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Proteomic analysis using BRG1-phosphorylation mutants

ABSTRACT: Proteins extracted from stable clones expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable BRG1 (brg1-S1452A) were trypsin-digested and analyzed by Q Exactive Quadrupole-Orbitrap LC-MS.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Ayuko Kimura

PROVIDER: PXD022681 | JPOST Repository | Wed Nov 24 00:00:00 GMT 2021

REPOSITORIES: jPOST

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Dataset's files

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			Action	DRS
	160824QE_Brg_MIX.raw	Raw
	160824QE_Brg_MM_1.raw	Raw
	160824QE_Brg_MM_2.raw	Raw
	160824QE_Brg_MM_3.raw	Raw
	160824QE_Brg_WT_1.raw	Raw

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1 - 5 of 11

Publications

Phosphorylation of Ser1452 on BRG1 inhibits the function of the SWI/SNF complex in chromatin activation.

Kimura Ayuko A Arakawa Noriaki N Kagawa Hiroyuki H Kimura Yayoi Y Hirano Hisashi H

Journal of proteomics 20210706

BRG1, one of core subunits of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancers. Previously, we reported significant downregulation of the phosphorylation level of BRG1 on Ser<sup>1452</sup> (<10%) in cell lines derived from ovarian clear cell carcinoma with frequent recurrence and acquired drug resistance. In this study, we tried to elucidate the roles of BRG1 phosphorylation, using cell lines expressing wild-type, phosphorylation-mimic (brg1-S<sup>1452</sup>D), or non- ...[more]

PMID: 34237461

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MS analysis of phosphopeptides enriched from BRG1-phospho mutants

Project description:Phosphopeptides enriched from stable clones expressing wild-type, phosphorylation-mimic (brg1-S1452D), or non-phosphorylatable BRG1 (brg1-S1452A) were analyzed by Q Exactive Quadrupole-Orbitrap LC-MS.

2021-11-24 | PXD022680 | JPOST Repository

Direct evidence of milk consumption from ancient human dental calculus, central Europe

Project description:This study investigated the consumption of milk products in the archaeological record, utilizing human dental calculus as a reservoir of dietary proteins from archaeological samples from across Eurasia. Protein extraction and generation of tryptic peptides from dental calculus was performed using a filter-aided sample preparation (FASP) protocol, modified for ancient samples, on 92 samples of archaeological dental calculus. Samples were extracted at three laboratories; the Functional Genomics Centre Zürich (FGCZ), the Centre for GeoGenetics at the National History Museum of Denmark, and BioArCh at the University of York. Sample extracts were sequenced (LC-MS/MS) using an LTQ-Orbitrap Velos (FGCZ), a Q-Exactive Hybrid Quadrupole Orbitrap and an LTQ-Orbitrap Elite (Central Proteomics Facility, Target Discovery Institute, Oxford).

2015-02-25 | PXD001360 | Pride

Direct evidence of milk consumption from ancient human dental calculus, UK

2015-02-26 | PXD001362 | Pride

Direct evidence of milk consumption from ancient human dental calculus, northern southwest Asia

2015-02-26 | PXD001359 | Pride

Direct evidence of milk consumption from ancient human dental calculus, northern Europe

2015-02-25 | PXD001361 | Pride

Direct evidence of milk consumption from ancient human dental calculus, St Helena

2015-02-25 | PXD001357 | Pride

Modeling protein destiny in developing tomato fruit

Project description:Proteomics and transcriptomics data of tomato fruits (Solanum lycopersicum L. var. Moneymaker) at 9 developmental stages were used to calculate with a mathematical model the rate constants of synthesis and degradation for over 1,000 proteins. Proteome and transcriptome were extracted from the pericarp tissue and analyzed using label-free LC-MS/MS (Orbitrap Q-Exactive) and RNA Sequencing (Illumina), respectively. Absolute quantification of transcriptome has been obtained by spiking-in internal standard before total-RNA extraction. Absolute quantification of the proteome has been approximated using the "Total Protein" approach. An OD equation defining the changes of protein content has been used to determine the synthesis and degradation rate constants (day -1). Almost 2,400 transcript-protein pairs were identified and the translation and degradation rate constants were determined for more than a thousand proteins. The model predicted median values of about 2 min for the translation and a lifetime of approximately 11 days. Proteins involved in protein synthesis had higher ks and kd values, indicating that the protein machinery is particularly flexible. None sequenced-based features were found that could be used to predict these rate constants.

2019-03-23 | GSE128739 | GEO

: Robust and reproducible large-scale label-free deep quantitative profiling of the MOLM-14 surfaceome using three mass spectrometry platforms over multiple years

Project description:Surface proteins are one of the most important and common matrices for clinical chemistry and proteomic analyses. With the rapid developments in mass spectrometry (MS)-based proteomics methods, label-free quantitative proteomics has become an increasingly popular tool for profiling global protein abundances. Here, we evaluate the performance of three mass spectrometers, namely Orbitrap Elite (Hybrid Ion Trap-Orbitrap), Q Exactive HF (Hybrid Quadrupole-Orbitrap) and Orbitrap Fusion (Tribrid Quadrupole-Ion Trap-Orbitrap), in label-free semiquantitative analysis of cell surface proteins spanning a four-year period. Sucrose gradient ultracentrifugation was used for surfaceome enrichment, following gel separation for in-depth protein identification. With the established workflow, we identify 2335 cell surface proteins in MOLM-14, a human acute myeloid leukemia cell line, with a high degree of reproducibility across three MS platforms over multiple years.

2021-12-30 | PXD022721 | Pride

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High Performance Quadrupole and an Ultra-High Field Orbitrap Analyzer

Project description:The quadrupole Orbitrap mass spectrometer (Q Exactive) has made a powerful proteomics instrument available in a benchtop format. It significantly boosted analyzable proteins per hour and has now evolved into a proteomics analysis workhorse for many laboratories. Here we describe the Q Exactive Plus and Q Exactive HF mass spectrometers, which feature several innovations in comparison to the original Q Exactive instrument. A low resolution pre-filter has been implemented within the injection flatapole, preventing unwanted ions from entering deep into the system, and thereby increasing its robustness. A new segmented quadrupole, with higher fidelity of isolation efficiency over a wide range of isolation windows, provides an almost two-fold improvement of transmission at narrow isolation widths. Additionally, the Q Exactive HF has a compact Orbitrap analyzer, leading to higher field strength and almost doubling resolution at the same transient times. With its very fast isolation and fragmentation capabilities, the instrument achieves overall cycle times of 1 s for a top 15 to 20 HCD (Higher energy Collisional Dissociation) method. We demonstrate identification of 5,000 proteins in standard 90-min gradients of tryptic digests of mammalian cell lysate, an increase of over 40% for detected peptides and over 20% for detected proteins. Additionally, we tested the instrument on peptide phosphorylation enriched samples, for which an improvement of up to 60% class I sites was observed.

2014-11-10 | PXD001203 | Pride

COL1 database samples for the Late Pleistocene of Western Eurasia

Project description:The project aimed to characterize the collagen type I (COL1) sequences from various modern, Holocene and Pleistocene bone, antler and skin samples for phylogenetic purposes. All extractions were performed at BioArCh, University of York (UK) or the Department of Human Evolution, MPI-EVA (Germany). Analyses took place on Q-Exactive Hybrid Quadrupole-Orbitrap MS.

2016-09-27 | PXD003190 | Pride

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