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Qi-Chang Xia

Publications and source records attributed to Qi-Chang Xia.

At least 19 recordsLinked to original sources
PubMed2004

A comparative proteomic strategy for subcellular proteome research: ICAT approach coupled with bioinformatics prediction to ascertain rat liver mitochondrial proteins and indication of mitochondrial localization for catalase.

Subcellular proteomics, as an important step to functional proteomics, has been a focus in proteomic research. However, the co-purification of "contaminating" proteins has been the major problem in all the subcellular proteomic research including all kinds of mitochondrial proteome research. It is often difficult to conclude whether these "contaminants" represent true endogenous partners or artificial associations induced by cell disruption or incomplete purification. To solve such a problem, we applied a high-throughput comparative proteome experimental strategy, ICAT approach performed with two-dimensional LC-MS/MS analysis, coupled with combinational usage of different bioinformatics tools, to study the proteome of rat liver mitochondria prepared with traditional centrifugation (CM) or further purified with a Nycodenz gradient (PM). A total of 169 proteins were identified and quantified convincingly in the ICAT analysis, in which 90 proteins have an ICAT ratio of PM:CM>1.0, while another 79 proteins have an ICAT ratio of PM:CM<1.0. Almost all the proteins annotated as mitochondrial according to Swiss-Prot annotation, bioinformatics prediction, and literature reports have a ratio of PM:CM>1.0, while proteins annotated as extracellular or secreted, cytoplasmic, endoplasmic reticulum, ribosomal, and so on have a ratio of PM:CM<1.0. Catalase and AP endonuclease 1, which have been known as peroxisomal and nuclear, respectively, have shown a ratio of PM:CM>1.0, confirming the reports about their mitochondrial location. Moreover, the 125 proteins with subcellular location annotation have been used as a testing dataset to evaluate the efficiency for ascertaining mitochondrial proteins by ICAT analysis and the bioinformatics tools such as PSORT, TargetP, SubLoc, MitoProt, and Predotar. The results indicated that ICAT analysis coupled with combinational usage of different bioinformatics tools could effectively ascertain mitochondrial proteins and distinguish contaminant proteins and even multilocation proteins. Using such a strategy, many novel proteins, known proteins without subcellular location annotation, and even known proteins that have been annotated as other locations have been strongly indicated for their mitochondrial location.

Animals↗
PubMed2004

A high-throughput approach for subcellular proteome: identification of rat liver proteins using subcellular fractionation coupled with two-dimensional liquid chromatography tandem mass spectrometry and bioinformatic analysis.

Four fractions from rat liver (a crude mitochondria (CM) and cytosol (C) fraction obtained with differential centrifugation, a purified mitochondrial (PM) fraction obtained with nycodenz density gradient centrifugation, and a total liver (TL) fraction) were analyzed with two-dimensional liquid chromatography tandem mass spectrometry analysis. A total of 564 rat proteins were identified and were bioinformatically annotated according to their physicochemical characteristics and functions. While most extreme alkaline ribosomal proteins were identified in the TL fraction, the C fraction mainly included neutral enzymes and the PM fraction enriched alkaline proteins and proteins with electron transfer activity or oxygen binding activity. Such characteristics were more apparent in proteins identified only in the TL, C, or PM fraction. The Swiss-Prot annotation and the bioinformatic prediction results proved that the C and PM fractions had enriched cytoplasmic or mitochondrial proteins, respectively. Combination usage of subcellular fractionation with two-dimensional liquid chromatography tandem mass spectrometry was proved to be a high-throughput, sensitive, and effective analytical approach for subcellular proteomics research. Using such a strategy, we have constructed the largest proteome database to date for rat liver (564 rat proteins) and its cytosol (222 rat proteins) and mitochondrial fractions (227 rat proteins). Moreover, the 352 proteins with Swiss-Prot subcellular location annotation in the 564 identified proteins were used as an actual subcellular proteome dataset to evaluate the widely used bioinformatics tools such as PSORT, TargetP, TMHMM, and GRAVY.

