High Accuracy Mass Spectrometry in Large-Scale Analysis of Protein Phosphorylation

2009 ◽  
pp. 131-142 ◽  
Author(s):  
Jesper V. Olsen ◽  
Boris Macek
Keyword(s):  
Mass Spectrometry ◽  
Protein Phosphorylation ◽  
Large Scale ◽  
High Accuracy ◽  
Scale Analysis ◽  
Large Scale Analysis

scholarly journals Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Chayaporn Suphavilai ◽  
Shumei Chia ◽  
Ankur Sharma ◽  
Lorna Tu ◽  
Rafael Peres Da Silva ◽  
...  
Keyword(s):  
Single Cell ◽  
Large Scale ◽  
Drug Response ◽  
Drug Repurposing ◽  
High Accuracy ◽  
Molecular Heterogeneity ◽  
Precision Oncology ◽  
Scale Analysis ◽  
Rna Seq ◽  
Large Scale Analysis

AbstractWhile understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of cancer omics datasets, we highlight the importance of intra-tumor transcriptomic heterogeneity (ITTH) for predicting clinical outcomes. Leveraging single-cell RNA-seq (scRNA-seq) with a recommender system (CaDRReS-Sc), we show that heterogeneous gene-expression signatures can predict drug response with high accuracy (80%). Using patient-proximal cell lines, we established the validity of CaDRReS-Sc’s monotherapy (Pearson r>0.6) and combinatorial predictions targeting clone-specific vulnerabilities (>10% improvement). Applying CaDRReS-Sc to rapidly expanding scRNA-seq compendiums can serve as in silico screen to accelerate drug-repurposing studies. Availability: https://github.com/CSB5/CaDRReS-Sc.

scholarly journals Structural elucidation of triacylglycerol using online acetone Paternò–Büchi reaction coupled with reversed-phase liquid chromatography mass spectrometry

The Analyst ◽  
2020 ◽  
Vol 145 (20) ◽  
pp. 6532-6540 ◽  
Author(s):  
Elissia T. Franklin ◽  
Yu Xia
Keyword(s):  
Mass Spectrometry ◽  
Liquid Chromatography ◽  
Large Scale ◽  
Reversed Phase ◽  
Structural Elucidation ◽  
Scale Analysis ◽  
Liquid Chromatography Mass Spectrometry ◽  
Reversed Phase Liquid Chromatography ◽  
Large Scale Analysis ◽  
Phase Liquid

The developed online RPLC-PB-MS/MS system allows large scale analysis of isomeric triacylglycerol lipids differing in CC locations.

scholarly journals Reliable identification of protein-protein interactions by crosslinking mass spectrometry

2020 ◽  
Author(s):  
Swantje Lenz ◽  
Ludwig R. Sinn ◽  
Francis J. O’Reilly ◽  
Lutz Fischer ◽  
Fritz Wegner ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Interactions ◽  
Large Scale ◽  
Protein Complexes ◽  
Estimation Procedure ◽  
Scale Analysis ◽  
Protein Protein Interactions ◽  
False Discovery ◽  
Large Scale Analysis ◽  
False Discovery Rate Estimation

Crosslinking mass spectrometry is widening its scope from structural analyzes of purified multi-protein complexes towards systems-wide analyzes of protein-protein interactions. Assessing the error in these large datasets is currently a challenge. Using a controlled large-scale analysis of Escherichia coli cell lysate, we demonstrate a reliable false-discovery rate estimation procedure for protein-protein interactions identified by crosslinking mass spectrometry.

