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ProteomicsComprehensive analysis of the proteome of S. cerevisiae wild-type and pdr5 cells in response to Bisphenol A (BPA) exposure
Bisphenol A, an endocrine-disrupting compound, is used widely in the industrial production of plastic products. Despite increasing concerns about its harmful effects on human health, animals and the environment, the use of BPA has been banned only in infant products and its effects on cellular proce...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2025-05-07 | PXD058913 | Pride
Bisphenol a (bpa) Tmt proteomics Stress Proteome S. cerevisiae 
ProteomicsLysine-specific demethylase 2A enhances binding of various nuclear factors to CpG-rich genomic DNAs by action of its CXXC-PHD domain
The lysine-specific demethylase 2A gene (KDM2A) is ubiquitously expressed and its transcripts consist of several alternatively spliced forms, including KDM2A and the shorter form N782 that lacks the 3’ end encoding F-box and LRR. KDM2A binds to numerous CpG-rich genomic loci and regulates various ce...
ORGANISM(S): Homo sapiens (Human) 
2019-06-28 | PXD012941 | Pride
Gelc-ms/ms Tandem mass tag 
ProteomicsmTMT: An alternative, non-isobaric, tandem mass tag allowing for precursor-based quantification
Stable isotope labeling of peptides is the basis for numerous mass spectrometry-based quantification strategies. Isobaric tagging and metabolic labeling, namely TMT and SILAC, are among the most widely used techniques for relative protein quantification. Here we report an alternative, precursor-base...
ORGANISM(S): Homo sapiens (Human) 
2019-09-16 | PXD014545 | Pride
Silac Tmt Isobaric Sh-sy5y Svgp12 Metabolic 
ProteomicsMultiplexed Proteome Profiling of Carbon Source Perturbations in Two Yeast Species with SL-SP3-TMT
Saccharomyces cerevisiae and Schizosaccharomyces pombe are the most commonly studied yeast model systems, yet comparisons of global proteome remodeling between these yeast species are scarce. Here, we profile the proteomes of S. cerevisiae and S. pombe cultured with either glucose or pyruvate as the...
ORGANISM(S): Homo sapiens (Human) 
2021-05-11 | PXD014546 | Pride
Sps-ms3 Cerevisiae Pombe Tmt Isobaric Pyruvate 
ProteomicsA Triple KnockOut Isobaric-labelling Quality Control Platform in an Integrated On-line Database Search
Sample multiplexing using isobaric tagging is a powerful strategy for proteome-wide protein quantification. One major caveat of isobaric tagging is ratio compression that results from the isolation, fragmentation, and quantification of co-eluting, near-isobaric peptides, a phenomenon typically refer...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-03-31 | PXD017803 | Pride
Tko standard  ion interference  tmt  itraq  sps-ms3  tvt  shiny application 
ProteomicsA Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments
Isobaric labeling is a powerful strategy for quantitative mass spectrometry-based proteomic investigations. A complication of such analyses has been the co-isolation of multiple analytes of similar mass-to-charge resulting in the distortion of relative protein abundance measurements across samples. ...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2019-08-23 | MSV000084230 | MassIVE
ProteomicsTemporal proteomic changes induced by nicotine in human cells: A quantitative proteomics approach
Nicotine is a prominent active compound in tobacco and many smoking cessation products. Some of the biological effects of nicotine are well documented in in vitro and in vivo systems; however, nominal data are available concerning the time-dependent changes on protein and phosphorylation events in r...
ORGANISM(S): Homo sapiens (Human) 
2021-05-11 | PXD023108 | Pride
Faims Tmtpro Covid19 Protein-protein interactions Orbitrap lumos Real time search Rts 
ProteomicsA Semi-automated Paramagnetic Bead-based Platform for Isobaric Tag Sample Preparation
The development of streamlined and high-throughput sample processing workflows is important for capitalizing on emerging advances and innovations in mass spectrometry-based applications. While the adaptation of new technologies and improved methodologies is fast paced, automation of upstream sample ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2022-01-06 | PXD024282 | Pride
Faims Sp3 Automation Tmtpro Rts Opentrons 
ProteomicsRNAmetasome, a multi-protein complex for the macromolecule biogenesis in human cells
The RNAmetasome, a multi-protein complex for the macromolecule biogenesis in human cells, is defined and characterized.
ORGANISM(S): Homo sapiens (Human) 
2021-12-10 | PXD024234 | Pride
Macromolecule biogenesis Metasome 
ProteomicsEnriching cysteine-containing peptides using a sulfhydryl-reactive alkylating reagent with a phosphonic acid group, and immobilized metal affinity chromatography
The reduction of disulfide bonds and their subsequent alkylation is commonplace in typical proteomics workflows. Here, we highlight a sulfhydryl-reactive alkylating reagent with a phosphonic acid group (iodoacetamido-LC-phosphonic acid, 6C-CysPAT) that facilitates the enrichment of cysteine-containi...
ORGANISM(S): Homo sapiens (Human) 
2023-12-28 | PXD038382 | Pride
Faims Tmtpro Cyspat Fe3+-nta Orbitrap eclipse Isobaric tagging 
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