Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Label-free vacuolar proteomics of wild-type and vps35Δ yeast using timsTOF Pro

ABSTRACT: Vacuoles were isolated from wild-type and vps35Δ S. cerevisiae cells grown to stationary phase. Peptides were digested using Preomics iST kit, analyzed by Bruker timsTOF Pro in DDA-PASEF mode. Data were searched against UniProt yeast database using PEAKS Studio X (1% FDR). This dataset was used to identify retromer cargoes accumulating in vps35Δ vacuoles.

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Prof. Jieqiong Gao

PROVIDER: PXD080941 | JPOST Repository | Mon Jul 13 00:00:00 BST 2026

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	WT-BY4741_Slot2-36_1_21442.d	Other
	WT-BY4741_Slot2-36_1_21442_5.3.556.mgf	Mgf
	protein-peptides-Vps35.csv	Csv
	protein-peptides-wt.csv	Csv
	protein-peptides.csv	Csv

Items per page:

1 - 5 of 7

Similar Datasets

Label-free vacuolar proteomics of wild-type and vps35Δ yeast using Orbitrap Eclipse

Project description:Vacuoles were isolated from wild-type and vps35Δ S. cerevisiae cells grown to stationary phase. Peptides were digested using Preomics iST kit, analyzed by Thermo Orbitrap Eclipse in DDA mode with FAIMS (-45V/-65V). Data were searched against UniProt yeast database using Proteome Discoverer 2.4.1.15 with 10 ppm precursor and 0.02 Da fragment tolerances, filtered at 1% FDR. This dataset was used to identify retromer cargoes accumulating in vps35Δ vacuoles.

2026-07-13 | PXD080926 | JPOST Repository

Vacuolar proteomic analysis of wild-type and vps35Δ Saccharomyces cerevisiae cells using Orbitrap Eclipse and timsTOF Pro

Project description:Label-free vacuolar proteomics comparing wild-type and vps35Δ Saccharomyces cerevisiae cells harvested at stationary phase, aiming to identify retromer cargoes that accumulate on vacuoles upon retromer dysfunction and promote vacuolar membrane curvature associated with lipid droplet degradation. Data were acquired in parallel on both Orbitrap Eclipse and timsTOF Pro mass spectrometers for cross-validation.

2026-07-13 | PXD080968 | JPOST Repository

Yeast Whole Genome Analysis - Wild-Type vs kap108∆ cells

Project description:A total cellular RNA analysis was performed to determine differential gene expression between wild-type and kap108∆ S. cerevisiae cells under both normal and oxidative stress conditions. Goal was to determine which genes are differentially expressed in the absence of the Kap108 importin, and to see how that differential expression changes with the addition of oxidative stress. This information can then be used to help elucidate the function and transport cargoes of Kap108, which are currently unknown.

2015-07-18 | GSE71068 | GEO

PASEF technology on timsTOF Pro improves quality of FPOP analysis

Project description:Fast photochemical oxidation of proteins (FPOP) is a modern technique for studying protein folding, conformations, interactions, etc. In this work, timsTOF Pro mass spectrometer coupled with trapped ion mobility spectrometry was used for identification of oxidative modifications in a model protein. Multiple modifications on the same residues, including six modifications of histidine, were successfully resolved. Moreover, PASEF technology allows successful sequencing even minor populations of modified peptides.

2021-06-10 | PXD020509 | Pride

dia-PASEF HeLa dilution series 0.2ng - 200ng on Bruker timsTOF Pro 2

Project description:Different sample preparation methods were tested for HeLa proteome analysis. A sample obtained using sodium deoxycholate-based lysis allowed identification of the highest number of proteins. For this sample, a dilution series was acquired in triplicates ranging from 0.2ng to 200ng. All measurements were performed on Bruker timsTOF Pro 2 operated in dia-PASEF mode and analysed library-free using DIA-NN 1.8.

2022-06-20 | PXD029836 | Pride

Comprehensive Proteomics Profiling of Zebrafish Retina Using a Hybrid DDA/DIA-PASEF Spectral Library on a timsTOF Pro 2 Mass Spectrometer

Project description:The zebrafish (Danio rerio) retina has been increasingly used for studying vertebrate visual processing and ocular growth regulation as it has a high anatomical and physiological similarity to the human eye. Recently, the integration of trapped ion mobility spectrometry (TIMS) with parallel accumulation–serial fragmentation (PASEF), has emerged as a powerful approach for proteomics analysis. In this study, a retina specific hybrid spectral library was constructed for quantitative proteomics analysis of the zebrafish retina. We integrated data dependent acquisition PASEF (DDA PASEF) and data independent acquisition PASEF (DIA PASEF) datasets acquired from 16 individual retinal protein lysates on a Bruker timsTOF Pro 2 mass spectrometer to generate the hybrid spectral library. The Pulsar search engine in Spectronaut 22 was used for hybrid library generation. The resulting hybrid library comprised 8,551 precursors, 7,866 unique peptides, and 1,494 protein groups (1% FDR), representing 44.5% of the reviewed zebrafish reference proteome.16 DIA PASEF runs from individual samples were then analyzed in both library based (using the hybrid library) and library free settings in Spectronaut (version 22) and DIA NN (version 2.3.2). It demonstrated that the hybrid library outperformed library free approaches, with improved peptide and precursor identifications across both proteomics platforms.

2026-06-17 | PXD076440 | Pride

Maximizing glycoproteomics identification depth in complex mixtures on the timsTOF Pro platform

Project description:Glycoproteins play important roles in numerous physiological processes and are often implicated in disease. Analysis of site-specific protein glycobiology through glycoproteomics is evolving rapidly in recent years thanks to hardware and software innovations. Introduction of Parallel Accumulation Serial Fragmentation (PASEF) on hybrid trapped ion mobility time-of-flight instruments combined deep proteome sequencing with separation of (near-)isobaric precursor ions or converging isotope envelopes through ion mobility separation. Despite these advantages, the use of PASEF in integrated glycoproteomics workflows to comprehensively capture the glycoproteome has received little attention. To address this gap, we have developed an integrated methodology using the timsTOF Pro2 to enhance N-glycopeptide identifications in complex mixtures. We explored its potential by systematically evaluating the impact of ion optics tuning, collision energies, mobility isolation width, and the use of dopant-enriched nitrogen gas (DEN) on glycopeptide identification rates. This comprehensive approach showed a marked increase in unique glycopeptide identification rates compared to standard proteomics settings while evaluating key parameters on a large set of glycopeptides. With short liquid chromatography gradients of 30 minutes, we increased the number of unique N-glycopeptide identifications in full human plasma glycopeptide samples from around 100 identifications under standard proteomics condition to over 1500 with our optimized glycoproteomics approach, highlighting the need for tailored solutions.

2024-01-03 | PXD047898 | Pride

Glycoproteomic Analyses of Influenza A Viruses Using timsTOF Pro MS.

Project description: Not available

| S-EPMC10225981 | biostudies-literature

A de novo MS1 feature detector for the Bruker timsTOF Pro.

Project description: Not available

| S-EPMC9710787 | biostudies-literature

Proteomic analysis of cooperating yeast metabolic communities during ageing

Project description:Yeast (Saccharomyces cerevisiae) cooperating metabolic communities (SeMeCos) were chronologically aged in minimal media (no amino acid supplementation). Samples were collected during exponential, early stationary and stationary phases for proteomic analysis. Comparison was performed between wild-type (knock-in, "kin"), 4p-SeMeCo ("4p") and MET15-3p-SeMeCo ("3p") cultures. Four independent biological replicates were acquired for each timepoint measured.

2022-11-08 | PXD036444 | Pride