MassIVE MSV000087841

Complete Public PXD027374

Multi-organ protein expression profile of Lewis Polycystic Kidney rat NPHP9 model

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Description

Tissue specimens were weighed, quantitated and processed for label free quantitation using standard in-gel digestion (trypsin) protocols. Kidney, liver, brain and skeletal muscle tissues from LPK (disease) rats(n=5) were compared to respective control tissues from Lewis (healthy) rats (n=5). Each sample was further fractionated (three fractions per sample) in gels before subjecting samples to trypsin digestion. Details provided in the manuscript. Label free quantitation (LFQ) was performed using Proteome Discoverer (Version 2.4 Thermo Scientific) (PD). Raw data files (.raw) were processed on PD using SEQUEST HT. The peptide identification was performed using NCBI RefSeq Database, Rattus norvegicus (NcbiAV TaxID=10116) (v2017-10-30). Protein modifications checked for variable modification were methionine oxidation, N-terminal acetylation, phosphorylation at serine, threonine and tyrosine. Carbamidomethylation of cysteine was fixed modifications. Trypsin with 2 missed cleavages. Fragment and peptide mass tolerance was set to 0.1 Da and 20 ppm respectively. Peptide and proteins were detected with 1 % FDR against decoy database. Stringent criterion: unique peptide le1 and amino acids less than equal to 6 and p-value less than equal to 0.05 was applied for significance.Unique and razor peptides were quantitated using precursor abundance. Protein abundance was computed using the sum of each peptide group abundances, while their ratios was calculated using the geometric median of peptide group ratios. [doi:10.25345/C5BZ55] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Nephronophthisis, Nek8, kidney, liver, brain, LPK

Contact

Principal Investigators:
(in alphabetical order) 		Prof. Jacqueline Phillips, Macquarie University, Australia
Submitting User: shabarni_gupta
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Number of distinct proteins found to be differentially abundant in at least one comparison across all analyses (original submission and reanalyses) associated with this dataset.

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