Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Label Free Quantitative Proteomic Analysis of Age-Related Protein Expression Changes in Mouse Brains

ABSTRACT: For this analysis, four young (2-month-old) and four aged (24-month-old) mice were used. The mouse brains were quickly dissected and sampled according to the procedure below. The proteomic analysis of PTS-soluble proteins was performed as follows: Homogenization and Collection of the Soluble Fraction: Mouse brain tissue is pulverized and then homogenized in PTS (Phase Transfer Surfactant) buffer. The homogenate is subsequently centrifuged at 15,000 × g for 15 minutes, and the resulting supernatant is collected as the "PTS-soluble fraction". Protein Reduction, Alkylation, and Digestion: The proteins within the collected supernatant (30 µg) are first reduced with DTT (dithiothreitol), followed by an alkylation step. The proteins are then digested with the enzyme trypsin to produce peptide fragments suitable for analysis. Peptide Purification: After the digested sample is treated with trifluoroacetic acid (TFA), the peptides are purified using a GL-tip SDB solid-phase extraction column. Mass Spectrometry: The purified peptides are subjected to label-free quantitative proteomic analysis using a Q-Exactive mass spectrometer.

ORGANISM(S): Mus Musculus (mouse)

SUBMITTER: Shigeo Murata

PROVIDER: PXD064908 | JPOST Repository | Mon Aug 04 00:00:00 BST 2025

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	250322_Old07_115w.mzid	Mzid
	250322_Old07_115w.raw	Raw
	250322_Old08_115w.mzid	Mzid
	250322_Old08_115w.raw	Raw
	250322_Old09_115w.mzid	Mzid

Items per page:

1 - 5 of 20

Similar Datasets

Quantitative Proteomic Analysis of Age-Related Protein Expression Changes in Mouse Brains Using TMT Labeling

Project description:This study investigates age-related alterations in the brain proteome of mice using quantitative proteomics. Brain tissues from young (2-month-old) and aged (24-month-old) mice were solubilized with PTS buffer, and the extracted proteins were subjected to tandem mass tag (TMT) labeling and mass spectrometry analysis.

2025-09-01 | PXD059962 | JPOST Repository

Gene expression in mouse leukocytes after CAWS administration

Project description:We performed DNA microarray analyses and compared the difference in the transcriptome between B6 and DBA/2 mice with modest or dramatic sensitivity to CAWS-vasculitis, respectively. Candida albicans water-soluble fraction (CAWS), a mannoprotein-β-glucan complex obtained from the culture supernatant of C. albicans NBRC1385, causes CAWS mediated vasculitis (CAWS-vasculitis) with distinct sensitivity among mouse strains.

2013-09-30 | GSE44803 | GEO

Identification of sarkosyl-insoluble proteins that accumulate in the brains of aged mice.

Project description:Five young (2-month-old) and five aged (24-month-old) mouse brains were bisected along the midline to separate the right and left hemispheres, then snap-frozen in liquid nitrogen. The frozen tissues were pulverized using a Multi-Beads Shocker (Yasui Kikai) and stored at -150°C until further use. The brain powder was homogenized in sarkosyl buffer (1% sarkosyl, 10 µg/mL RNase, 1 mM PMSF, 1 mM EDTA in PBS) using a Potter-Elvehjem homogenizer at 800 rpm. After a 10-minute incubation on ice, the homogenate was centrifuged at 15,000 g for 5 minutes at 4°C to separate the supernatant and pellet (P1). The supernatant was centrifuged again at 15,000 g for 5 minutes at 4°C, followed by a third centrifugation at 15,000 g for 15 minutes at 4°C to obtain the final supernatant (S1) and a pellet. S1 was then subjected to ultracentrifugation at 100,000 g for 1 hour at 4°C, resulting in a supernatant (S2) and a pellet. This pellet was resuspended in sarkosyl buffer using a vortex mixer and centrifuged again at 100,000 g for 1 hour at 4°C. The supernatant was discarded, and the final pellet (P2), representing the sarkosyl-insoluble fraction, was retained.

