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: The mass spectra of the proteins captured on Q10 chips were recorded on the PCS 4000 ProteinChip array reader (Bio-Rad laboratories, Hercules, CA).

Techniques:

Journal: BMC Microbiology

Article Title: Candidate proteomic biomarkers for three genogroups of the swine pathogen Streptococcus suis serotype 2

doi: 10.1186/s12866-015-0401-0

Figure Lengend Snippet: Heatmap/hierarchical clustering of 136 proteins of 45 S. suis strains discriminated by MLST into three sequence type (ST) groups: ST1 (n = 15), ST25 (n = 15), and ST28 (n = 15). The clusters were obtained by combining the average intensity values of all samples tested in duplicate on CM10 and Q10 ProteinChip arrays (acquisition protocol 1). The consecutive numbers of each strain used in the SELDI expression difference mapping (EDM) are indicated above the image (S1-S15 for the ST1 group (in red); S16-S30 for the ST25 group (in blue), and S31-S45 for the ST28 group (in green) followed by the respective sequence types and original names of the S. suis strains (in brackets). The protein masses detected on the CM10 (red) and Q10 (blue) ProteinChip arrays are indicated on the right side of the image. Specific EDM conditions: First pass: peak S/N ≥ 5, valley depth S/N ≥ 3, minimal peak threshold – 20% for all spectra; second pass: peak S/N ≥ 2, valley depth S/N ≥ 2; third pass: adding estimated (missing) peaks to complete the clusters, clustered mass window width – 0.1%, autocentroid marks on peaks, M/Z range of analysis (z = 1): 3000–20000 Da.

Article Snippet: Two types of ProteinChip ion-exchange arrays (Q10 and CM10; Bio-Rad Laboratories, Mississauga, ON, Canada) were assembled in a 96-well bioprocessor (Bio-Rad Laboratories) and were preactivated for 30 min with their respective buffers (100 mM Tris–HCl, pH 9.0, and 100 mM sodium acetate, pH 4.0, respectively).

Techniques: Sequencing, Expressing

Journal: Diagnostic Pathology

Article Title: Comparative proteomic analysis of normal and tumor stromal cells by tissue on chip based mass spectrometry (toc-MS)

doi: 10.1186/1746-1596-5-10

Figure Lengend Snippet: Principle of tissue on chip based mass spectrometry (toc-MS): (A) Head and neck cancer (HNC) tissue sections were stained H&E to obtain an overview of the tissue architecture . (B) Exemplary cutting lines of laser microdissection. (C) Stroma areas with about 100 square μm were cut out using the laser microdissection and transferred on a ProteinChip array (D). The same procedure was performed with normal connective tissue (not to scale).

Article Snippet: A Q10 ProteinChip array (strong anion exchanger; BioRad) was activated (see [ ]) and wetted with 0.5 μl lysis buffer (100 mM Na-phosphate (pH 7.5), 5 mM EDTA, 2 mM MgCl 2 , 3 mM 2-β-mercaptoethanol, 0.1% CHAPS, 500 μM leupeptine, and 0.1 mM PMSF).

Techniques: Mass Spectrometry, Staining, Laser Capture Microdissection

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