Dual roles of drug or its metabolite−protein conjugate: Cutting‐edge strategy of drug discovery using shotgun proteomics
Sign Up to like & getrecommendations! Published in 2022 at "Medicinal Research Reviews"
DOI: 10.1002/med.21889
Abstract: Many drugs can bind directly to proteins or be bioactivated by metabolizing enzymes to form reactive metabolites (RMs) that rapidly bind to proteins to form drug−protein conjugates or metabolite−protein conjugates (DMPCs). The close relationship between… read more here.
Keywords: drug discovery; shotgun proteomics; using shotgun; metabolite protein ... See more keywords
Scavager: A Versatile Postsearch Validation Algorithm for Shotgun Proteomics Based on Gradient Boosting
Sign Up to like & getrecommendations! Published in 2019 at "PROTEOMICS"
DOI: 10.1002/pmic.201800280
Abstract: Shotgun proteomics workflows for database protein identification typically include a combination of search engines and postsearch validation software based mostly on machine learning algorithms. Here, a new postsearch validation tool called Scavager employing CatBoost, an… read more here.
Keywords: gradient boosting; postsearch validation; scavager; postsearch ... See more keywords
Shotgun Proteomics of Plant Plasma Membrane and Microdomain Proteins Using Nano-LC-MS/MS.
Sign Up to like & getrecommendations! Published in 2020 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-0528-8_7
Abstract: Shotgun proteomics allows for the comprehensive analysis of proteins extracted from plant cells, subcellular organelles, and membranes. Previously, two-dimensional gel electrophoresis-based proteomics was used for mass spectrometric analysis of plasma membrane proteins. However, this method… read more here.
Keywords: using nano; membrane; shotgun proteomics; plasma membrane ... See more keywords
Shotgun Proteomics for L3 and L4 Anisakis simplex Development Stages.
Sign Up to like & getrecommendations! Published in 2021 at "Methods in molecular biology"
DOI: 10.1007/978-1-0716-1178-4_5
Abstract: Anisakis simplex s.s. is a parasitic nematode that causes anisakiasis in humans. L3 stage larvae, which are present in many fish species and cephalopods all over the globe, might be consumed and develop occasionally into… read more here.
Keywords: simplex development; development stages; proteomics anisakis; anisakis simplex ... See more keywords
iTRAQ-Based Shotgun Proteomics Approach for Relative Protein Quantification.
Sign Up to like & getrecommendations! Published in 2017 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-6730-8_23
Abstract: Shotgun proteomics has a key role in quantitative estimation of proteins from biological systems under different conditions, which is crucial in the understanding of their functional roles. Isobaric tagging for relative and absolute quantitation (iTRAQ)… read more here.
Keywords: proteomics approach; based shotgun; itraq; quantification ... See more keywords
The extraradical proteins of Rhizophagus irregularis: A shotgun proteomics approach.
Sign Up to like & getrecommendations! Published in 2020 at "Fungal biology"
DOI: 10.1016/j.funbio.2019.12.001
Abstract: Arbuscular Mycorrhizal fungi (AMF, Glomeromycota) form obligate symbiotic associations with the roots of most terrestrial plants. Our understanding of the molecular mechanisms enabling AMF propagation and AMF-host interaction is currently incomplete. Analysis of AMF proteomes… read more here.
Keywords: proteins rhizophagus; extraradical proteins; rhizophagus irregularis; irregularis shotgun ... See more keywords
Common Decoy Distributions Simplify False Discovery Rate Estimation in Shotgun Proteomics.
Sign Up to like & getrecommendations! Published in 2022 at "Journal of proteome research"
DOI: 10.1021/acs.jproteome.1c00600
Abstract: In shotgun proteomics, false discovery rate (FDR) estimation is a necessary step to ensure the quality of accepted peptide-spectrum matches (PSMs) from a database search. Popular statistical validation tools for FDR control tend to rely… read more here.
Keywords: false discovery; common decoy; estimation; discovery rate ... See more keywords
Philosopher: a versatile toolkit for shotgun proteomics data analysis
Sign Up to like & getrecommendations! Published in 2020 at "Nature Methods"
DOI: 10.1038/s41592-020-0912-y
Abstract: To the Editor — Here we introduce Philosopher (https://philosopher.nesvilab. org), a free, open-source, versatile and robust data analysis toolkit designed to bring easy access to a powerful and comprehensive set of computational tools for shotgun… read more here.
Keywords: philosopher; data analysis; proteomics data; analysis ... See more keywords
Shotgun Proteomics of Human Dentin with Different Prefractionation Methods
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-41144-x
Abstract: Human dentin is not only a composite material of a collagenous matrix and mineral to provide strength and elasticity to teeth, but also a precious reservoir full of bioactive proteins. They are released after demineralization… read more here.
Keywords: prefractionation; different prefractionation; dentin different; human dentin ... See more keywords
A sample preparation workflow for adipose tissue shotgun proteomics and proteogenomics
Sign Up to like & getrecommendations! Published in 2018 at "Biology Open"
DOI: 10.1242/bio.036731
Abstract: ABSTRACT Animals with large adipose stores, such as marine mammals, may provide insights into the evolution and function of this multifunctional tissue in health and disease. In the absence of sequenced genomes, molecular information can… read more here.
Keywords: preparation workflow; tissue; sample preparation; adipose tissue ... See more keywords
Does filter-aided sample preparation provide sufficient method linearity for quantitative plant shotgun proteomics?
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Plant Science"
DOI: 10.3389/fpls.2022.874761
Abstract: Due to its outstanding throughput and analytical resolution, gel-free LC-based shotgun proteomics represents the gold standard of proteome analysis. Thereby, the efficiency of sample preparation dramatically affects the correctness and reliability of protein quantification. Thus,… read more here.
Keywords: method; sample preparation; shotgun proteomics; plant ... See more keywords