Animals↗
PubMed2004

Accurate qualitative and quantitative proteomic analysis of clinical hepatocellular carcinoma using laser capture microdissection coupled with isotope-coded affinity tag and two-dimensional liquid chromatography mass spectrometry.

Laser capture microdissection (LCM) is a powerful tool that enables the isolation of specific cell types from tissue sections, overcoming the problem of tissue heterogeneity and contamination. This study combined the LCM with isotope-coded affinity tag (ICAT) technology and two-dimensional liquid chromatography to investigate the qualitative and quantitative proteomes of hepatocellular carcinoma (HCC). The effects of three different histochemical stains on tissue sections have been compared, and toluidine blue stain was proved as the most suitable stain for LCM followed by proteomic analysis. The solubilized proteins from microdissected HCC and non-HCC hepatocytes were qualitatively and quantitatively analyzed with two-dimensional liquid chromatography tandem mass spectrometry (2D-LC-MS/MS) alone or coupled with cleavable ICAT labeling technology. A total of 644 proteins were qualitative identified, and 261 proteins were unambiguously quantitated. These results show that the clinical proteomic method using LCM coupled with ICAT and 2D-LC-MS/MS can carry out not only large-scale but also accurate qualitative and quantitative analysis.

Affinity Labels↗
PubMed2004

Proteome analysis of hepatocellular carcinoma cell strains, MHCC97-H and MHCC97-L, with different metastasis potentials.

To better understand the mechanism underlying hepatocellular carcinoma (HCC) metastasis and to search for potential markers for HCC prognosis, differential proteome analysis on two HCC cell strains with high and low metastatic potentials, MHCC97-H and MHCC97-L, was conducted using two-dimensional (2-D) gel electrophoresis followed by matrix-assisted laser desorption/time of flight mass spectrometry and liquid chromatography ion trap mass spectrometry. Image analysis of silver-stained 2-D gels revealed that 56 protein spots showed significant differential expression in MHCC97-H and MHCC97-L cells (Student's t-test, P < 0.05) and 4 protein spots were only detected in MHCC97-H cells. Fourteen protein spots were further identified using in-gel tryptic digestion, peptide mass fingerprinting and tandem mass spectrometry. The expressions of pyruvate kinase M2, ubiquitin carboxy-terminal hydrolase L1, laminin receptor 67 kDa, S100 calcium-binding protein A4, thioredoxin and cytokeratin 19 were elevated in MHCC97-H cells. However, manganese superoxide dismutase, calreticulin precursor, cathepsin D, lactate dehydrogenase B, non-metastatic cell protein 1, cofilin 1 and calumenin precursor were down-regulated in MHCC97-H cells. Intriguingly, most of these identified proteins have been reported to be associated with tumor metastasis. The functional implications of alterations in the levels of these proteins are discussed.

Animals↗
PubMed2004

Phosphoproteome analysis of mouse liver using immobilized metal affinity purification and linear ion trap mass spectrometry.

Since protein phosphorylation is a dominant mechanism of information transfer in cells, there is a great need for methods capable of accurately elucidating sites of phosphorylation. In recent years mass spectrometry has become an increasingly viable alternative to more traditional methods of phosphorylation analysis. The present study used immobilized metal affinity chromatography (IMAC) coupled with a linear ion trap mass spectrometer to analyze phosphorylated proteins in mouse liver. A total of 26 peptide sequences defining 26 sites of phosphorylation were determined. Although this number of identified phosphoproteins is not large, the approach is still of interest because a series of conservative criteria were adopted in data analysis. We note that, although the binding of non-phosphorylated peptides to the IMAC column was apparent, the improvements in high-speed scanning and quality of MS/MS spectra provided by the linear ion trap contributed to the phosphoprotein identification. Further analysis demonstrated that MS/MS/MS analysis was necessary to exclude the false-positive matches resulting from the MS/MS experiments, especially for multiphosphorylated peptides. The use of the linear ion trap considerably enabled exploitation of nanoflow-HPLC/MS/MS, and in addition MS/MS/MS has great potential in phosphoproteome research of relatively complex samples.

