Dataset Information

Mouse kidney glomeruli. Control vs. podocin(R231Q/A268V)

ABSTRACT: Similar to human patients, mice with the compound heterozygous mutation podocin R231Q/A268V, develop a late onset FSGS. Here, we did a proteomics anaylsis of kidney glomeruli before the onset of disease (mice at 3 weeks of age). Analysis of the data reveals that there are no developmental changes in the proteome of compund heterozygous mice.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Kidney

DISEASE(S): Focal Segmental Glomerulosclerosis

SUBMITTER: Martin Hoehne

LAB HEAD: Thomas Benzing

PROVIDER: PXD018326 | Pride | 2020-05-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20180412_Q2_UC_ColID_562_ProjID_1129_Benzing_sample_1.raw	Raw
	20180412_Q2_UC_ColID_562_ProjID_1129_Benzing_sample_2.raw	Raw
	20180412_Q2_UC_ColID_562_ProjID_1129_Benzing_sample_3.raw	Raw
	20180412_Q2_UC_ColID_562_ProjID_1129_Benzing_sample_4.raw	Raw
	20180412_Q2_UC_ColID_562_ProjID_1129_Benzing_sample_5.raw	Raw

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Publications

A molecular mechanism explaining albuminuria in kidney disease.

Butt Linus L Unnersjö-Jess David D Höhne Martin M Edwards Aurelie A Binz-Lotter Julia J Reilly Dervla D Hahnfeldt Robert R Ziegler Vera V Fremter Katharina K Rinschen Markus M MM Helmstädter Martin M Ebert Lena K LK Castrop Hayo H Hackl Matthias J MJ Walz Gerd G Brinkkoetter Paul T PT Liebau Max C MC Tory Kálmán K Hoyer Peter F PF Beck Bodo B BB Brismar Hjalmar H Blom Hans H Schermer Bernhard B Benzing Thomas T

Nature metabolism 20200511 5

Mammalian kidneys constantly filter large amounts of liquid, with almost complete retention of albumin and other macromolecules in the plasma. Breakdown of the three-layered renal filtration barrier results in loss of albumin into urine (albuminuria) across the wall of small renal capillaries, and is a leading cause of chronic kidney disease. However, exactly how the renal filter works and why its permeability is altered in kidney diseases is poorly understood. Here we show that the permeability ...[more]

PMID: 32694662

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Project description:Isolated murine kidney glomeruli were lysed in buffer containing 8M urea, and proteins were reduced and alkylated. Proteins were digested with trypsin. After reverse-phase chomatrography, peptides were fractionated using strong cation exchange chromatography. Phosphopeptides were enriched using IMAC (FeNTA) columns. Peptides were analyzed by LC-MS/MS on a Q Exactive mass spectrometer or an LTQ Orbitrap XL mass spectrometer. Metadata for Orbitrap samples (MaxQuant Output files include „Orbi“) 1. General features – 1.1 Global descriptors a. Responsible person or role: Markus Rinschen. markus.rinschen@uk-koeln.de; tobias.lamkemeyer@uni-koeln.de b. Instrument manufacturer, model: LTQ-Orbitrap XL, Thermo Scientific c. customization 2. Ion sources – ESI fed by nLC 2 (Proxeon) 3. Post source component 3.1. Analyser: MS1 survey scan in an Orbitrap and MS2 analysed in Linear Trap. 3.2. Activation/Dissociation: CID 4. Spectrum and peak list generation and annotation 4.1. Data acquisition: MaxQuant v. 1.3.05 Top one method with a cycle of one full MS1 scan in the Orbitrap, followed by the fragmentation with dynamic exclusion window of 60 seconds and followed by the acquisition of 5 product ion scans generated in the LTQ analyser, and detected in the LTQ. Unselected fragmentation. For further details, see .raw files. URL of file: Filename 4.2. Data analysis: MaxQuant v 1.3.05 Parameters used in the generation of peak lists or processed spectra: see annotation in “parameters” file. The mouse uniprot reference database “complete proteome” obtained on January 2nd, 2013 was used. Metadata for QExactive samples (Max Quant output files include „QE“) 1. General features – 1.1 Global descriptors a. Responsible person or role: Markus Rinschen. markus.rinschen@uk-koeln.de; Marcus Krüger marcus.krueger@mpi-bn.mpg.de b. Instrument manufacturer, model: Q Exactive Thermo Scientific c. customization 2. Ion sources – ESI fed by nLC 1000 (Proxeon) 3. Post source component 3.1. Analyser: MS1 survey scan in an Orbitrap and MS2 analysed in Orbitrap/HCD cell 3.2. Activation/Dissociation: HCD 4. Spectrum and peak list generation and annotation 4.1. Data acquisition: MaxQuant v. 1.3.05 Top one method with a cycle of one full MS1 scan in the Orbitrap, followed by the fragmentation with dynamic exclusion window of 20 seconds in the HCD cell and followed by the acquisition of 10 product ion scans generated in the LTQ analyser, and detected in the LTQ. Unselected fragmentation. For further details, see .raw files. URL of file: Filename 4.2. Data analysis: MaxQuant v 1.3.05 Parameters used in the generation of peak lists or processed spectra: see annotation in “parameters” file. The mouse uniprot reference database “complete proteome” obtained on January 2nd, 2013 was used.