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.

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

2011 ◽  
Vol 2011 ◽  
pp. 1-13 ◽  
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.

scholarly journals Proteomics in Diagnosis of Prostate Cancer/ Протеомика Во Дијагноза На Простатниот Карцином

PRILOZI ◽  
2015 ◽  
Vol 36 (1) ◽  
pp. 5-36 ◽  
Author(s):  
Katarina Davalieva ◽  
Momir Polenakovic
Keyword(s):  
Prostate Cancer ◽  
Tumor Tissue ◽  
Biomarker Discovery ◽  
Molecular Level ◽  
Specific Antigen ◽  
Shotgun Proteomics ◽  
Comparative Proteomics ◽  
Label Free ◽  
The Past ◽  
Proteomics Research

Abstract Prostate cancer (PCa) is the second most frequently diagnosed malignancy in men worldwide. The introduction of prostate specific antigen (PSA) has greatly increased the number of men diagnosed with PCa but at the same time, as a result of the low specificity, led to overdiagnosis, resulting to unnecessary biopsies and high medical cost treatments. The primary goal in PCa research today is to find a biomarker or biomarker set for clear and effecttive diagnosis of PCa as well as for distinction between aggressive and indolent cancers. Different proteomic technologies such as 2-D PAGE, 2-D DIGE, MALDI MS profiling, shotgun proteomics with label-based (ICAT, iTRAQ) and label-free (SWATH) quantification, MudPIT, CE-MS have been applied to the study of PCa in the past 15 years. Various biological samples, including tumor tissue, serum, plasma, urine, seminal plasma, prostatic secretions and prostatic-derived exosomes were analyzed with the aim of identifying diagnostic and prognostic biomarkers and developing a deeper understanding of the disease at the molecular level. This review is focused on the overall analysis of expression proteomics studies in the PCa field investigating all types of human samples in the search for diagnostics biomarkers. Emphasis is given on proteomics platforms used in biomarker discovery and characterization, explored sources for PCa biomarkers, proposed candidate biomarkers by comparative proteomics studies and the possible future clinical application of those candidate biomarkers in PCa screening and diagnosis. In addition, we review the specificity of the putative markers and existing challenges in the proteomics research of PCa.

A peptide-centric approach to breast cancer biomarker discovery utilizing label-free multiple reaction monitoring mass spectrometry

2008 ◽  
Vol 3 (1) ◽  
pp. 78-82 ◽  
Author(s):  
Gergana Metodieva ◽  
Christina Greenwood ◽  
Louise Alldridge ◽  
Paul Sauven ◽  
Metodi Metodiev
Keyword(s):  
Breast Cancer ◽  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Multiple Reaction Monitoring ◽  
Cancer Biomarker ◽  
Reaction Monitoring ◽  
Label Free

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

Stealth modified bottom up SERS substrates for label-free therapeutic drug monitoring of doxorubicin in blood serum

Talanta ◽  
2020 ◽  
Vol 218 ◽  
pp. 121138 ◽  
Author(s):  
Sandeep Surendra Panikar ◽  
Nehla Banu ◽  
Elia-Reza Escobar ◽  
Gonzalo-Ramírez García ◽  
Jesús Cervantes-Martínez ◽  
...  
Keyword(s):  
Therapeutic Drug Monitoring ◽  
Blood Serum ◽  
Drug Monitoring ◽  
Therapeutic Drug ◽  
Label Free ◽  
Bottom Up ◽  
Sers Substrates

scholarly journals A simple serum depletion method for proteomics analysis

BioTechniques ◽  
2020 ◽  
Vol 69 (2) ◽  
pp. 148-151
Author(s):  
Alexandre Zougman ◽  
John P Wilson ◽  
Rosamonde E Banks
Keyword(s):  
Sample Preparation ◽  
Serum Protein ◽  
Body Fluid ◽  
Biomarker Discovery ◽  
The Body ◽  
Protein Digestion ◽  
Proteomics Analysis ◽  
Serum Proteome ◽  
Serum Fractions

Serum is the body fluid most often used in biomarker discovery. Albumin, the most abundant serum protein, contributes approximately 50% of the serum protein content, with an additional dozen abundant proteins dominating the rest of the serum proteome. To profile this challenging protein mixture by proteomics, the abundant proteins must be depleted to allow for detection of the low-abundant proteins, the primary biomarker targets. Current serum depletion approaches for proteomics are costly and relatively complex to couple with protein digestion. We demonstrate a simple, affordable serum depletion methodology that, within a few minutes of processing, results in two captured serum fractions – albumin-depleted and albumin-rich – which are digested in situ. We believe our method is a useful addition to the biomarker sample preparation toolbox.

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.

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