anion exchange proteinchip q10 arrays  (Bio-Rad)

Journal: BMC Neurology

Article Title: Identification of novel biomarker candidates by proteomic analysis of cerebrospinal fluid from patients with moyamoya disease using SELDI-TOF-MS

doi: 10.1186/1471-2377-10-112

Figure Lengend Snippet: Mass spectra of representative single biomarker candidate proteins in CSF under different pH conditions. Protein profiles of the MMD and control groups were generated using Q10 (strong anion exchanger) array. For each pH condition, the upper two spectra are protein profiles obtained between m/z 2,000 and 10,000, and the lower two spectra are expansions showing the peak intensities around m/z 4473, 4588 and 4476 for pH 5, 7 and 9, respectively. All representative peaks (red arrows) are larger for the MMD than control group under each pH condition, as determined by SELDI-TOF-MS.

Article Snippet: Q10 (strong anion exchanger) ProteinChip array (Bio-Rad Laboratories) was used for protein profile analysis.

Techniques: Biomarker Assay, Generated

Journal: BMC Neurology

Article Title: Identification of novel biomarker candidates by proteomic analysis of cerebrospinal fluid from patients with moyamoya disease using SELDI-TOF-MS

doi: 10.1186/1471-2377-10-112

Figure Lengend Snippet: CART analysis using peaks obtained by SELDI-TOF-MS to discriminate between patients with MMD and control patients. The decision tree was constructed using CSF samples from 32 patients with MMD and control patients. The classification is determined starting at the roof node, following by appropriate splitting decisions based on the peak intensity at each node. If the peak intensity is lower than the cutoff intensity value, the left node is selected. This splitting process is continued until no further classification is achieved and terminal nodes are produced. Using m/z 4473, 2406 and 6338 peaks (pH 5), m/z 4588 and 7250 peaks (pH 7), and m/z 4746 and 1044 peaks (pH 9), CART for Q10 ProteinChip was applied to identify patients with MMD and control patients. The analysis correctly classified all 20 patients with MMD under pH 5 condition and 19 of 20 under the pH 7 and 9 conditions; all 12 control patients were classified under all pH conditions.

Article Snippet: Q10 (strong anion exchanger) ProteinChip array (Bio-Rad Laboratories) was used for protein profile analysis.

Techniques: Construct, Produced

Journal: Molecular & Cellular Proteomics

Article Title: A Proteomic Analysis Reveals Differential Regulation of the σS-Dependent yciGFE(katN) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

doi: 10.1074/mcp.m110.002493

Figure Lengend Snippet: FIG. 1. Identification of protein targets for YncC regulation in Salmonella. A, Selective capture of proteins from cell lysates of S. Typhimurium wild-type and mutant strains onto Q10 ProteinChip Array. Clear lysates from ATCC14028 (WT) and its mutant derivatives ATCCyncC, ATCCrpoS and ATCCyci were applied to the surface of a Q10 ProteinChip as described in the Experimental Procedures section. The captured proteins were detected using surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry. The normalized mass (m/z) for each peak (in Da) is demonstrated on the x-axis, whereas intensity (A) is plotted on the y-axis. Extracts were examined several times at different laser energies, and energies of 4500 nJ and 3200 nJ were found to be optimal for detection of peaks 1, 2, and peak 3, respectively. To pick out peak 3, the first pass peak detection was performed with a s/n threshold of two instead of five (Experimental Procedures). The relevant portion of the spectra from a representative experiment is shown. Similar results were obtained in two other experiments. The arrows indicate proteins expressed at different levels in the wild-type and the mutant strains. B, Partial purification of proteins of interest for identification by mass spectrometry. The pH 5 fraction (25 l) of the Q Ceramic HYPERD F exchange resin from lysates of 2: ATCCkatN-lacZ, 3: ATCC14028; 4: ATCC-F1; 5: ATCC-F12; and 6: ATCCrpoS were loaded on the gel. 1: molecular weight markers (in kDa). The stars indicate the protein bands that were excised from the gel and identified as the YciF and YciE proteins by mass spectrometry. C, Schematic representation of the yciGFE(katN) loci in Salmonella (STM) and E. coli K-12 (ECO). The molecular sizes of the gene products are indicated in Daltons (Da). D, The yciG promoters in Salmonella and E. coli K-12. The relevant portion of the sequence in Salmonella ATCC14028 (STM) and E. coli MG1655 (ECO) is shown.

