Faculty Opinions recommendation of Label-free protein quantification using LC-coupled ion trap or FT mass spectrometry: Reproducibility, linearity, and application with complex proteomes.

Nanoscience becomes one of the most cutting-edge research directions in recent years since it is gradually matured from basic to applied science. Nanoparticles (NPs) and nanomaterials (NMs) play important roles in various aspects of biomedicine science, and their influences on the environment have caused a whole range of uncertainties which require extensive attention. Due to the quantitative and dynamic information provided for human proteome, mass spectrometry (MS)-based quantitative proteomic technique has been a powerful tool for nanomedicine study. In this article, recent trends of progress and development in the nanomedicine of proteomics were discussed from quantification techniques and publicly available resources or tools. First, a variety of popular protein quantification techniques including labeling and label-free strategies applied to nanomedicine studies are overviewed and systematically discussed. Then, numerous protein profiling tools for data processing and postbiological statistical analysis and publicly available data repositories for providing enrichment MS raw data information sources are also discussed.

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Comparative Study of Targeted and Label-free Mass Spectrometry Methods for Protein Quantification

Journal of Proteome Research ◽

10.1021/pr301221f ◽

2013 ◽

Vol 12 (4) ◽

pp. 2005-2011 ◽

Cited By ~ 7

Author(s):

Linda IJsselstijn ◽

Marcel P. Stoop ◽

Christoph Stingl ◽

Peter A. E. Sillevis Smitt ◽

Theo M. Luider ◽

...

Keyword(s):

Mass Spectrometry ◽

Comparative Study ◽

Protein Quantification ◽

Label Free

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In-depth Exploration of Cerebrospinal Fluid by Combining Peptide Ligand Library Treatment and Label-free Protein Quantification

Molecular & Cellular Proteomics ◽

10.1074/mcp.m900513-mcp200 ◽

2010 ◽

Vol 9 (5) ◽

pp. 1006-1021 ◽

Cited By ~ 98

Author(s):

Emmanuelle Mouton-Barbosa ◽

Florence Roux-Dalvai ◽

David Bouyssié ◽

François Berger ◽

Eric Schmidt ◽

...

Keyword(s):

Cerebrospinal Fluid ◽

Protein Quantification ◽

Peptide Ligand ◽

Label Free ◽

Free Protein

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Label-free protein quantification on tandem mass spectra acquired in a data-independent mode provides accurate measurements over five orders of concentration magnitude in complex matrices

Journal of Integrated OMICS ◽

10.5584/jiomics.v1i2.45 ◽

2011 ◽

Vol 1 (2) ◽

Author(s):

Alexander Scherl ◽

HuiSong Pak ◽

Carla Pasquarello

Keyword(s):

Mass Spectra ◽

Protein Quantification ◽

Tandem Mass ◽

Label Free ◽

Complex Matrices ◽

Free Protein ◽

Tandem Mass Spectra ◽

Independent Mode

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Label-free protein quantification after ultrafast digestion of complex proteomes using ultrasonic energy and immobilized-trypsin magnetic nanoparticles

Talanta ◽

10.1016/j.talanta.2018.12.066 ◽

2019 ◽

Vol 196 ◽

pp. 262-270 ◽

Cited By ~ 3

Author(s):

Gonçalo Martins ◽

Javier Fernández-Lodeiro ◽

Jamila Djafari ◽

Carlos Lodeiro ◽

J.L. Capelo ◽

...

Keyword(s):

Magnetic Nanoparticles ◽

Protein Quantification ◽

Ultrasonic Energy ◽

Label Free ◽

Free Protein ◽

Immobilized Trypsin

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Proteomic Characterization of Cerebrospinal Fluid from Ataxia-Telangiectasia (A-T) Patients Using a LC/MS-Based Label-Free Protein Quantification Technology

International Journal of Proteomics ◽

10.1155/2011/578903 ◽

2011 ◽

Vol 2011 ◽

pp. 1-13 ◽

Cited By ~ 8

Author(s):

Monika Dzieciatkowska ◽

Guihong Qi ◽

Jinsam You ◽

Kerry G. Bemis ◽

Heather Sahm ◽

...

Keyword(s):

Cerebrospinal Fluid ◽

Biomarker Discovery ◽

Functional Characterization ◽

Therapeutic Targets ◽

Bioinformatic Analysis ◽

Protein Quantification ◽

Label Free ◽

Free Protein ◽

Potential Biomarker

Cerebrospinal fluid (CSF) has been used for biomarker discovery of neurodegenerative diseases in humans since biological changes in the brain can be seen in this biofluid. Inactivation of A-T-mutated protein (ATM), a multifunctional protein kinase, is responsible for A-T, yet biochemical studies have not succeeded in conclusively identifying the molecular mechanism(s) underlying the neurodegeneration seen in A-T patients or the proteins that can be used as biomarkers for neurologic assessment of A-T or as potential therapeutic targets. In this study, we applied a high-throughput LC/MS-based label-free protein quantification technology to quantitatively characterize the proteins in CSF samples in order to identify differentially expressed proteins that can serve as potential biomarker candidates for A-T. Among 204 identified CSF proteins with high peptide-identification confidence, thirteen showed significant protein expression changes. Bioinformatic analysis revealed that these 13 proteins are either involved in neurodegenerative disorders or cancer. Future molecular and functional characterization of these proteins would provide more insights into the potential therapeutic targets for the treatment of A-T and the biomarkers that can be used to monitor or predict A-T disease progression. Clinical validation studies are required before any of these proteins can be developed into clinically useful biomarkers.

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