In Silico Tools and Phosphoproteomic Software Exclusives

Abstract

Proteomics and phosphoproteomics have been emerging as new dimensions of omics. Phosphorylation has a profound impact on the biological functions and applications of proteins. It influences everything from intrinsic activity and extrinsic executions to cellular localization. This post-translational modification has been subjected to detailed study and has been an object of analytical curiosity with the advent of faster instrumentation. The major strength of phosphoproteomic research lies in the fact that it gives an overall picture of the workforce of the cell. Phosphoproteomics gives deeper insights into understanding the mechanism behind development and progression of a disease. This review for the first time consolidates the list of existing bioinformatics tools developed for phosphoproteomics. The gap between development of bioinformatics tools and their implementation in clinical research is highlighted. The challenge facing progress is ideally believed to be the interdisciplinary arena this field of research is associated with. For meaningful solutions and deliverables, these tools need to be implemented in clinical studies for obtaining answers to pharmacodynamic questions, saving time, costs and energy. This review hopes to invoke some thought in this direction.

Special Issue on “Big Data in Biology, Life Sciences and Healthcare”

“…The Special Issue includes two review papers in the area of bioinformatics and machine learning tools for proteomics, which has emerged as an important dimension of omics. Paul et al [9] reviewed bioinformatics tools developed for phosphoproteomics. The study is inspired by the profound impact phosphorylation has on biological functions from intrinsic activity and extrinsic executions to cellular localization and the strength of phosphoproteomics research in that it provides an overall picture of the workforce of the cell.…”

Phosphopeptide enrichment for phosphoproteomic analysis - A tutorial and review of novel materials

“…A range of computational tools and MS data analysis for p-peptide and site localisation are available, which are well catalogued and described, alongside proteomic data analysis pipelines by Paul et al, 2019 [37]. Locard-Paulet et al [38] compared 22 pipelines for bottom-up phosphoproteomics analysis involving data base search tools (MaxQuant, Proteome Discoverer, PeptideShaker), search engines (Andromeda, Comet, Mascot, MS Amanda, SequestHT, and X!Tandem), and localization scoring algorithms (delta score, D-score, PTM-score, phosphoRS, and Ascore) for a defined dataset.…”

“…Phosphotyrosine antibody cocktails [102]. Phosphotyrosine-imprinted polymer with TiO 2 [100] Figure 2 Schemes for the creation and use of three novel enrichment materials: a) MagG@PEI@PA-Ti 4+ , which can adsorb 53.5 μg mg -1 p-peptide with 90% recovery, and is sensitive to concentrations as low as 0.8 fmol.μl -1 [49], b) Ti 4+ @PDA@GA, aerogel, 1518 formed from graphene oxide (GO), is used in a lab-in-syringe methodology that preferentially enriches p-proteins (1300-1345 μg mg −1 vs 4.8-160 μg mg −1 ), can adsorb up to 1340 μg mg -1 , and is sensitive to concentrations as low as 2 fmol.μl -1 [37], and c) 1521 loading buffer (50% ACN, 0.1% or 0.25% TFA, v/v), washed 3 times, and then eluted by 1550 ammonia solutions (0.4 M or 10% wt%) after min's treatment. (c) TiO 2 -NH 2 modified MALDI plate (β-casein, BSA, horseradish peroxidase, human serum, human saliva) [113], for which 5 min of incubation (50% ACN, 1% TFA, or 95% ACN, 0.1% TFA, v/v), after 5 times washing, DHB was added for direct LC-MS/MS analysis.…”

Deep Learning in Phosphoproteomics: Methods and Application in Cancer Drug Discovery

“…PTM research has made remarkable progress over the years, especially after the emergence of new computational techniques. Combined with experimental methods, the application of bioinformatics tools in PTM analysis enables a more efficient exploration of the phosphorylation network, resulting in the timely analysis of datasets and providing insights for biological research and drug discovery [ 19 ].…”