Amino Acid Sequence↗
PubMed2003

From proteomic analysis to clinical significance: overexpression of cytokeratin 19 correlates with hepatocellular carcinoma metastasis.

To better understand the mechanism underlying the hepatocellular carcinoma (HCC) metastasis and to search potential markers for HCC prognosis, differential proteomic analysis on two well-established HCC cell strains with high and low metastatic potentials, MHCC97-H and MHCC97-L, was conducted using two-dimensional gel electrophoresis followed by matrix-assisted laser desorption/time-of-flight mass spectrometry. Cytokeratin 19 (CK19) was identified and found to be overexpressed in MHCC97-H as compared with MHCC97-L. This result was further confirmed by two-dimensional Western blot analysis and immunofluorescence assay. Furthermore, one-dimensional Western blot analysis showed consistently increased CK19 expression in progressively more metastatic cells. Immunohistochemical study on 102 human HCC specimens revealed that more patients in the CK19-positive group had overt intrahepatic metastases (satellite nodules, p < 0.05; vascular tumor emboli, p < 0.001; tumor node metastatis staging, p < 0.001). CK19 fragment CYFRA 21-1 levels measured in sera from nude mice model of human HCC metastasis with radioimmunoassay increased in parallel with tumor progression and rose remarkably when pulmonary metastases occurred. The results demonstrated that overexpression of CK19 in HCC cells is related to metastatic behavior. Serum CK19 level might reflect the pathological progression in some HCC and may be a useful marker for predicting tumor metastasis and a therapeutic target for the treatment of HCC patients with metastases.

Animals↗
PubMed2003

Unique physiological and pathogenic features of Leptospira interrogans revealed by whole-genome sequencing.

Leptospirosis is a widely spread disease of global concern. Infection causes flu-like episodes with frequent severe renal and hepatic damage, such as haemorrhage and jaundice. In more severe cases, massive pulmonary haemorrhages, including fatal sudden haemoptysis, can occur. Here we report the complete genomic sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroup Icterohaemorrhagiae consisting of a 4.33-megabase large chromosome and a 359-kilobase small chromosome, with a total of 4,768 predicted genes. In terms of the genetic determinants of physiological characteristics, the facultatively parasitic L. interrogans differs extensively from two other strictly parasitic pathogenic spirochaetes, Treponema pallidum and Borrelia burgdorferi, although similarities exist in the genes that govern their unique morphological features. A comprehensive analysis of the L. interrogans genes for chemotaxis/motility and lipopolysaccharide synthesis provides a basis for in-depth studies of virulence and pathogenesis. The discovery of a series of genes possibly related to adhesion, invasion and the haematological changes that characterize leptospirosis has provided clues about how an environmental organism might evolve into an important human pathogen.

Bacterial Adhesion↗
PubMed2003

Identification of proteins separated by one-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis with matrix-assisted laser desorption/ionization ion trap mass spectrometry; comparison with matrix-assisted laser desorption/ionization time-of-flight mass fingerprinting.

Digests from ten gel bands containing low abundance proteins were analyzed by both matrix-assisted laser desorption/ionization ion trap (MALDI-IT) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) methods. MALDI-TOF techniques were able to identify only one protein from all 10 gel bands, while MALDI-IT identified eight proteins from the same 10 bands. The ability to perform MS/MS experiments with a MALDI-IT instrument leads to protein identifications based on both peptide molecular mass and sequence information, and is much less prone to errors and uncertainties introduced by peptide fingerprinting methodologies in which protein identification is based on peptide molecular masses alone.

Amino Acid Sequence↗
PubMed2002

Protein isoforms observed by ultrahigh resolution capillary isoelectric focusing electrospray ionization mass spectrometry.

