proteinchip array bioprocessor  (Ciphergen inc)

Journal: Proteome Science

Article Title: Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid

doi: 10.1186/1477-5956-4-7

Figure Lengend Snippet: Representative SELDI-TOF MS spectra of CSF in denaturing buffer on CM10, Q10, H50 and IMAC30 arrays. a) CSF was diluted 1:1 in denaturing buffer 9.5 M urea, 2% CHAPS, 50 mM Tris-HCl, pH 9.0. Denatured CSF samples were diluted 1:4 in appropriate binding buffer and processed on: CM10 with 100 mM ammonium acetate pH 4.0; Q10 with 100 mM Tris-HCl pH 9.0; H50 with 10% AcN, 01% TFA; and IMAC30 with 100 mM Na phosphate, 0.5 M NaCl pH 7.0 and 100 mM Cu sulphate activation. ProteinChip arrays were prepared with SPA. b) Enlargement of the shaded spectra region showing peaks between m/z range of 4–11 kDa.

Article Snippet: Following 20 min incubation at 4°C, the CSF samples were then added to separate spots on the array surface using a Biomek laboratory station (Beckman-Coulter, CA) modified to make use of a ProteinChip array bioprocessor (Ciphergen Biosystems Inc.).

Techniques: Binding Assay, Activation Assay

Journal: Proteome Science

Article Title: Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid

doi: 10.1186/1477-5956-4-7

Figure Lengend Snippet: Venn diagram representing the overlap of peaks between ProteinChip array types. CSF prepared in denaturing buffer was processed on CM10, Q10, H50 and IMAC30 ProteinChip arrays using (a) SPA, and (b) CHCA. Peaks with a signal-to-noise ratio of 3 or greater, between the m/z range of 25–20 kD, were considered. When assigning peak clusters across spectra, two peaks on different surfaces were assumed to be the same protein if both their respective m/z were within 0.3%.

Article Snippet: Following 20 min incubation at 4°C, the CSF samples were then added to separate spots on the array surface using a Biomek laboratory station (Beckman-Coulter, CA) modified to make use of a ProteinChip array bioprocessor (Ciphergen Biosystems Inc.).

Techniques:

Journal: Proteome Science

Article Title: Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid

doi: 10.1186/1477-5956-4-7

Figure Lengend Snippet: Assessment of inter-chip variability. Spectra were obtained from a CSF sample of equal volume loaded across twelve chips used for one bioprocessor plate, and CVs calculated on normalized peak intensities. Four peaks, representing various intensities, are indicated along with their calculated CVs across the 12 chips.

Article Snippet: Following 20 min incubation at 4°C, the CSF samples were then added to separate spots on the array surface using a Biomek laboratory station (Beckman-Coulter, CA) modified to make use of a ProteinChip array bioprocessor (Ciphergen Biosystems Inc.).

Techniques:

Journal: Proteome Science

Article Title: Optimization and evaluation of surface-enhanced laser-desorption/ionization time-of-flight mass spectrometry for protein profiling of cerebrospinal fluid

doi: 10.1186/1477-5956-4-7

Figure Lengend Snippet: Assessment of systematic variability across bioprocessor plates using principle component analysis. Variability was evaluated across three bioprocessor plates processed 4 and 24 hours apart. Spectra were obtained from pooled CSF sample randomly placed on a single spot across each of twelve different CM10 chips on one bioprocessor plate. The same was repeated for the other plates 4 and 24 hr later. Following baseline subtraction, normalization and spectra alignment, 45 peaks which appeared in all spectra were used for PCA analysis. The PCA results were color coded for the three bioprocessor plates: blue, 0 hr; red, 4 hr; black, 24 h.

Article Snippet: Following 20 min incubation at 4°C, the CSF samples were then added to separate spots on the array surface using a Biomek laboratory station (Beckman-Coulter, CA) modified to make use of a ProteinChip array bioprocessor (Ciphergen Biosystems Inc.).

Techniques:

Journal: American Journal of Translational Research

Article Title: Targeting TNFα in severe psoriasis-mass spectrometry reveals a time-dependent specific inhibition of Factor H in responding patients

doi:

Figure Lengend Snippet: Progression of specific intensity peaks within mass profiles during Etanercept treatment. Shown is the progression of intensities (relative units) of the 4326 Da (A), 6632 Da (B) and 133977 Da (C) peaks of the mass profiles over time. W0, W12 and W24 correspond to duration of Etanercept treatment expressed in weeks. Samples exhibiting a significant difference for C (healthy controls) vs W0, W0 vs W12 and W0 vs W24 are shown. Horizontal lines correspond to the mean of the 10 samples for each condition. P-values were calculated using the non-parametric Mann-Whitney test when comparing C to W0 (unpaired data), and the non-parametric Wilcoxon signed-rank test when comparing W0 to W12, or W0 to W24 (paired data). *Statistically significant difference between C and W0. **Statistically significant difference between W0 and W12, or between W0 and W24. The 4.3 and 134 kDa masses were detected using fraction 2, and the 6.6 kDa mass was detected using fraction 4. ProteinChip®, matrix and laser intensity conditions are detailed in Table 2.

Article Snippet: Conditioning, sample incubation, and washings of the ProteinChip® arrays were performed with the Bio-Rad ProteinChip® Bioprocessor®.

Techniques: MANN-WHITNEY