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Proteomic analysis of residues from experimental ceramics

ABSTRACT: Ceramic vessels were used to cook fish/duck/black grouse, and proteomic studies were conducted on the ceramics to study how the choice of various database can affect the species identification and whether they can allow us to differentiate between fish and bird processing in ceramic vessels. We also employed a novel urea-GuHCl DES as the extraction reagent, and compared its efficiency with the conventional 6M GuHCl used for protein extraction (data available in project PXD027720). The samples used were same as the samples used in Peoject PXD027720, with a urea-GuHCl DES used as the extraction reagent instead of 6M GuHCl solution.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Esocidae Cyprinidae Anatidae Phasianidae

SUBMITTER: Manasij Pal Chowdhury

LAB HEAD: Dr. Michael Buckley

PROVIDER: PXD029035 | Pride | 2022-11-11

REPOSITORIES: Pride

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			Action	DRS
	1A_DES_Custom.dat	Other
	1A_DES_Custom.mzid	Mzid
	1A_DES_SwissProt.dat	Other
	1B_DES_Custom.dat	Other
	1B_DES_Custom.mzid	Mzid

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Proteomic analysis of residues from experimental ceramics

Project description:Ceramic vessels were used to cook fish/duck/black grouse, and proteomic studies were conducted on the ceramics to study how the choice of various database can affect the species identification and whether they can allow us to differentiate between fish and bird processing in ceramic vessels.

2022-11-11 | PXD027720 | Pride

Proteomic analysis of residues from experimental ceramics used for cooking a mixture of milk, meat and cereals

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Ancient proteins extracted from ceramic residues

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Evaluating the protein extraction methods for gut metaproteomics

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Mining the cellular inventory of pyridoxal phosphate-dependent enzymes with functionalized cofactor mimics

Project description:Pyridoxal phosphate (PLP) is an enzyme cofactor required for the chemical transformation of biological amines in numerous essential cellular processes. PLP-dependent enzymes (PLP-DEs) are ubiquitous and evolutionarily diverse, making their classification based on sequence homology challenging. This calls for a more direct approach for identifying new PLP-DEs and uncovering novel roles of PLP within the cell. We present a chemical proteomic method for reporting on PLP-DEs using functionalized cofactor probes. PL-analogs designed to be taken up by cells and metabolized in situ were synthesized. The probes are phosphorylated to functional cofactor surrogates by cellular PL kinases and bind to PLP-DEs via a reversible aldimine bond, which can be fixed by NaBH4-reduction. Conjugation to a reporter tag permits the identification of PLP-DEs using quantitative, label-free mass spectrometry via confidence ranking and profile searches. We label a significant portion of the PLP-ome in Staphylococcus aureus (41%) and annotate uncharacterized proteins as novel PLP-DEs. In applying our method, we were able to study structural tolerance within PLP-DE active sites and to screen for off-targets of the PLP-DE inhibitor D-cycloserine. Our cofactor profiling method represents a robust way to mine the cellular inventory of PLP-DEs which can be used for genome annotation, comparative profiling and drug development.

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Escherichia coli biofilm: mono-species culture vs. mixed-species culture

Project description:Transcription profile of Escherichia coli cells in mono-species pure biofilms was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species biofilms. E. coli cells were separated from dual-species biofilms before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli biofilms were processed with the same separation protocol before RNA extraction.

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Escherichia coli planktonic cultures: mono-species culture vs. mixed-species culture

Project description:Transcription profile of Escherichia coli cells in mono-species pure planktonic cultures was compared to that of E. coli cells in E. coli-Stenotrophomonas maltophilia dual-species planktonic cultures E. coli cells were separated from dual-species planktonic cultures before total RNA extraction to eliminate possible cross hybridization from S. maltophilia transcripts. The separation method was developed by combining the use of reagent RNAlater and immuno-magnetic separation. Pure E. coli planktonic cultures were processed with the same separation protocol before RNA extraction.

2013-12-30 | GSE24913 | GEO

Metaproteomics: Optimization and evaluation of protein extraction from activated sludge

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