br Data analysis The data acquired by

Data analysis The data acquired by Analyst QS 2.0 software was further processed for peak list generation, protein identification, and peptide quantification using ProteinPilot™ software 3.0 (revision number 114732; Applied Biosystems, Foster City, CA). The Paragon algorithm in the ProteinPilot™ software was used for the peptide identification. The user defined parameters were as: (i) Sample type-iTRAQ 4-plex (Peptide Labeled); (ii) Cysteine alkylation-MMTS; (iii) Digestion-trypsin; (iv) Instrument-QSTAR Elite ESI; (v) Special factors—none; (vi) Species—none; (vii) Specify processing—Quantitate; (viii) ID Focus—biological modifications, amino GDC-0994 substitutions; (ix) Database—concatenated JGI downloaded from (http://www.aspgd.org/, http://genome.jgi.doe.gov/Aspfu1/Aspfu1.home.html); (x) Search effort-thorough. The precursors and fragment mass tolerances were default as adopted by the software. For iTRAQ quantitation, peptides were automatically selected by Pro Group algorithm for calculations of the reporter peak area, p-value etc. The final data was auto bias-corrected and a strict cut-off of unused ProteinScore ≥2, which corresponds to a confidence limit of 99% was applied. Proteins quantified with at least two peptides with 95% confidence were considered for further analysis. The data was classified according to glycosyl hydrolase (GH) family following KEGG database. These proteins were sorted using N-terminal Sec-dependant secretion signal using SignalP 3.0 (http://www.cbs.dtu.dk/services/ SignalP/)[7]
Conflict of interest
Acknowledgments This work is in part supported by grants from the Singapore Ministry of Education (Tier1: RGT15/13) and NTU-NHG Ageing Research Grant (ARG/14017) and NTU iFood (Grant no.: S006).
Specifications table
Value of the data
Experimental design, materials and methods
Specifications table
Value of the data
Data, experimental design, materials and methods
Specifications table Value of the data Experimental design, materials and methods Amphoteric azo dyes were used for the control of the first dimension (pI) in horizontal Comparative two-dimensional Fluorescence Gel Electrophoresis (hCoFGE) [1]. CoFGE itself uses an internal reference grid formed by internal protein standards to correct for the gel-to-gel variation in the second dimension of 2D polyacrylamide GE improving protein spot coordinate assignment [2–4].
Data
Value of the data
Methods 6–7 week old male Sprague–Dawley rats weighing between 150 and 200g were used for this study. Animals were housed in a temperature-controlled environment (maintained at 25°C) with a 12-h light–dark cycle and provided water and standard chow ad libitum. All experimental procedures were in accordance with the National Research Council guidelines and approved by the Rutgers University Animal Care and Facilities Committee.
Burn injury A hypermetabolic response was induced by administering a full-thickness dorsal-skin burn to an area corresponding to 20% of the total body surface area (TBSA). Rats were randomly assigned to either a Burn group or a control Shamburn group. Rats were anesthetized by intraperitoneal injection of ketamine (80–100mg/kg) and xylazine (12–10mg/kg), and all hair was removed from the dorsal abdominal area using electric clippers. In the experimental Burn group, the animal׳s back was immersed in water at 100°C for 10s to produce a full-thickness scald injury covering 20% TBSA. An intraperitoneal injection of saline solution (50ml/kg) was used to resuscitate the rats immediately after administering the burn injury. Rats sustaining the burn injury had a 100% survival rate with no evidence of systemic hypo-perfusion and no significant alterations in feeding patterns. Rats in the negative control, Shamburn group, were treated identically but were immersed in lukewarm water maintained at 37°C. Rats were caged individually after burn or shamburn procedures and given standard rat chow and water ad libitum until sacrifice. Consistent with other studies with this full thickness burn model, no post-burn analgesics were administered since the nerve endings in the skin are destroyed and the skin becomes insensate. Furthermore, after animals woke up, they ate, drank and moved freely around the cage, responded to external stimuli, and did not show clinical signs of pain or distress. Animal body weights were monitored daily and found to increase at the same rate in both groups [1].