and acid-cleavable detergent gave similar results; 203 identified proteins of which 93 (46%) were mapped integral membrane proteins. However, employing PPS 216 proteins were identified of which 75 (35%) were mapped as integral membrane proteins. These results indicate that methanol alone or in combination with PPS yielded significantly higher membrane protein identification/enrichment than the PPS alone.     

Identification of membrane proteins from mammalian cell/tissue using methanol-facilitated solubilization and tryptic digestion coupled with 2D-LC-MS/MS

The core prerequisites for an efficient proteome-scale analysis of mammalian membrane proteins are effective isolation, solubilization, digestion and multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). This protocol is for analysis of the mammalian membrane proteome that relies on solubilization and tryptic digestion of membrane proteins in a buffer containing 60% (vol/vol) methanol. Tryptic digestion is followed by strong cation exchange (SCX) chromatography and reversed phase (RP) chromatography coupled online with MS/MS for protein identification. The use of a methanol-based buffer eliminates the need for reagents that interfere with chromatographic resolution and ionization of the peptides (e.g., detergents, chaotropes, inorganic salts). Sample losses are minimized because solubilization and digestion are carried out in a single tube avoiding any sample transfer or buffer exchange between these steps. This protocol is compatible with stable isotope labeling at the protein and peptide level, enabling identification and quantitation of integral membrane proteins. The entire procedure--beginning with isolated membrane fraction and finishing with MS data acquisition--takes 4-5 d.     

Peroxidatic catecholestrogen production by human breast cancer tissue in vitro

The ability of breast cancer tissues from postmenopausal women to form catechol estrogens was examined by using a product isolation assay. Initial assays were carried out in the presence of either: (a) NADPH, the co-factor for monooxygenase mediated catecholestrogen (CE) formation or; (b) light-activated Tween 80 (LAT-80), a putative organic hydroperoxide co-factor for peroxidatic activity. Under monooxygenase conditions, CE formation by homogenates of 10 tumors did not exceed that obtained with heat denatured tissue. In contrast, 17 of 20 tumors incubated with LAT-80 synthesized significant amounts of CE (8.5 +/- 1.17 2-hydroxyestradiol [2-OH-E2] and 12.8 +/- 2.4 nmol/g protein/10 min 4-hydroxyestradiol [4-OH-E2]). Substitution of cumene hydroperoxide, an organic hydroperoxide, for LAT-80 enhanced estrogen 2/4 hydroxylase (E-2/4-H) activity over 200-fold, making it possible to characterize systematically the peroxidatic activity. The properties of peroxidatic E-2/4-H activity were similar to those of soluble peroxidases isolated from brain, including an acidic pH optimum, localization in the soluble fraction, an apparent Km in the range of 80 microM and an apparent Vmax in the range of 4000 nmol/g/protein/10 min for both 2- and 4-OH-E2. Under optimal assay conditions, peroxidatic E-2/4-H activity was identified in 10 of 13 tumors (2480 +/- 580 nmol/g protein/10 min for 2-OH-E2 and 2790 +/- 600 for 4-OH-E2). The level of activity detected suggests a biological relevance for CE formation by breast cancer tissue.     

Proteomic analysis in human breast cancer: identification of a characteristic protein expression profile of malignant breast epithelium

Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Surprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow proteins of interest to be identified by their expression and/or modification pattern in 2-DE rather than using the traditional approach of translating gene expression data. To identify a proteomic pattern that is characteristic for malignant breast epithelium, we performed differential 2-DE analysis in sets of microdissected malignant breast epithelia and corresponding adjacent normal breast epithelia from five patients with invasive breast carcinoma. Thirty-two protein spots were found to be selectively regulated in malignant epithelium, and were subjected to MALDI-TOF and/or immunoblotting for protein identification. Thirteen of the identified proteins had previously not been associated with breast cancer. The validity of these findings was confirmed by literature review and immunohistochemistry for identified proteins in an independent cohort of 50 breast cancer specimens. We here describe, for the first time, a proteomic analysis of matched normal and malignant epithelia from invasive breast carcinomas. This strategy leads to a better understanding of oncogenesis at an operational level and helps to characterize the malignant phenotype of individual tumors, and thereby to identify novel targets for antineoplastic therapy.     