On-line coupling of capillary isoelectric focusing (CIEF) to electrospray ionization mass spectrometry (ESI-MS) as a two-dimensional separation/analysis system was employed for high-resolution analysis of the protein isoforms observed during CIEF process. The analytical system was established by using neutral coated long capillary (80 cm), active capillary positioning and sheath-liquid interface. Proteins were separated and resolved in CIEF according to their differences in isoelectric point (pI), and then characterized by ESI-MS. The focused protein zones were eluted to the entrance of MS by combining cathodic mobilization with gravity. The ultrahigh resolution (difference in pI<0.04) of this technique obtained under certain conditions led to the detection of three isoforms in hemoglobin A and in sickle cell hemoglobin (with similar charge distribution and same molecular weight, but their differences in pIranging from 0.04 to 0.08) and two isoforms of beta-lactoglobulin A (difference in pI is 0.6). The isoelectric points, relative amounts, and molecular masses of these isoforms were determined simultaneously by CIEF-ESI-MS.

Carbonic Anhydrase II↗
PubMed2000

Synthesis of Human Proinsulin C-peptide and Preparation of Specific Antibody to It.

A HPLC and CE pure human proinsulin C-peptide was synthesized by solid-phase method and TSK column purification. Its amino acid sequence and MS were consistent with theoretical values. In comparison with the formly reported chemical synthesis of C-peptide, this method has the advantage of simplicity and higher overall yield (41%). To improve the immunogenicity and specificity of oligopeptide antibody, the acrylyl-C-peptides were transformed into a polymer the product had a poly-propionyl-core matrix with C-peptide branches. This treatment gave a macromolecule with a M(r) about 25 kD. By using the polymer to immunize New Zealand rabbits for 30 days, specific antiserum was obtained with titer of 2.5x10(4) (by ELISA), which did not cross react with BSA. Thus, the poly-propionyl-peptide system provided a new approach for preparing synthetic peptide antibody and therefore is promising for the preparation of synthetic peptide-based vaccine.

Journal Article↗
PubMed2000

Thiophosphorylation and Fluorescent Labeling of Substrate Peptide of Protein Kinase.

Study on the conditions of thiophosphorylation reaction and fluorescent labeling reaction of the substrate of protein kinase A was carried out by using Kemptide LRRASLG as a model. The suitable concentration of the fluorescent regent 5-{ ((2-iodoacetyl)amino)ethyl amino} naphthelene-1-sulfonic acid (1,5-IAEDANS) and the suitable pH of labeling reaction buffer were 1.6 mmol/L and 8, respectively. Stability of the labeled peptide under the conditions of automatic N-terminal protein sequencing, electrospray mass spectrometry and in the presence of 0.1% trifluoroacetic acid was investigated, respectively. The specific differences in UV spectra between the labeled and unlabeled peptides were observed. Therefore, the possibility to detect the thiophosphorylated and fluorophore labeled peptide during high performance liquid chromatography peptide mapping was primarily shown.

Journal Article↗
PubMed1999

Analysis of Peptide Mapping Glycosylated Site and Glycan Structure in Ribonuclease B by Liquid Chromatography-Electrospray Mass Spectrometry.

Liquid chromatography-electrospray mass spectrometry was utilized to analyze peptide mapping of a glycoprotein ribonuclease B to obtain its primary structure. The glycosylated site was determined by comparison of peptide mapping before and after glycanase treatment.Tandem MS(MS/MS)was performed to analyze the structure of N-linked glycan and deglycosylated peptide. The nature of glycan was determined to be of highmannose type by mass spectrometry after the treatment with alpha-mannosidase. In addition the relative abundance of heterogeneous glycopeptides was quantified. This method is rapid and sensitive for the characterization of glycoproteins with N-linked glycan.

Journal Article↗
PubMed1999

Application of Free-flow Electrophoresis to the Separation of Murine Lymphocytes.

