Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins DOI Creative Commons
Ismael Rodríguez Palomo, Bharath Nair, Yun Chiang

et al.

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: Nov. 21, 2024

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses interpretations of complex, degraded protein mixtures. The community has also established standards good practice to interrogate our data. However, there lack systematic exploration how these affect identification peptides, post-translational modifications (PTMs), proteins their significance (through False Discovery Rate) correctness. We systematically investigated performance wide range sequencing tools search engines in controlled system: experimental degradation single purified bovine β-lactoglobulin (BLG), heated at 95°C pH 7 0, 4 128 days. target BLG since it one most robust ubiquitous archaeological record. tested different reference database choices, targeted dairy one, whole proteome three digestion options (tryptic-, semi-tryptic- non-specific searches), order evaluate effects space peptides. explored alternative strategies, including open that allows global PTMs based upon precursor mass tolerance de novo boost sequence coverage. analysed samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked discuss optimal strategy characterisation ancient proteins. studied physicochemical properties correlate with bias

Language: Английский

Acetylation, ADP-ribosylation and methylation of malate dehydrogenase DOI
Misty L. Kuhn, John F. Rakus, Delphine Quénet

et al.

Essays in Biochemistry, Journal Year: 2024, Volume and Issue: 68(2), P. 199 - 212

Published: July 12, 2024

Abstract Metabolism within an organism is regulated by various processes, including post-translational modifications (PTMs). These types of chemical alter the molecular, biochemical, and cellular properties proteins allow to respond quickly different environments, energy states, stresses. Malate dehydrogenase (MDH) a metabolic enzyme that conserved in all domains life extensively modified post-translationally. Due central role MDH, its modification can flux, Krebs cycle, glycolysis, lipid amino acid metabolism. Despite importance both MDH post-translationally landscape, comprehensive characterization PTMs, their effects on structure, function, flux remains underexplored. Here, we review three PTMs – acetylation, ADP-ribosylation, methylation explore what known literature how these potentially affect 3D enzymatic activity, interactome MDH. Finally, briefly discuss potential involvement dynamics metabolons include

Language: Английский

Citations

1
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins DOI Creative Commons
Ismael Rodríguez Palomo, Bharath Nair, Yun Chiang

et al.

Peer Community Journal, Journal Year: 2024, Volume and Issue: 4

Published: Nov. 21, 2024

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses interpretations of complex, degraded protein mixtures. The community has also established standards good practice to interrogate our data. However, there lack systematic exploration how these affect identification peptides, post-translational modifications (PTMs), proteins their significance (through False Discovery Rate) correctness. We systematically investigated performance wide range sequencing tools search engines in controlled system: experimental degradation single purified bovine β-lactoglobulin (BLG), heated at 95°C pH 7 0, 4 128 days. target BLG since it one most robust ubiquitous archaeological record. tested different reference database choices, targeted dairy one, whole proteome three digestion options (tryptic-, semi-tryptic- non-specific searches), order evaluate effects space peptides. explored alternative strategies, including open that allows global PTMs based upon precursor mass tolerance de novo boost sequence coverage. analysed samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked discuss optimal strategy characterisation ancient proteins. studied physicochemical properties correlate with bias

Language: Английский

Citations

1