Proteins regulated in the brain of diving rats in both orbitrap and Iontrap analyses.

<p>Proteins regulated in the brain of diving rats in both orbitrap and Iontrap analyses.</p

Synaptic vesicle fusion and recycling in nerve terminals.

<p>The thermometers indicates upregulation (red) or downregulation (blue). Pathway symbol explanations: <a href="https://ftp.genego.com/files/A4_MetaCore_qrg_en.pdf" target="_blank">https://ftp.genego.com/files/A4_MetaCore_qrg_en.pdf</a>.</p

Network analysis of the >20% significantly regulated proteins.

<p>The proteins significantly regulated (>20% regulation) due to fast decompression (Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185765#pone.0185765.t002" target="_blank">2</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185765#pone.0185765.t003" target="_blank">3</a>) were analysed for potential protein-protein interactions and GO enrichments using String. Green circles indicate the significantly downregulated proteins in the datasets, all proteins without a green circle were significantly upregulated. Explanation of protein name abbreviations, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0185765#pone.0185765.t003" target="_blank">Table 3</a>.</p

Protein S100B levels in serum after hyperbaric exposure.

<p>Box plots of serum S100B concentration one week before, 2–3 hours after, and one week after the dive in the fast decompression rate group (FD, 1 bar/20 s), and one week after the dive in the slow decompression rate group (SD, 1 bar/10 min). The plot shows the 25th and 75th percentiles with median and bars at maximum and minimum values.</p

Proteins only detected in either orbitrap or Iontrap and significantly regulated.

<p>Proteins only detected in either orbitrap or Iontrap and significantly regulated.</p

Enriched ontologies and networks in Metacore.

<p>The number of proteins (n) in each enriched terminology is shown. The -log2 (p-value) is plotted and the p = 0.05 illustrated with a stippled line.</p

An overview of number of rats, saturation time and decompression rates.

<p>An overview of number of rats, saturation time and decompression rates.</p

Collagen fibrils were analyzed using transmission electron microscopy (TEM).

<p>Collagen fibril diameter distribution and average fibril diameter per tumor in 4T1 (n = 7 and n = 5) tumors (A, B), showed a shift towards thinner fibrils in SCID integrin α11-deficient (α11-KO) mice. RM11 tumors (n = 4 and n = 3) (C, D) and dermis (n = 4 and n = 3) (E, F) showed no significant differences in average collagen fibril diameter in SCID integrin α11 wild type (WT) and SCID integrin α11-deficient (α11-KO) mice (RM11 p = 0.20, dermis p = 0.47) using unpaired two-tailed t-test. Mean ± SD. * p < 0.006. Representative TEM images of collagen fibrils from both genotypes in 4T1 tumors (G, H), RM11 tumors (I, J) and dermis (K, L) are shown. Scale bars indicate 0.2 μm.</p

Proteins quantified using iontrap and orbitrap LC-MS.

<p>The total number of proteins quantified using the different methods are presented in parenthesis outside the diagram. The overlapping identifications are shown within the sections and the intersection. The numbers at the top in the diagram show number of proteins without significant regulation. The significantly regulated proteins due to fast decompression, according to two-sided t-tests, are denoted with an asterisk (*, p<0.05). The significantly regulated proteins which in addition passed the filtering criteria (>20% regulation and significant in both datasets) are illustrated with arrows.</p

Clustering analyses of all significantly regulated proteins.

<p>The normalized protein quantification values, from significantly regulated proteins in the orbitrap analysis (A, B) and iontrap analysis (C, D) were imported into Perseus. Log2 transformed data were analysed with principal component analysis for the orbitrap dataset (A) and the iontrap dataset (C), NaN values were replaced with 0 for the latter. The log2 data was then z-normalized by row and unsupervised hierarchically clustered (distance: Spearman, linkage: average) for the orbitrap dataset (B) and the iontrap dataset (D), including NaN illustrated as grey cells for the latter. Green cells represent downregulated proteins and red cells upregulated proteins. FD, fast decompression rate; SD, slow decompression rate.</p