PXD027374

PXD027374 is an original dataset announced via ProteomeXchange.

Dataset Summary

Title	Multi-organ protein expression profile of Lewis Polycystic Kidney rat NPHP9 model
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.
HostingRepository	MassIVE
AnnounceDate	2021-07-17
AnnouncementXML	Submission_2021-07-17_07:37:16.990.xml
DigitalObjectIdentifier
ReviewLevel	Non peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Shabarni Gupta
SpeciesList	scientific name: Rattus norvegicus; common name: Norway rat; NCBI TaxID: 10116;
ModificationList	Acetyl; Phospho; Carbamidomethyl; Met-loss
Instrument	Q Exactive Plus

Dataset History

Revision	Datetime	Status	ChangeLog Entry
0	2021-07-17 01:08:05	ID requested
⏵ 1	2021-07-17 07:37:17	announced

Publication List

no publication

no publication

Keyword List

submitter keyword: Nephronophthisis, Nek8, kidney, liver, brain, LPK

submitter keyword: Nephronophthisis, Nek8, kidney, liver, brain, LPK

Contact List

Prof. Jacqueline Phillips
contact affiliation	Macquarie University
contact email	jacqueline.phillips@mq.edu.au
lab head
Shabarni Gupta
contact affiliation	Macquarie University
contact email	shabarni.gupta@hdr.mq.edu.au
dataset submitter

Full Dataset Link List

MassIVE dataset URI
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MassIVE dataset URI

Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000087841/