Understanding platelets

2005 ◽  
Vol 94 (11) ◽  
pp. 916-925 ◽  
Author(s):  
Marcus Dittrich ◽  
Ingvild Birschmann ◽  
Christiane Stuhlfelder ◽  
Albert Sickmann ◽  
Sabine Herterich ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
Building Blocks ◽  
Clinical Implications ◽  
Scale Analysis ◽  
New Techniques ◽  
Analysis Techniques ◽  
Large Scale Analysis ◽  
Sage Data ◽  
New Framework

SummaryNew large-scale analysis techniques such as bioinformatics, mass spectrometry and SAGE data analysis will allow a new framework for understanding platelets. This review analyses some important options and tasks for these tools and examines an outline of the new, refined picture of the platelet outlined by these new techniques. Looking at the platelet-specific building blocks of genome, (active) transcriptome and proteome (notably secretome and phospho-proteome), we summarize current bioinformatical and biochemical approaches, tasks as well as their limitations. Understanding the surprisingly complex platelet regarding compartmentalization, key cascades, and pathways including clinical implications will remain an exciting and hopefully fruitful challenge for the future.

Biochemical and Computational Approaches for the Large-Scale Analysis of Protein Arginine Methylation by Mass Spectrometry

2020 ◽  
Vol 21 (7) ◽  
pp. 725-739
Author(s):  
Daniele Musiani ◽  
Enrico Massignani ◽  
Alessandro Cuomo ◽  
Avinash Yadav ◽  
Tiziana Bonaldi
Keyword(s):  
Mass Spectrometry ◽  
Large Scale ◽  
High Resolution Mass Spectrometry ◽  
Arginine Methylation ◽  
Research Field ◽  
Scale Analysis ◽  
Post Translational Modification ◽  
Large Scale Analysis ◽  
Protein Arginine Methylation

: The absence of efficient mass spectrometry-based approaches for the large-scale analysis of protein arginine methylation has hindered the understanding of its biological role, beyond the transcriptional regulation occurring through histone modification. In the last decade, however, several technological advances of both the biochemical methods for methylated polypeptide enrichment and the computational pipelines for MS data analysis have considerably boosted this research field, generating novel insights about the extent and role of this post-translational modification. : Here, we offer an overview of state-of-the-art approaches for the high-confidence identification and accurate quantification of protein arginine methylation by high-resolution mass spectrometry methods, which comprise the development of both biochemical and bioinformatics methods. The further optimization and systematic application of these analytical solutions will lead to ground-breaking discoveries on the role of protein methylation in biological processes.

Large-scale analysis of protein phosphorylation in Populus leaves

2013 ◽  
Vol 23 (4) ◽  
pp. 410-420 ◽  
Author(s):  
Jinwen Liu ◽  
Deli Ning ◽  
Guiling Zhao ◽  
Yuxiang Cheng ◽  
Baichen Wang
Keyword(s):  
Protein Phosphorylation ◽  
Large Scale ◽  
Scale Analysis ◽  
Large Scale Analysis

scholarly journals Quantitative model suggests both intrinsic and contextual features contribute to the transcript coding ability determination in cells

2021 ◽  
Author(s):  
Yu-jian Kang ◽  
Jing-Yi Li ◽  
Lan Ke ◽  
Shuai Jiang ◽  
De-chang Yang ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Large Scale ◽  
Protein Translation ◽  
Quantitative Model ◽  
High Accuracy ◽  
Biological Information ◽  
Scale Analysis ◽  
Large Scale Analysis ◽  
Context Dependent ◽  
Key Steps

Gene transcription and protein translation are two key steps of the "central dogma". It is still a major challenge to quantitatively deconvolute factors contributing to the coding ability of transcripts in mammals. Here, we propose Ribosome Calculator (RiboCalc) for quantitatively modeling the coding ability of RNAs in human genome. In addition to effectively predicting the experimentally confirmed coding abundance via sequence and transcription features with high accuracy, RiboCalc provides interpretable parameters with biological information. Large-scale analysis further revealed a number of transcripts with a variety of coding ability for distinct types of cells (i.e., context-dependent coding transcripts, CDCTs), suggesting that, contrary to conventional wisdom, a transcript's coding ability should be modeled as a continuous spectrum with a context-dependent nature.

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