Post-Translational Modification (PTM) Proteomics: Challenges and Perspectives

Darie, Costel C.

doi:10.4172/2329-6798.1000e114

Cited by 3 publications

(1 citation statement)

References 37 publications

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“…Therefore, understanding the nature, quantity, and temporal progression of PTMs has arguably been one of the most substantial contributions of MS-based proteomics to modern biology 1 . However, the sub-stoichiometric nature and dynamic regulation of PTMs makes it challenging to capture and detect PTMs 11 . Thus, unique enrichment techniques and sample-processing workflows are often required for enriching PTMs before analysis by mass spectrometry 12 .…”

Section: Mainmentioning

confidence: 99%

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Nickchi

Mirzaie

Baumann

et al. 2022

Preprint

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Post-translational modifications (PTMs) are under significant focus in molecular biomedicine due to their importance in signal transduction in most cellular and organismal processes. Characterization of PTMs, discrimination between functional and inert PTMs, quantification of their occupancies and PTM crosstalk are demanding tasks in each biosystem. On top of that, the study of each PTM often necessitates a particular laborious experimental design. Here, we present a PTM-centric proteome informatic pipeline for prediction of most probable and relevant PTMs in mass spectrometry-based proteomics data. Upon prediction, such PTMs can be incorporated in a refined database search. To demonstrate the applicability of our approach, using expression profiling, we identified cellular proteins that are differentially regulated in response to multikinase inhibitors dasatinib and staurosporine. Computational enrichment analysis was employed to determine the potential PTMs of protein targets for both drugs. Finally, we conducted an additional round of database search with the predicted probable PTMs. Our pipeline helped analyze the enriched PTMs and even detected proteins that were not picked up in the initial search. Our findings support the idea of PTM-centric searching of MS data in proteomics based on computational enrichment analysis and we believe this strategy should be incorporated in futuristic proteomics search engines.

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Section: Mainmentioning

confidence: 99%

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Nickchi

Mirzaie

Baumann

et al. 2022

Preprint

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Characterizing disease-associated changes in post-translational modifications by mass spectrometry

Thygesen

Boll

Finsen

et al. 2018

Expert Review of Proteomics

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Exploring post-translational modifications (PTMs) with the use of mass spectrometry (PTMomics) is a rapidly developing area, with methods for discovery/quantification being developed and advanced on a regular basis. PTMs are highly important for the regulation of protein function, interaction and activity, both in physiological and disease states. Changes in PTMs can either cause, or be the result of a disease, making them central for biomarker studies and studies of disease pathogenesis. Recently, it became possible to study multiple PTMs simultaneously from low amount of sample material, thereby increasing coverage of the PTMome obtainable from a single sample. Thus, quantitative PTMomics holds great potential to discover biomarkers from tissue and body fluids as well as elucidating disease mechanisms through characterization of signaling pathways. Areas covered: Recent mass spectrometry-based methods for assessment of the PTMome, with focus on the most studied PTMs, are highlighted. Furthermore, both data dependent and data independent acquisition methods are evaluated. Finally, current challenges in the field are discussed. Expert commentary: PTMomics holds great potential for clinical and biomedical research, especially with the generation of spectral libraries of peptides and PTMs from individual patients (permanent PTM maps) for use in personalized medicine.

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Application of mass-spectrometry compatible photocleavable surfactant for next-generation proteomics using rice leaves

et al. 2021

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The solubilization of isolated proteins into the adequate buffer containing of surfactants is primary step for proteomic analysis. Particularly, sodium dodecyl sulfate (SDS) is the most widely used surfactant, however, it is not compatible with mass spectrometry (MS). Therefore, it must be removed prior to MS analysis through rigorous washing, which eventually results in inevitable protein loss. Recently, photocleavable surfactant, 4-hexylphenylazosulfonate (Azo), was reported which can be easily degraded by UV irradiation and is compatible with MS during proteomic approach using animal tissues. In this study, we employed comparative label-free proteomic analysis for evaluating the solubilization efficacies of the Azo and SDS surfactants using rice leave proteins. This approach led to identification of 3,365 proteins of which 682 proteins were determined as significantly modulated. Further, according to the subcellular localization prediction in SDS and Azo, proteins localized in the chloroplast were the major organelle accounting for 64% of the total organelle in the SDS sample, while only 37.5% of organelle proteins solubilized in the Azo were predicted to be localized in chloroplast. Taken together, this study validates the efficient solubilization of total protein isolated from plant material for bottom-up proteomics. Azo surfactant is suitable as substitute of SDS and promising for bottom-up proteomics as it facilitates robust protein extraction, rapid washing step during enzymatic digestion, and MS analysis.

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Post-Translational Modification (PTM) Proteomics: Challenges and Perspectives

Cited by 3 publications

References 37 publications

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Monitoring Functional Post-Translational Modifications Using a Data-Driven Proteome Informatic Pipeline Based on PEIMAN2

Characterizing disease-associated changes in post-translational modifications by mass spectrometry

Application of mass-spectrometry compatible photocleavable surfactant for next-generation proteomics using rice leaves

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