Free-flow electrophoresis offers not only the all-in-solution separation process but also very gentle separation conditions, and it can be used for continuous separation and preparation, so it has been widely applied in the fields of biochemistry and cell biology. Using this technique to separate insoluble particles such as cells, both high separation efficiency and high activity and viability could be obtained. Murine lymphocytes were separated in low ionic strength triethanolamine buffer by free-flow electrophoresis, the cell fractions were detected and characterized by means of UV spectrometry, immune fluorescence labeling and flow cytometry. Results indicated that T and B lymphocytes were well separated with high viability.

Journal Article↗
PubMed1999

Protein and Peptide Identification by Capillary Zone Electrophoresis-Tandem Mass Spectrometry.

A method for highly sensitive protein and peptide identification by capillary zone electrophoresis/electrospray ionization-tandem mass spectrometry (CZE/ESI/MS/MS) was described. A mixture of peptides Met-enkephalin and Leu-enkephalin was analyzed, and their amino acid sequences were identified, respectively, using CZE/MS/MS. Peptide mapping for a tryptic digest of horse cytochrome c was performed by the same method. The results indicated that almost all peptides generated by tryptic digestion were identified, and their sequences were interpreted by their collision-induced (CID) mass spectra. Applying the uninterpreted CID spectra of the protein digest to searching in sequence database by the SEQUEST program could identify proteins conveniently and rapidly. The samples consumed in the CZE/MS/MS experiments were at picomole level, so this method is quite suitable for quality control of recombinant proteins and trace amount protein identification in the proteome research.

Journal Article↗
PubMed1999

Peptide Mapping and Primary Structure Analysis of hEGFby Mass Spectrometry.

Liquid chromatography-mass spectrometry(LC-MS) was adopted to analyze peptide mapping of the hEGF digested by TPCK-trypsin and V8 to determine the molecular weight of each peptide fragment. Most of the peptide fragments were sequenced by tandem MS(MS-MS) to obtain the amino acid sequence. In addition, the number of disulfide bonds was confirmed. This method will facilitate the determination and structural analysis for nature, synthesis and recombinant proteins and peptides. The accuracy and resolution are both better than that of the routine method.

Journal Article↗
PubMed1998

C-terminal Analysis of Proteins and Peptides.

A chemical method for C-terminal sequencing has been used to analyze the C-terminus of proteins and peptides, which can be converted to proteinyl alkylated thiohydantoin (proteinyl-ATH) or peptidyl-ATH via activated with acetic anhydride, coupled with [NCS](-) and alkylated with bromomethylene. The C-terminal ATH-amino acid can be cleaved and detected at 254 nm. The C-terminal sequences with varied lengths have been obtained from natural and recombinant proteins and peptides by the C-terminal analysis, and modifications and mutations of C-terminus have been found. By this method, important information of C-terminus of proteins and peptides can be obtained for the identification of recombinant products and sythetic peptides. At present, starting with samples of 1-2 nmole, C-terminal of 3-5 residues or that of over 10 residues in some case, can be successfully determined.

Journal Article↗
PubMed1998

Separation and Electrophoretic Behaviour of 8-aminonaphthalene-1,3,6-trisulfonic Acid-derivatized Oligosaccharides by Capillary Electrophoresis.

The mixture of the hydrolyzate of dextran was derivatized with 8-aminonaphthalene-1,3,6-trisulfonic acid(ANTS) by reductive amination, then the derivatives were separated by capillary zone electrophoresis in 50 mmol/L phosphate, pH 2.5 electrophoretic buffer and in the buffer of 100mmol/L disodium tetraborate, pH 9.3, respectively. Two-dimensional mapping of the series of linear dextranoligosaccharide derivatives was obtained by plotting their relative electrophoretic mobilities in acidic buffer vs those in alkaline buffer. The relative electrophoretic mobilities of the derivatives were linearly correlated to the negative two-thirds power of the molecular weights. The effects of triethylamine (TEA) added into the electrophoretic buffer on the electrophoretic behavior of the oligosaccharide derivatives were discussed. Those effects may arise from the interaction between the oligosaccharide derivatives and TEA. Similar results were found when we applied the methods above to mannan-, xylan- and chitin-oligosaccharide derivatives, respectively.

Journal Article↗