MassIVE MSV000096588

Partial Public

LC-MS data of trypsin-digested urinary proteins of clinical cases of diabetic nephropathy.

Subscribe Comment Reanalyze Spectra Add Reanalysis

Description

The LC-MS study was carried out to identify the proteins in urine samples of clinical cases of diabetic nephropathy (Healthy control, Diabetic group, Microalbuminuria, Overt albuminuria group). Study design The urine samples (10 ml) of patients with HbA1c greater than 6.5 percent were collected in a sterile container from the endocrinology OPD, PGIMER, Chandigarh, India, after obtaining informed consent. The study was carried out following the Helsinki Declaration. The Institute Ethics Committee approved the study protocol via (IEC) vide No INT/IEC/2020/SPL-1031. The spot dipstick method was used to screen urine samples for the presence of blood (haematuria) and pus cells (leucocytes). Samples showing the presence of both blood and leucocytes were further excluded from the study. After screening, 90 patient samples (30 diabetic controls, 30 microalbuminuria, and 30 overt albuminuria) were included in the study. For control, urine samples of 30 healthy controls were also included in the study. The albumin excretion rate parameters (Albumin to creatinine ratio (ACR)) was measured in Alere Afinion TM AS100 Analyser with ACR test kits. The ACR was expressed in mg per gram. Based on the obtained ACR, the patient groups were categorized following criteria as detailed under inclusion criteria. The inclusion and exclusion criteria are mentioned below. Inclusion criteria Microalbuminuria (meant as diabetic microalbuminuria)- Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate 30 to 300 mg per gram of creatinine in a spot urine sample. Overt albuminuria (meant as diabetic overt albuminuria): Established case of Diabetes Mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin concentration more than or equal to 300 mg per gram of creatinine in a spot urine sample. Diabetic Control- Established case of diabetes mellitus with glycated hemoglobin more than or equal to 6.5 percent and urinary albumin excretion rate of less than 30 mg per gram of creatinine in a spot urine. Exclusion criteria Patients with any evidence of urine tract infection or haematuria by dipstick test. Separation of urinary proteins The urinary proteins are separated from the urine matrix through centrifugation (15000 g for 1 hour at 4 degrees Celsius. The pellet obtained was expected to contain the proteins. For this, a 2 ml urine sample was subjected to centrifugation for each participant. After centrifugation (1ml in different aliquots), 2 pellets from the same sample were obtained. The pellets were suspended in PB (200 microlitres, pH 7.38, 0.1 M) and mixed well with a vortex. The pellets obtained from the same group were pooled. A similar treatment was provided to all the samples to obtain pellets. Protein quantification was done using the BCA method. LC-MS protocol: For this, 100 micrograms of urinary protein in 10 mM Tris HCl buffer, pH 7.38 was denatured by boiling with 10 mM dithiothreitol for 10 mins followed by the addition of Iodoacetamide (90 mM, SIGMA) and incubation for 30 mins in the dark at 37 degrees Celsius. These were then subjected to trypsin digestion (2 micrograms, Promega, MS grade, prepared in acetic acid) and kept overnight at 37 degrees Celsius. The reaction was stopped by the addition of 1 percent trifluoroacetic acid (TCI, LC-MS grade). The sample clean-up with C18 resins column was performed and the aliquots were then sent for data acquisition (PMID 39216816). The different raw files obtained are named as follows and uploaded. 1- Healthy Control 2- Diabetic Controls 3- Microalbuminuria 4- Overt albuminuria Prof Dibyajyoti Banerjee, Dr. Rajasri Bhattacharyya, Dr. Sheemona Chowdhary, Dr. Deepak Kumar, and Ms Monu Kumari acknowledge ICMR, New Delhi, India, sanctioned project titled Pseudoesterase activity of albumin as a determinant for serum cholesterol in rabbits for financial support. [doi:10.25345/C5MP4W07N] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: Urinary proteins, Diabetic nephropathy, Diabetes, Microalbuminuria, Overt albuminuria, LC-MS, Trypsin digestion ; Clinical samples ; DatasetType:Proteomics

Contact

Principal Investigators:
(in alphabetical order) 		Dibyajyoti Banerjee, Postgraduate Institute of Medical Education and Research, Chandigarh, India, India
Submitting User: deepakk1812
Number of Files:
Total Size:
Spectra:
Subscribers:
 
Owner Reanalyses
Experimental Design
    Conditions:
    Biological Replicates:
    Technical Replicates:
 
Identification Results
    Proteins (Human, Remapped):
    Proteins (Reported):
    Peptides:
    Variant Peptides:
    PSMs:
 
Quantification Results
    Differential Proteins:
    Quantified Proteins:
 
Browse Dataset Files
 
FTP Download Link (click to copy):

Species

Instrument

Modifications

- Dataset Reanalyses

+ Dataset History

Click here to queue conversion of this dataset's submitted spectrum files to open formats (e.g. mzML). This process may take some time.

When complete, the converted files will be available in the "ccms_peak" subdirectory of the dataset's FTP space (accessible via the "FTP Download" link to the right).
Number of distinct conditions across all analyses (original submission and reanalyses) associated with this dataset.

Distinct condition labels are counted across all files submitted in the "Metadata" category having a "Condition" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct biological replicates across all analyses (original submission and reanalyses) associated with this dataset.

Distinct replicate labels are counted across all files submitted in the "Metadata" category having a "BioReplicate" or "Replicate" column in this dataset.

"N/A" means no results of this type were submitted.
Number of distinct technical replicates across all analyses (original submission and reanalyses) associated with this dataset.

The technical replicate count is defined as the maximum number of times any one distinct combination of condition and biological replicate was analyzed across all files submitted in the "Metadata" category. In the case of fractionated experiments, only the first fraction is considered.

"N/A" means no results of this type were submitted.
Originally identified proteins that were automatically remapped by MassIVE to proteins in the SwissProt human reference database.

"N/A" means no results of this type were submitted.
Number of distinct protein accessions reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct unmodified peptide sequences reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct peptide sequences (including modified variants or peptidoforms) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Total number of peptide-spectrum matches (i.e. spectrum identifications) reported across all analyses (original submission and reanalyses) associated with this dataset.

"N/A" means no results of this type were submitted.
Number of distinct proteins quantified across all analyses (original submission and reanalyses) associated with this dataset.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
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.

A protein is differentially abundant if its change in abundance across conditions is found to be statistically significant with an adjusted p-value <= 0.05 and lists no issues associated with statistical tests for differential abundance.

Distinct protein accessions are counted across all files submitted in the "Statistical Analysis of Quantified Analytes" category having a "Protein" column in this dataset.

"N/A" means no results of this type were submitted.
This dataset may not contain all raw spectra data as originally deposited in PRIDE. It has been imported to MassIVE for reanalysis purposes, so its spectra data here may consist solely of processed peak lists suitable for reanalysis with most software.