Proteomic analysis of the tetraspanin web using LC-ESI-MS/MS and MALDI-FTICR-MS

Tetraspanins are integral membrane proteins involved in a variety of physiological and pathological processes. In cancer, clinical and experimental studies have reported a link between tetraspanin expression levels and metastasis. Tetraspanins play a role as organizers of a molecular network of interactions, the "tetraspanin web". Here, we have performed a proteomic characterization of the tetraspanin web using a model of human colon cancer consisting of two cell lines derived from primary tumor and metastasis from the same patient. The tetraspanin complexes were isolated after immunoaffinity purification and the proteins were identified by MS using LC-ESI-MS/MS and MALDI-FTICR. The high resolution and mass accuracy of FTICR MS allowed reliable identification using mass finger printing with only two peptides. Thus, it could be used to resolve the composition of complex peptide mixtures from membrane proteins. Different types of membrane proteins were identified, including adhesion molecules (integrins, Lu/B-CAM, GA733 proteins), receptors and signaling molecules (BAI2, PKC, G proteins), proteases (ADAM10, TADG15), and membrane fusion proteins (syntaxins) as well as poorly characterized proteins (CDCP1, HEM-1, CTL1, and CTL2). Some components were differentially detected in the tetraspanin web of the two cell lines. These differences may be relevant for tumor progression and metastasis.     

Determination of acylated anthocyanin in human urine after ingesting a purple-fleshed sweet potato beverage with various contents of anthocyanin by LC-ESI-MS/MS

Eighty-seven healthy volunteers ingested a purple-fleshed sweet potato beverage with various contents of anthocyanin (beverage A; 22.1 mg/250 ml, B; 107.8, C; 84.9). An acylated anthocyanin, peonidin 3-caffeoylsophoroside-5-glucoside, was detected in the urine 2 h after ingestion. The concentrations were 15.1+/-2.2 microg/l of urine (mean+/-SEM), 46.6+/-5.3, and 53.3+/-2.2 for beverages A, B, and C respectively.     

LC-ESI-MS/MS method for the quantification of entecavir in human plasma and its application to bioequivalence study

Liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) was used for a quantitative estimation of entecavir (EV) in human plasma using lamivudine (LM) as internal standard (IS). The method herein described is simple, sensitive, and specific. Chromatographic separation was performed on XBridge-C18, 4.6 mm × 50 mm, 5-μm column with an isocratic mobile phase composed of 10 mM ammonium hydrogen carbonate (pH 10.5):methanol (85:15 v/v), pumped at 0.3 ml/min. EV and LM were detected using proton adducts at m/z 278.1→152.1 and 230.2→112.0 in multiple reaction monitoring (MRM) positive mode. Solid phase extraction method was employed in the extraction of EV and LM from the biological matrix. This method was validated over a linear concentration range of 50.0-20000.0 pg/ml with a correlation coefficient (r) ≥0.9983. Intra and inter-day precision of EV was found within the range of 1.2-4.2 for EV and 4.4-4.5 for LM. EV was stable throughout three freeze/thaw cycles, bench top and postoperative studies. This method was successfully used in the analysis of plasma samples following oral administration of EV (0.5 mg) in 26 healthy human volunteers.     

