Journal: FEBS Open Bio

Article Title: Proteomic pattern of breast milk discriminates obese mothers with infants of delayed weight gain from normal‐weight mothers with infants of normal weight gain

doi: 10.1002/2211-5463.12610

Figure Lengend Snippet: Heat map/hierarchical clustering of 15 breast milk proteins of 52 mothers divided into two groups, normal weight ( n = 26) and obese ( n = 26). The clusters are obtained by combining the average intensity values of the samples tested in duplicate on CM 10 and Q10 ProteinChip arrays using the following acquisition protocol: laser energy, 3500 nJ; focus mass, 10 000 Da; matrix attenuation, 3000 Da. Above the heat map are shown the sample names (numbered from 1 to 26 in each group, in red for the mothers of normal weight (normoponderal), and in blue for the obese mothers). On the right side of the image are the molecular masses detected on ProteinChip arrays of CM 10 (red) and Q10 (blue) type. EDM conditions: first pass: peak S/N, ≥ 5; valley depth S/N, ≥ 2; minimal peak threshold, 20% of all spectra; second pass: peak S/N, ≥ 2; valley depth S/N, ≥ 2; third pass: adding estimated (missing) peaks to complete clusters; clustered mass window width, 0.1%; m / z range of analysis ( z = 1), 3000–30 000 Da.

Article Snippet: For spectra processing, expression difference mapping (EDM) was carried out using proteinchip data manager 3.0.7 software (Bio‐Rad).

Techniques:

Journal:

Article Title: Nitrated alpha-synuclein and microglial neuroregulatory activities

doi: 10.1007/s11481-008-9100-z

Figure Lengend Snippet: SELDI-TOF, 1D SDS PAGE, and Western blot analyses of supernatant fluids obtained from N-α-syn-activated microglial. Representative SELDI-TOF spectral analysis (region 10–20 kDa) of untreated-control (top panel) and N-α-syn-stimulated microglia (bottom panel) at 16 h post-stimulation, shown in A. Marked by an asterisk are upregulated and uniquely expressed peaks corresponding in molecular weight within 1% of mass tolerance to proteins identified by LC-MS/MS. These include calcyclin (10,051 Da), thioredoxin (11,544 Da), calvasculin (11,721 Da), calmodulin (16,706 Da), and TNF-α (17,907 Da). Bands were excised from 1D SDS PAGE gel, digested by trypsin, and sequenced by LC-MS/MS. Lanes are supernatant fluids obtained from control (unstimulated) microglial = [Lanes 1–3] and supernatants from N-α-syn-activated microglia [Lanes 4–6] collected 8 h, 16 h, and 24 h post-stimulation, respectively. (B). Representative Western blots of supernatant fluids from control and N-α-syn-stimulated microglia 16 h post-stimulation for proteins identified by LC-MS/MS (C).

Article Snippet: Protein profiling of culture supernatants was performed using SELDI-TOF ProteinChip ® assays ( Enose et al., 2005 ; Kadiu et al., 2007 ) (Ciphergen Biosystems, Fremont, CA).

Techniques: SDS Page, Western Blot, Molecular Weight, Liquid Chromatography with Mass Spectroscopy

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: The ProteinChip All-in-One Protein Standard II (Bio-Rad) was used for external calibration.

Techniques: Biomarker Discovery, Electrophoresis, Purification