scholarly journals A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments

PROTEOMICS ◽  
2012 ◽  
Vol 13 (3-4) ◽  
pp. 493-503 ◽  
Author(s):  
Melissa M. Matzke ◽  
Joseph N. Brown ◽  
Marina A. Gritsenko ◽  
Thomas O. Metz ◽  
Joel G. Pounds ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Protein Quantification ◽  
Label Free ◽  
Computational Approaches ◽  
Peptide Peak

scholarly journals LFAQ: Toward Unbiased Label-Free Absolute Protein Quantification by Predicting Peptide Quantitative Factors

2018 ◽  
Vol 91 (2) ◽  
pp. 1335-1343 ◽  
Author(s):  
Cheng Chang ◽  
Zhiqiang Gao ◽  
Wantao Ying ◽  
Yan Fu ◽  
Yan Zhao ◽  
...  
Keyword(s):  
Protein Quantification ◽  
Label Free

Recent Technological Advances in the Mass Spectrometry-based Nanomedicine Studies: An Insight from Nanoproteomics

2019 ◽  
Vol 25 (13) ◽  
pp. 1536-1553 ◽  
Author(s):  
Jing Tang ◽  
Yunxia Wang ◽  
Yi Li ◽  
Yang Zhang ◽  
Runyuan Zhang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Information Sources ◽  
Protein Quantification ◽  
Protein Profiling ◽  
Label Free ◽  
Dynamic Information ◽  
Data Repositories ◽  
Research Directions ◽  
Technological Advances ◽  
Recent Trends

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.

scholarly journals Electrochemical detection of different p53 conformations by using nanostructured surfaces

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Sarah Tonello ◽  
Francesca Stradolini ◽  
Giulia Abate ◽  
Daniela Uberti ◽  
Mauro Serpelloni ◽  
...  
Keyword(s):  
Quantitative Analysis ◽  
Limit Of Detection ◽  
Direct Electrochemistry ◽  
Protein Quantification ◽  
Label Free ◽  
Limited Information ◽  
Clinical Practices ◽  
Nanostructured Surfaces ◽  
Integrated Devices ◽  
Biochemical Assays

AbstractProtein electrochemistry represents a powerful technique for investigating the function and structure of proteins. Currently available biochemical assays provide limited information related to the conformational state of proteins and high costs. This work provides novel insights into the electrochemical investigation of the metalloprotein p53 and its redox products using label-free direct electrochemistry and label-based antibody-specific approaches. First, the redox activities of different p53 redox products were qualitatively investigated on carbon-based electrodes. Then, focusing on the open p53 isoform (denatured p53), a quantitative analysis was performed, comparing the performances of different bulk and nanostructured materials (carbon and platinum). Overall, four different p53 products could be successfully discriminated, from wild type to denatured. Label-free analysis suggested a single electron exchange with electron transfer rate constants on the order of 1 s−1. Label-based analysis showed decreasing affinity of pAb240 towards denatured, oxidized and nitrated p53. Furthermore, platinum nanostructured electrodes showed the highest enhancement of the limit of detection in the quantitative analysis (100 ng/ml). Overall, the obtained results represent a first step towards the implementation of highly requested complex integrated devices for clinical practices, with the aim to go beyond simple protein quantification.

scholarly journals Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs

2012 ◽  
Vol 13 (Suppl 16) ◽  
pp. S6 ◽  
Author(s):  
Timothy Clough ◽  
Safia Thaminy ◽  
Susanne Ragg ◽  
Ruedi Aebersold ◽  
Olga Vitek
Keyword(s):  
Protein Quantification ◽  
Label Free ◽  
Significance Analysis

scholarly journals Genetics Meets Proteomics: Correlating the Portuguese Water Dog Blood Serum Proteome with Genetic Markers

2011 ◽  
Vol 4 ◽  
pp. PRI.S6470
Author(s):  
Sandra Sénéchal ◽  
Martin Kussmann
Keyword(s):  
Blood Serum ◽  
Biomarker Discovery ◽  
Protein Quantification ◽  
Label Free ◽  
Blood Profile ◽  
Serum Proteome ◽  
Genetic Level ◽  
Portuguese Water ◽  
Dog Blood ◽  
Genetically Determined

Blood serum is a body fluid widely used for biomarker discovery and therefore numerous studies aim at defining its proteome. The serum proteome is subject to fluctuations resulting from biological variability (eg, diurnal variations) reflecting both healthy and/or disease-related conditions. Inter-individual differences originate partly at the genetic level and may influence clinical blood profile including the serum proteome. Therefore we investigated whether serum protein abundance is genetically determined: we report the study of a cohort of 146 Portuguese Water Dogs, a dog breed whose genetic background has been well characterized. We generated protein profiles of dog sera on 1D-gels and correlated them with microsatellite markers. We detected correlations between 7 gel bands and 11 genetic regions and developed a label-free protein quantification method to identify and quantify the proteins most accountable for serum proteome variation. An association between the abundance of RBP4 in dog serum and the adiponectin gene was detected.

Label-Free Comparative Analysis of Proteomics Mixtures Using Chromatographic Alignment of High-Resolution μLC−MS Data

2008 ◽  
Vol 80 (4) ◽  
pp. 961-971 ◽  
Author(s):  
Gregory L. Finney ◽  
Adele R. Blackler ◽  
Michael R. Hoopmann ◽  
Jesse D. Canterbury ◽  
Christine C. Wu ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
High Resolution ◽  
Label Free

scholarly journals Label-free single-cell protein quantification using a drop-based mix-and-read system

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Alireza Abbaspourrad ◽  
Huidan Zhang ◽  
Ye Tao ◽  
Naiwen Cui ◽  
Haruichi Asahara ◽  
...  
Keyword(s):  
Single Cell ◽  
Single Cell Protein ◽  
Protein Quantification ◽  
Cell Protein ◽  
Label Free
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