Article Snippet: A strong anion exchange ProteinChip array (Q10, Bio-Rad), for which the complementary resin Q Ceramic HYPERD F (BioSepra-Pall, Cergy St Christophe, France) can be used for protein purification, was employed to capture negatively charged proteins.

Techniques: Mutagenesis, Mass Spectrometry, Purification, Molecular Weight, Sequencing

Journal: Molecular & Cellular Proteomics

Article Title: A Proteomic Analysis Reveals Differential Regulation of the σS-Dependent yciGFE(katN) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

doi: 10.1074/mcp.m110.002493

Figure Lengend Snippet: FIG. 4. Expression of the yciGFE locus in E. coli K-12 strains. A, SELDI-TOF-MS profiles of E. coli MG1655 and its mutant derivatives using the Q10 ProteinChip array. Clear lysates from MG1655 (WT) and its mutants MG655hns, MG1655hnsyciE, and MG1655hnsyciF were applied to the surface of a Q10 ProteinChip as described in the Experimental Procedures section. The captured proteins were de- tected using surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry. Normalized mass (m/z) for each peak (in Daltons (Da)) is demonstrated on the x-axis, whereas intensity (A) is plotted on the y-axis. A laser energy of 3200 nJ was used. The relevant portion of the spectra is shown. The arrows indicate the YciE and YciF proteins. B, Expression of the yciE-lacZ fusion in the E. coli strains indicated was determined in overnight LB cultures at 37 °C. Lanes 1 to 5: (1) MC4100 yciE-lacZ, (2) MC4100hns yciE-lacZ, (3) MC4100mcbR yciE-lacZ, (4) MC4100hnsmcbR yciE-lacZ, (5) MC4100hnsrpoS yciE-lacZ. Lanes 6 to 15: MC4100 yciE-lacZ harbor- ing pCABg (6), pmcbRHIS (7), pQE30 (12), and pyncCHIS (13); MC4100hns yciE-lacZ harboring pCABg (8), pmcbRHIS (9), pQE30 (14), and pyncCHIS (15); and MC4100hnsmcbR yciE-lacZ harboring pCABg (10), and pmcbRHIS (11).

Article Snippet: A strong anion exchange ProteinChip array (Q10, Bio-Rad), for which the complementary resin Q Ceramic HYPERD F (BioSepra-Pall, Cergy St Christophe, France) can be used for protein purification, was employed to capture negatively charged proteins.

Techniques: Expressing, Mutagenesis, Mass Spectrometry

Journal: Molecular & Cellular Proteomics : MCP

Article Title: A Proteomic Analysis Reveals Differential Regulation of the ? S -Dependent yciGFE ( katN ) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

doi: 10.1074/mcp.M110.002493

Figure Lengend Snippet: Identification of protein targets for YncC regulation in Salmonella. A, Selective capture of proteins from cell lysates of S. Typhimurium wild-type and mutant strains onto Q10 ProteinChip Array. Clear lysates from ATCC14028 (WT) and its mutant derivatives ATCCyncC, ATCCrpoS and ATCCyci were applied to the surface of a Q10 ProteinChip as described in the Experimental Procedures section. The captured proteins were detected using surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry. The normalized mass (m/z) for each peak (in Da) is demonstrated on the x-axis, whereas intensity (μA) is plotted on the y-axis. Extracts were examined several times at different laser energies, and energies of 4500 nJ and 3200 nJ were found to be optimal for detection of peaks 1, 2, and peak 3, respectively. To pick out peak 3, the first pass peak detection was performed with a s/n threshold of two instead of five (Experimental Procedures). The relevant portion of the spectra from a representative experiment is shown. Similar results were obtained in two other experiments. The arrows indicate proteins expressed at different levels in the wild-type and the mutant strains. B, Partial purification of proteins of interest for identification by mass spectrometry. The pH 5 fraction (25 μl) of the Q Ceramic HYPERD F exchange resin from lysates of 2: ATCCkatN-lacZ, 3: ATCC14028; 4: ATCC-F1; 5: ATCC-F12; and 6: ATCCrpoS were loaded on the gel. 1: molecular weight markers (in kDa). The stars indicate the protein bands that were excised from the gel and identified as the YciF and YciE proteins by mass spectrometry. C, Schematic representation of the yciGFE(katN) loci in Salmonella (STM) and E. coli K-12 (ECO). The molecular sizes of the gene products are indicated in Daltons (Da). D, The yciG promoters in Salmonella and E. coli K-12. The relevant portion of the sequence in Salmonella ATCC14028 (STM) and E. coli MG1655 (ECO) is shown.

