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: Proteome Science

Article Title: A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass

doi: 10.1186/1477-5956-10-45

Figure Lengend Snippet: Classification results

Article Snippet: Protein profiles of serum and tissue samples were generated using anionic surfaces of CM10 and cationic surfaces of Q10 ProteinChip arrays (Ciphergen Biosystems Inc., Fremont, CA.).

Techniques:

Journal: Proteome Science

Article Title: A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass

doi: 10.1186/1477-5956-10-45

Figure Lengend Snippet: Pairwise comparisons between tumors of low malignant potential and hierarchical clustering of tissue data. Table with pairwise comparisons between mucinous and serous tumors of low malignant potential, cancer and benign tumor tissue. The number of upregulated (+) and downregulated (−) peaks is given for each comparison. Hierarchical clustering of CM10 tissue data. Clustering of 84 tissue samples using complete linkage and Pearson correlation distance on the 62 peaks that were differentially expressed (adjusted p-value < 0.05) between cancer, low malignant potential (divided in mucinous and serous), and benign tumor. The Z-score is calculated on the columns by subtracting the mean expression value of a column from each of the values and then dividing the resulting values by the standard deviation of the column. Color in the heat maps, therefore, indicates the relative expression level, with red being higher and blue lower than the mean expression value. The vertical side bar indicates the sample type: benign (red), mucinous LMP (green), serous LMP (purple), cancer (blue).

Article Snippet: Protein profiles of serum and tissue samples were generated using anionic surfaces of CM10 and cationic surfaces of Q10 ProteinChip arrays (Ciphergen Biosystems Inc., Fremont, CA.).

Techniques: Expressing, Standard Deviation

Journal: Proteome Science

Article Title: A critical assessment of SELDI-TOF-MS for biomarker discovery in serum and tissue of patients with an ovarian mass

doi: 10.1186/1477-5956-10-45

Figure Lengend Snippet: Comparison of detected peaks in serum and tissue

Article Snippet: Protein profiles of serum and tissue samples were generated using anionic surfaces of CM10 and cationic surfaces of Q10 ProteinChip arrays (Ciphergen Biosystems Inc., Fremont, CA.).

Techniques:

Journal: Frontiers in Molecular Neuroscience

Article Title: Sample Pooling and Inflammation Linked to the False Selection of Biomarkers for Neurodegenerative Diseases in Top–Down Proteomics: A Pilot Study

doi: 10.3389/fnmol.2018.00477

Figure Lengend Snippet: Identification of the candidate biomarker in outliers. (A) Four CJD samples with a 10–15 kDa band of different intensity (arrow). (B) Electrophoresis analysis of the purified candidate biomarker. The arrow marks the position of the peak. (C) After passive elution of the band in (B) , the presence of the candidate biomarker was confirmed by SELDI-TOF analysis with a Q10 ProteinChip Array.

Article Snippet: Each serum sample was diluted 1.5 times with a solution of 8 M urea, 1% CHAPS and stirred at room temperature for 15 min. ProteinChip Q10 Arrays (anion exchanger) (Bio-Rad) were pre-equilibrated with 150 μl of binding buffer (100 mM Tris pH 9 (made from TrisBase adjusted using HCl solution) and 0.1% Triton X-100) in a 96-well bioprocessor with gentle agitation for 5 min. Then, 2 μl of denaturated sample was mixed with 100 μl of binding buffer.

Techniques: Biomarker Discovery, Electrophoresis, Purification