scholarly journals A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization

2017 ◽  
Vol 65 (2) ◽  
pp. 361-370 ◽  
Author(s):  
Brian K. Erickson ◽  
Christopher M. Rose ◽  
Craig R. Braun ◽  
Alison R. Erickson ◽  
Jeffrey Knott ◽  
...  
Keyword(s):  
High Throughput ◽  
Targeted Proteomics ◽  
Combine Sample ◽  
Protein Signature

scholarly journals A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer

EBioMedicine ◽  
2019 ◽  
Vol 44 ◽  
pp. 322-333 ◽  
Author(s):  
Qiujin Shen ◽  
Karol Polom ◽  
Coralie Williams ◽  
Felipe Marques Souza de Oliveira ◽  
Mariana Guergova-Kuras ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Serum Protein ◽  
Targeted Proteomics ◽  
Diagnostic Biomarker ◽  
Proteomics Approach ◽  
Resectable Gastric Cancer ◽  
Protein Signature

scholarly journals Peptide barcoding for one-pot evaluation of sequence–function relationships of nanobodies

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yusei Matsuzaki ◽  
Wataru Aoki ◽  
Takumi Miyazaki ◽  
Shunsuke Aburaya ◽  
Yuta Ohtani ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Size Exclusion Chromatography ◽  
High Throughput ◽  
Size Exclusion ◽  
Targeted Proteomics ◽  
One Pot ◽  
Unique Peptide ◽  
Exclusion Chromatography ◽  
Protein Binders

AbstractOptimisation of protein binders relies on laborious screening processes. Investigation of sequence–function relationships of protein binders is particularly slow, since mutants are purified and evaluated individually. Here we developed peptide barcoding, a high-throughput approach for accurate investigation of sequence–function relationships of hundreds of protein binders at once. Our approach is based on combining the generation of a mutagenised nanobody library fused with unique peptide barcodes, the formation of nanobody–antigen complexes at different ratios, their fine fractionation by size-exclusion chromatography and quantification of peptide barcodes by targeted proteomics. Applying peptide barcoding to an anti-GFP nanobody as a model, we successfully identified residues important for the binding affinity of anti-GFP nanobody at once. Peptide barcoding discriminated subtle changes in KD at the order of nM to sub-nM. Therefore, peptide barcoding is a powerful tool for engineering protein binders, enabling reliable one-pot evaluation of sequence–function relationships.

scholarly journals ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments

2017 ◽  
Vol 12 (2) ◽  
pp. 1600180 ◽  
Author(s):  
Yassene Mohammed ◽  
Jingxi Pan ◽  
Suping Zhang ◽  
Jun Han ◽  
Christoph H. Borchers
Keyword(s):  
High Throughput ◽  
Standard Addition ◽  
Standard Addition Method ◽  
Targeted Proteomics ◽  
Addition Method ◽  
External Standard

scholarly journals A targeted proteomics toolkit for high-throughput absolute quantification of Escherichia coli proteins

2014 ◽  
Vol 26 ◽  
pp. 48-56 ◽  
Author(s):  
Tanveer S. Batth ◽  
Pragya Singh ◽  
Vikram R. Ramakrishnan ◽  
Mirta M.L. Sousa ◽  
Leanne Jade G. Chan ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Throughput ◽  
Absolute Quantification ◽  
Targeted Proteomics

scholarly journals A Targeted Proteomics Approach Reveals a Serum Protein Signature as Diagnostic Biomarker for Resectable Gastric Cancer

2019 ◽  
Author(s):  
Qiujin Shen ◽  
Karol Polom ◽  
Coralie Williams ◽  
Felipe Marques Souza de Oliveira ◽  
Mariana Guergova-Kuras ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Serum Protein ◽  
Targeted Proteomics ◽  
Diagnostic Biomarker ◽  
Proteomics Approach ◽  
Resectable Gastric Cancer ◽  
Protein Signature

High-throughput production of a stable isotope-labeled peptide library for targeted proteomics using a wheat germ cell-free synthesis system

2016 ◽  
Vol 12 (8) ◽  
pp. 2389-2393 ◽  
Author(s):  
Nobuaki Takemori ◽  
Ayako Takemori ◽  
Yuki Tanaka ◽  
Jun Ishizaki ◽  
Hitoshi Hasegawa ◽  
...  
Keyword(s):  
High Throughput ◽  
Wheat Germ ◽  
Peptide Library ◽  
Selected Reaction Monitoring ◽  
Reaction Monitoring ◽  
Targeted Proteomics ◽  
Synthesis System ◽  
System P ◽  
Reference Peptide ◽  
Protein Synthesis System

Development of a reference peptide library for selected reaction monitoring (SRM)-based targeted proteomics using a high-throughput protein synthesis system.

scholarly journals High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440

2020 ◽  
Vol 8 ◽  
Author(s):  
Yuqian Gao ◽  
Thomas L. Fillmore ◽  
Nathalie Munoz ◽  
Gayle J. Bentley ◽  
Christopher W. Johnson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Systems Biology ◽  
Pseudomonas Putida ◽  
High Throughput ◽  
High Speed ◽  
Large Scale ◽  
Protein Quantification ◽  
Selected Reaction Monitoring ◽  
Targeted Proteomics ◽  
Pseudomonas Putida Kt2440

Targeted proteomics is a mass spectrometry-based protein quantification technique with high sensitivity, accuracy, and reproducibility. As a key component in the multi-omics toolbox of systems biology, targeted liquid chromatography-selected reaction monitoring (LC-SRM) measurements are critical for enzyme and pathway identification and design in metabolic engineering. To fulfill the increasing need for analyzing large sample sets with faster turnaround time in systems biology, high-throughput LC-SRM is greatly needed. Even though nanoflow LC-SRM has better sensitivity, it lacks the speed offered by microflow LC-SRM. Recent advancements in mass spectrometry instrumentation significantly enhance the scan speed and sensitivity of LC-SRM, thereby creating opportunities for applying the high speed of microflow LC-SRM without losing peptide multiplexing power or sacrificing sensitivity. Here, we studied the performance of microflow LC-SRM relative to nanoflow LC-SRM by monitoring 339 peptides representing 132 enzymes in Pseudomonas putida KT2440 grown on various carbon sources. The results from the two LC-SRM platforms are highly correlated. In addition, the response curve study of 248 peptides demonstrates that microflow LC-SRM has comparable sensitivity for the majority of detected peptides and better mass spectrometry signal and chromatography stability than nanoflow LC-SRM.

scholarly journals Efficient visualization of high-throughput targeted proteomics experiments: TAPIR: Fig. 1.

2015 ◽  
Vol 31 (14) ◽  
pp. 2415-2417 ◽  
Author(s):  
Hannes L. Röst ◽  
George Rosenberger ◽  
Ruedi Aebersold ◽  
Lars Malmström
Keyword(s):  
High Throughput ◽  
Targeted Proteomics

High-throughput targeted proteomics discovery approach and spontaneous reperfusion in ST-segment elevation myocardial infarction

2020 ◽  
Vol 220 ◽  
pp. 137-144 ◽  
Author(s):  
Jay S. Shavadia ◽  
Christopher B. Granger ◽  
Wendimagegn Alemayehu ◽  
Cynthia M. Westerhout ◽  
Thomas J. Povsic ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
High Throughput ◽  
Targeted Proteomics ◽  
St Segment Elevation ◽  
Segment Elevation Myocardial Infarction ◽  
St Segment
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