Proteome analysis and tissue microarray for profiling protein markers associated with lymph node metastasis in colorectal cancer

BACKGROUND: Understanding the proteins associated with lymph node metastasis (LNM) in colorectal cancer (CRC) will benefit us in the prediction of CRC prognosis and provide us new potential targets in the intervention of CRC. The aim of this study is to investigate the LNM-associated proteins and to evaluate the clinicopathological characteristics of these target proteins' expression in CRC. METHODS: Fresh tumor and paired normal mucosa from five cases for each group of non-LNM CRC and LNM CRC were analyzed by two-dimensional electrophoresis coupled with MALDI-TOF-MS, followed by Western blotting confirmation. In 40 paraffin-embedded CRC samples, each for non-LNM CRC and LNM CRC, four differentially expressed proteins identified by proteomics analysis were detected by tissue microarray with immunohistochemistry staining to access the clinicopathological characteristics of these proteins in LNM of CRC. RESULTS: Twenty-five proteins were found to be differentially expressed between normal mucosa and CRC tissue. Increased expression levels of heat shock protein-27 (HSP-27), glutathione S-transferase (GST), and Annexin II, but a decreased expression level of liver-fatty acid binding protein (L-FABP), existed in LNM CRC as compared with non-LNM CRC (p<0.01 or p<0.05, respectively). CONCLUSION: The techniques of proteomic analysis combined with tissue microarray provide us a dramatic tool for screening of LNM-associated proteins in cancer research. The increased expression of HSP-27, GST, and Annexin II, but decreased expression of L-FABP, suggests a significantly elevated incidence of LNM in CRC.     

Characterization of an antiestrogen-binding protein in high salt extracts of human breast cancer tissue

An antiestrogen binding protein which binds [3H]tamoxifen (1-[4-(2-dimethylaminoethoxy)-phenyl]1,2-diphenylbut-1(Z)-ene) with high affinity (Kd = 1.1 X 10(-9) M) is present in high salt (0.6 M KCl) extracts of washed breast cancer tissue pellets. Its concentration in high salt extract is higher than its concentration in cytosol. The characteristics of the antiestrogen binding protein from cytosol and salt extract of breast cancer tissue are indistinguishable. It specifically binds triphenylethylene and other nonsteroidal antiestrogens and displays little or no binding affinity for estrogens, progesterone, dihydrotestosterone and cortisol. The antiestrogen binding protein is of unusually large size as judged by gel filtration on agarose 0.5 m and sedimentation analysis on 5-20% sucrose density gradients. Differential centrifugation studies indicate that it is not principally microsomal in origin. This protein is more thermostable than the estrogen receptor from which it can also be distinguished by ion exchange chromatography. The antiestrogen binding protein was eluted from DEAE-Sephacel by 0.05 M KCl indicating that it is less negatively charged than the estrogen receptor which was eluted by 0.1 M KCl. Lipoprotein fractionation of breast cancer cytosol using potassium bromide density gradients did not reveal specific antiestrogen binding activity associated with any recognized class of lipoprotein. Specific [3H]tamoxifen binding sites were pelleted in potassium bromide gradients consistent with the apparent large size of this protein. The physical characteristics of the antiestrogen binding protein in normal human tissue (myometrium) and neoplastic tissue (breast cancer) are remarkably similar, possibly reflecting a highly conserved structure.     

Proteome analysis of a human uveal melanoma primary cell culture by 2-DE and MS

We present here the first proteomics analysis of uveal melanoma (UM) cells. These cells represent a good model for the identification of polypeptide markers, which could be developed as diagnostic tools. UM is the most common primary intraocular tumour in adults. In contrast to other cancers, the survival rate of patients with this malignancy has changed little over the past few decades; a better understanding of the molecular biology of UM oncogenesis and metastasis is needed to build the basis for the identification of novel drug targets. In the study presented here, proteins from a UM primary cell culture were separated by 2-DE using a pI 3-10 gradient; 270 spots were analysed by LC-MS/MS, identifying 683 proteins derived from 393 different genes. Of those, 69 (18%) are related to cancer processes involving cell division, proliferation, invasion, metastasis, oncogenesis, drug resistance and others. To our knowledge, 96% of the proteins identified, including 16 hypothetical proteins, have never been reported in UM before. This study represents the first step towards the establishment of a UM protein database as a valuable resource for the study of this malignancy.