2025-08-04 | PXD060043 | JPOST Repository

Identification of XL peptides in Bik1 variants and different conditions

Project description:Identification of crosslinks in Bik1 variants and different conditions (phase separation, soluble, supernatant, pellet).

2025-01-06 | PXD050929 | Pride

Targeted quantification of XL peptides in Bik1 variants and different conditions

Project description:Quantification of crosslinks in Bik1 variants and different conditions (phase separation, soluble, supernatant, pellet)

2025-01-06 | PXD055703 | Pride

TMT analysis of detergent-soluble and insoluble fractions from HEK293T cells in normal conditions and upon heat shock

Project description:HEK293T cells were cultured according to standard protocols and heat shocked at 42oC for 6 hours. Detergent-soluble and insoluble fractions from HEK293T cells were obtained following the procedures described before. Specifically, HEK293T cells were lysed in NP40 lysis buffer (Invitrogen #FNN0021) with protease inhibitors by gentle pipetting. The cell homogenate was centrifuged at 14000 rpm and the supernatant was retrieved (detergent-soluble fraction). The remaining pellet was washed twice in ice-cold NP40 lysis buffer and then resuspended in urea buffer (RIPA buffer with 8M urea). The samples were then centrifuged at 14000 rpm for 10 min to pellet any remaining cell debris. The resulting supernatant (detergent-insoluble fraction) was retrieved and analyzed as explained below.

2025-08-01 | PXD046967 | Pride

Functional partitioning of transcriptional regulators by patterned charge blocks

Project description:GFP-MED1-IDR forms condensates when added to a soluble nuclear extract. Centrifugation fractionates the extract into a pellet fraction containing the proteins partitioned into MED1-IDR condensates and supernatant fraction containing proteins excluded from the MED1-IDR condensates. Two independent supernatant (LUM1_854558, LUM1_854560) and pellet (LUM1_854559, LUM1_854561) fractions were collected and subject to proteomic analysis to identify protein enriched in MED1-IDR condensates.

2022-04-22 | MSV000089301 | MassIVE

Profiling of 18 - 40 nt small RNAs and transcriptomes in the testis and epididymis of WT and Gpx5 KO mice.

Project description:Total RNAs were extracted from the Testis and Epididymal Caput, Corpus and Cauda tissues of 2-month and 13-month-old WT and Gpx5 KO mice (C57BL/6). The 18 - 40 nt fraction small RNAs and transcriptomes were subjected to library construction and deep sequencing, using Illumina GAIIx or Hiseq 2000.

2019-07-01 | GSE122087 | GEO

Comparing gene expression in livers of 1-month vs 6-month old mice following DEN treatment

Project description:To look for age-related changes in the liver that take place during DNA damage resolution, we used RNAseq gene expression analysis to characterize mRNA expression profile in livers from 1-month vs. 6-month-old mice either before or 2 days (representing the peak of DNA damage response) and 6 days (representing the resolution phase of DNA damage) after DEN treatment.

2018-09-01 | GSE103200 | GEO

Transdifferentiation as a mechanism of treatment resistance in a mouse model of castration-resistant prostate cancer

Project description:Analysis of transcriptome of prostate tissue from the anterior lobe or tumor from 9, 12, 13, 14, and 16 months old mouse Prostate tissue or tumor from 9 month old Nkx3.1CreERT2/+ mice, 14 month old Nkx3.1CreERT2/+;Ptenflox/flox mice (intact, treated with vehicle), 16 month old Nkx3.1CreERT2/+;Ptenflox/flox mice (castrated, treated with vehicle or abiraterone), 12 month old Nkx3.1CreERT2/+;Ptenflox/flox;P53flox/flox mice(intact, treated with vehicle), 13 month old Nkx3.1CreERT2/+;Ptenflox/flox;P53flox/flox mice (castrated, treated with vehicle or abiraterone) was harvested, and snap frozen for subsequent molecular analysis

2017-04-18 | GSE92721 | GEO