Biomedical subjects

Yet-Ran Chen

Publications and source records attributed to Yet-Ran Chen.

8 recordsLinked to original sources

PubMed2006

Multi-Q: a fully automated tool for multiplexed protein quantitation.

The iTRAQ labeling method combined with shotgun proteomic techniques represents a new dimension in multiplexed quantitation for relative protein expression measurement in different cell states. To expedite the analysis of vast amounts of spectral data, we present a fully automated software package, called Multi-Q, for multiplexed iTRAQ-based quantitation in protein profiling. Multi-Q is designed as a generic platform that can accommodate various input data formats from search engines and mass spectrometer manufacturers. To calculate peptide ratios, the software automatically processes iTRAQ's signature peaks, including peak detection, background subtraction, isotope correction, and normalization to remove systematic errors. Furthermore, Multi-Q allows users to define their own data-filtering thresholds based on semiempirical values or statistical models so that the computed results of fold changes in peptide ratios are statistically significant. This feature facilitates the use of Multi-Q with various instrument types with different dynamic ranges, which is an important aspect of iTRAQ analysis. The performance of Multi-Q is evaluated with a mixture of 10 standard proteins and human Jurkat T cells. The results are consistent with expected protein ratios and thus demonstrate the high accuracy, full automation, and high-throughput capability of Multi-Q as a large-scale quantitation proteomics tool. These features allow rapid interpretation of output from large proteomic datasets without the need for manual validation. Executable Multi-Q files are available on Windows platform at http://ms.iis.sinica.edu.tw/Multi-Q/.

Chromatography, Liquid↗

PubMed2006

Quantitative proteomic and genomic profiling reveals metastasis-related protein expression patterns in gastric cancer cells.

Gastric cancer is a leading cause of death worldwide, and patients have an overall 5-year survival rate of less than 10%. Using quantitative proteomic techniques together with microarray chips, we have established comprehensive proteome and transcriptome profiles of the metastatic gastric cancer TMC-1 cells and the noninvasive gastric cancer SC-M1 cell. Our qualitative protein profiling strategy offers the first comprehensive analysis of the gastric cancer cell proteome, identifying 926 and 909 proteins from SC-M1 and TMC-1 cells, respectively. Cleavable isotope-coded affinity tagging analysis allows quantitation of a total of 559 proteins (with a protein false-positive rate of <0.005), and 240 proteins were differentially expressed (>1.3-fold) between the SC-M1 and TMC-1 cells. We identified numerous proteins not previously associated with gastric cancer. Notably, a large subset of differentially expressed proteins was associated with tumor metastasis, including proteins functioning in cell-cell and cell-extracellular matrix (cell-ECM) adhesion, cell motility, proliferation, and tumor immunity. Gene expression profiling by DNA microarray revealed differential expression (of >2-fold) of about 1000 genes. The weak correlation observed between protein and mRNA profiles highlights the important complementarities of DNA microarray and proteomics approaches. These comparative data enabled us to map the disease-perturbed cell-cell and cell-ECM adhesion and Rho GTPase-mediated cytoskeletal pathways. Further validation of a subset of genes suggests the potential use of vimentin and galectin 1 as markers for metastasis. We demonstrate that combining proteomic and genomic approaches not only provides a rapid, robust, and sensitive platform to elucidate the molecular mechanisms underlying gastric cancer metastasis but also may identify candidate diagnostic markers and therapeutic targets.

Biomarkers, Tumor↗

PubMed2005

Design and performance of a low-flow capillary electrophoresis-electrospray-mass spectrometry interface using an emitter with dual beveled edge.

A low-flow electrophoresis-mass spectrometry (CE-MS) interface has been developed for interfacing capillary zone electrophoresis (CZE) with electrospray- ionization-mass spectrometry (ESI-MS). The interface consists of two parallel capillary columns (a separation column and a makeup column), and an emitter with a dual beveled edge. While maintaining a relatively low optimum flow rate, the dual-beveled-edge ESI emitter allows the use of a tip with larger orifice. Therefore, this interface is less prone to column blocking in comparison with a flat tip. Primarily attributed to low sample dilution and smaller initial droplet, the interface showed better sensitivity than a conventional sheath liquid interface. Furthermore, the interface was found to be more resistant to the presence of nonvolatile salts. By using 40 mM borate and 20 mM alpha-cyclodextrin (alpha-CD) as the running buffer, four major forms of gangliosides were detected by CE-MS.

Electrophoresis, Capillary↗

PubMed2004

A low-makeup beveled tip capillary electrophoresis /electrospray ionization mass spectrometry interface for micellar electrokinetic chromatography and nonvolatile buffer capillary electrophoresis.

