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High-Throughput Proteotyping of Bacterial Isolates by Double Barrel Chromatography-Tandem Mass Spectrometry Based on Microplate Paramagnetic Beads and Phylopeptidomics

Journal of Proteomics, 2020
Corresponding author : Jean Armengaud (jean.armengaud@cea.fr)International audienceTandem mass spectrometry-based proteotyping of microorganisms presents several advantages over whole-cell MALDI-TOF mass spectrometry: because a larger number of signals ...
Béatrice M Alpha-Bazin, Karim Hayoun, Jean Armengaud   +2 more
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Computational prediction of proteotypic peptides

Expert Review of Proteomics, 2007
Evaluation of: Mallick P, Schirle M, Chen SS et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25(1), 125–131 (2007).Mass spectrometry, the driving analytical force behind proteomics, is primarily used to identify and quantify as many proteins in a complex biological mixture as possible.
Josip, Blonder, Timothy D, Veenstra
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Proteotyping pluripotency with mass spectrometry

Expert Review of Proteomics, 2019
Pluripotency emerges transiently during embryogenesis in two main forms with different developmental potential, termed naïve and primed states. Importantly, these pluripotent states can be recapitulated in vitro under specific culture conditions, representing a unique model to study the regulatory principles of development and cellular plasticity ...
Cristina, Sayago, Ana, Martinez-Val, Javier, Munoz   +2 more
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Scoring proteomes with proteotypic peptide probes

Nature Reviews Molecular Cell Biology, 2005
Technologies for genome-wide analyses typically undergo a transition from a discovery phase to a scoring phase. In the discovery phase, the genomic universe is explored and all pertinent data are noted. In the scoring phase, relevant entities are screened to reveal groups of genes that are associated with specific biological processes or conditions. In
Bernhard, Kuster, Markus, Schirle, Parag, Mallick, Ruedi, Aebersold   +3 more
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Proteotypic Peptides and Their Applications

2016
Recent advances in mass spectrometry based proteomic techniques and publicly available large proteomic repositories are being exploited to characterize the proteome of multiple organisms. While humongous amount of proteomic data is being acquired and analyzed, many biological questions still remain unanswered.
Shivakumar, Keerthikumar, Suresh, Mathivanan   +1 more
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Proteotype Co-evolution and Diversity in Mammals

2022
Abstract Evolutionary profiling has been largely limited to the nucleotide level. Using consistent proteomic methods, we quantified proteomic and phosphoproteomic layers in fibroblasts from 11 common mammalian species, with transcriptomic variability as reference.
Qian Ba, Yuanyuan Hei, Anasuya Dighe, Wenxue Li, Jamie Maziarz, Irene Pak, Shisheng Wang, Günter P. Wagner, Yansheng Liu   +8 more
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The use of proteotypic peptide libraries for protein identification

Rapid Communications in Mass Spectrometry, 2005
Abstract This paper describes an algorithm to apply proteotypic peptide sequence libraries to protein identifications performed using tandem mass spectrometry (MS/MS). Proteotypic peptides are those peptides in a protein sequence that are most likely to be confidently observed by current MS‐based proteomics ...
Robertson, Craig, John P, Cortens, Ronald C, Beavis   +2 more
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Proteotyping: Proteomic Characterization, Classification and Identification of Microorganisms – A Prospectus

Systematic and Applied Microbiology, 2015
Modern microbial systematics requires a range of methodologies for the comprehensive characterization, classification and identification of microorganisms. While whole-genome sequences provide the ultimate reference for defining microbial phylogeny and taxonomy, selected biomarker-based strategies continue to provide the means for the bulk of microbial
Stefan Hulth, Lucia Gonzales Strömberg, Edward R. B. Moore   +2 more
exaly   +4 more sources

Computational prediction of proteotypic peptides for quantitative proteomics

Nature Biotechnology, 2006
Mass spectrometry-based quantitative proteomics has become an important component of biological and clinical research. Although such analyses typically assume that a protein's peptide fragments are observed with equal likelihood, only a few so-called 'proteotypic' peptides are repeatedly and consistently identified for any given protein present in a ...
Parag, Mallick, Markus, Schirle, Sharon S, Chen, Mark R, Flory, Hookeun, Lee, Daniel, Martin, Jeffrey, Ranish, Brian, Raught, Robert, Schmitt, Thilo, Werner, Bernhard, Kuster, Ruedi, Aebersold   +11 more
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Proteotyping of the Parainfluenza Virus with High-Resolution Mass Spectrometry

Analytical Chemistry, 2013
Parainfluenza viruses (PIVs) are one of the most common causes of respiratory tract infections in children and can be life-threatening when the airway becomes obstructed. Infection results in a spectrum of respiratory disease symptoms that makes diagnosis difficult.
An P, Nguyen, Kevin M, Downard
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