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