A robust interface has been developed for interfacing micellar electrokinetic chromatography (MEKC) and nonvolatile buffer capillary electrophoresis (CE) to electrospray ionization mass spectrometry (ESI-MS). The interface consists of two parallel capillaries for separation (50 microm i.d. x 155 microm o.d.) and makeup (50 microm i.d. x 155 microm o.d.) housed within a larger capillary (530 microm i.d. x 690 microm o.d.). The capillaries terminate in a single tapered tip having a beveled edge. The use of a tapered beveled edge results in a greater tip orifice diameter (75 microm) than in a previous design from our laboratory (25 microm) that used a flat tip. While maintaining a similar optimum flow rate and consequently similar sample dilution, a 75-microm beveled emitter is more rugged than a 25-microm flat tip. Furthermore, the incorporation of a sheath liquid capillary allows the compositions of the final spray solution to be controlled. The application of this novel CE/ESI-MS interface was demonstrated for MEKC using mixtures of triazines (positive ion mode) and phenols (negative ion mode). The ability to perform CE/ESI-MS using a nonvolatile buffer was demonstrated by the analysis of gangliosides with a buffer consisting of 40 mM borate and 20 mM alpha-cyclodextrin.

Journal Article↗

PubMed2004

Quantitative proteomic analysis of metabolic regulation by copper ions in Methylococcus capsulatus (Bath).

Copper ions switch the oxidation of methane by soluble methane monooxygenase to particulate methane monooxygenase in Methylococcus capsulatus (Bath). Toward understanding the change in cellular metabolism related to this transcriptional and metabolic switch, we have undertaken genomic sequencing and quantitative comparative analysis of the proteome in M. capsulatus (Bath) grown under different copper-to-biomass ratios by cleavable isotope-coded affinity tag technology. Of the 682 proteins identified, the expressions of 60 proteins were stimulated by at least 2-fold by copper ions; 68 proteins were down-regulated by 2-fold or more. The 60 proteins overexpressed included the methane and carbohydrate metabolic enzymes, while the 68 proteins suppressed were mainly responsible for cellular signaling processes, indicating a role of copper ions in the expression of the genes associated with the metabolism of the organism downstream of methane oxidation. The study has also provided a complete map of the C1 metabolism pathways in this methanotroph and clarified the interrelationships between them.

Bacterial Proteins↗

PubMed2004

A beveled tip sheath liquid interface for capillary electrophoresis-electrospray ionization-mass spectrometry.

A simple and durable sheath liquid interface for capillary zone electrophoresis-electrospray ionization-mass spectrometry (CZE-ESI-MS) has been developed. This interface utilized a beveled tip emitter and was found to be more sensitive than the conventional sheath liquid interface. The use of a beveled tip reduces the optimal flow rate and therefore decreases sample dilution. The interface utilized a 380 microm inner diameter and 400 microm outer diameter beveled tapered tip. Because of the large inner diameter and outer diameter of the tip, the interface is robust and can be easily implemented. The performance of this interface for CZE-ESI-MS and micelle electrokinetic capillary electrophoresis-electrospray-mass spectrometry, as demonstrated by the analysis of synthetic drugs and triazine mixtures, was significantly better than results obtained using a conventional sheath liquid interface.

Electrophoresis, Capillary↗

PubMed2003

A low-flow ce/electrospray ionization MS interface for capillary zone electrophoresis, large-volume sample stacking, and micellar electrokinetic chromatography.

A simple and versatile low-flow interface has been developed for interfacing capillary electrophoresis (CE) with electrospray ionization (ESI) mass spectrometry. This low-flow interface showed better sensitivity than a conventional sheath liquid interface, primarily attributed to a low dilution factor and a reduction in the sprayer orifice size. The interface was also found to be more tolerant to the presence of nonvolatile salts. Because of tolerance to the surfactant SDS, this interface can be used to couple micellar electrokinetic chromatography (MEKC) with ESI-MS. The performance of the interface in an MEKC-MS application, as demonstrated in the analysis of triazines, was significantly better than that obtained with a conventional sheath liquid interface. Moreover, this interface can be easily used for large-volume sample-stacking (LVSS) applications. Using a series of phenols as a test case, an approximate 500-fold enrichment was achieved by LVSS in conjunction with the low-flow CE/MS interface described.

Journal Article↗

PubMed2003

A simple method for fabrication of silver-coated sheathless electrospray emitters.

A simple and time-saving procedure is proposed for preparing a silver-coated fused-silica capillary tip. The tapered capillary tip was coated with silver using an acrylic-based silver conductive pen. The fabrication of a silver-coated fused-silica capillary tip takes less than 5 minutes. The silver-coated fused-silica capillary tip is rugged and durable for sheathless capillary electrophoresis/electrospray mass spectrometry and also for microspray applications.

Animals↗