Article Snippet: A strong anion exchange ProteinChip array (Q10, Bio-Rad), for which the complementary resin Q Ceramic HYPERD F (BioSepra-Pall, Cergy St Christophe, France) can be used for protein purification, was employed to capture negatively charged proteins.

Techniques: Mutagenesis, Mass Spectrometry, Purification, Molecular Weight, Sequencing

Journal: Molecular & Cellular Proteomics : MCP

Article Title: A Proteomic Analysis Reveals Differential Regulation of the ? S -Dependent yciGFE ( katN ) Locus by YncC and H-NS in Salmonella and Escherichia coli K-12

doi: 10.1074/mcp.M110.002493

Figure Lengend Snippet: Expression of the yciGFE locus in E. coli K-12 strains. A, SELDI-TOF-MS profiles of E. coli MG1655 and its mutant derivatives using the Q10 ProteinChip array. Clear lysates from MG1655 (WT) and its mutants MG655hns, MG1655hnsyciE, and MG1655hnsyciF were applied to the surface of a Q10 ProteinChip as described in the Experimental Procedures section. The captured proteins were detected using surface enhanced laser desorption/ionization (SELDI) time-of-flight mass spectrometry. Normalized mass (m/z) for each peak (in Daltons (Da)) is demonstrated on the x-axis, whereas intensity (μA) is plotted on the y-axis. A laser energy of 3200 nJ was used. The relevant portion of the spectra is shown. The arrows indicate the YciE and YciF proteins. B, Expression of the yciE-lacZ fusion in the E. coli strains indicated was determined in overnight LB cultures at 37 °C. Lanes 1 to 5: (1) MC4100 yciE-lacZ, (2) MC4100hns yciE-lacZ, (3) MC4100mcbR yciE-lacZ, (4) MC4100hnsmcbR yciE-lacZ, (5) MC4100hnsrpoS yciE-lacZ. Lanes 6 to 15: MC4100 yciE-lacZ harboring pCABg (6), pmcbRHIS (7), pQE30 (12), and pyncCHIS (13); MC4100hns yciE-lacZ harboring pCABg (8), pmcbRHIS (9), pQE30 (14), and pyncCHIS (15); and MC4100hnsmcbR yciE-lacZ harboring pCABg (10), and pmcbRHIS (11).

Article Snippet: A strong anion exchange ProteinChip array (Q10, Bio-Rad), for which the complementary resin Q Ceramic HYPERD F (BioSepra-Pall, Cergy St Christophe, France) can be used for protein purification, was employed to capture negatively charged proteins.

Techniques: Expressing, Mutagenesis, Mass Spectrometry

Journal: Journal of Biomedicine and Biotechnology

Article Title: Proteomic Analysis of Pichindé virus Infection Identifies Differential Expression of Prothymosin- α

doi: 10.1155/2010/956823

Figure Lengend Snippet: Identification and validation of peak 3790 as prothymosin- α . Mass spectrum of proteins from fraction Q3 that bound to Q10 ProteinChip array and was analyzed on QSTAR XL instrument (mass range from 1000 to 4000 m/z).

Article Snippet: 10 μ L of each fraction was added to 90 μ L 50 mM Tris (pH 8) buffer and was captured on Q10 anion exchange ProteinChip array surfaces (Bio-Rad Laboratories, Hercules, CA) with a bioprocessor Biomek 3000 (Beckman Coulter, Fullerton, CA).

Techniques: Biomarker Discovery

Journal: Journal of Biomedicine and Biotechnology

Article Title: Proteomic Analysis of Pichindé virus Infection Identifies Differential Expression of Prothymosin- α

doi: 10.1155/2010/956823

Figure Lengend Snippet: (a) The peptide with m/z approximately 3790 was identified as the fragment of prothymosin alpha by the following MS/MS microsequencing. (b) Mass spectrum of proteins pulled out from cytoplasmic fraction of murine macrophage samples by antiprothymosin alpha which was coupled to protein G agarose beads (mass range from 1000 to 20,000 m/z). Antiprothymosin alpha-coupled protein G agarose beads were incubated with cytoplasmic fraction and eluted proteins were analyzed on NP 20 ProteinChip array.

Article Snippet: 10 μ L of each fraction was added to 90 μ L 50 mM Tris (pH 8) buffer and was captured on Q10 anion exchange ProteinChip array surfaces (Bio-Rad Laboratories, Hercules, CA) with a bioprocessor Biomek 3000 (Beckman Coulter, Fullerton, CA).

Techniques: Tandem Mass Spectroscopy, Incubation