scholarly journals Challenges for Biomarker Discovery in Body Fluids Using SELDI-TOF-MS

2010 ◽  
Vol 2010 ◽  
pp. 1-15 ◽  
Author(s):  
Muriel De Bock ◽  
Dominique de Seny ◽  
Marie-Alice Meuwis ◽  
Jean-Paul Chapelle ◽  
Edouard Louis ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Biological Fluids ◽  
Protein Profiling ◽  
Sample Collection ◽  
Sample Handling ◽  
Biomarker Identification ◽  
The Past ◽  
Set Up ◽  
And Storage ◽  
Tof Ms

Protein profiling using SELDI-TOF-MS has gained over the past few years an increasing interest in the field of biomarker discovery. The technology presents great potential if some parameters, such as sample handling, SELDI settings, and data analysis, are strictly controlled. Practical considerations to set up a robust and sensitive strategy for biomarker discovery are presented. This paper also reviews biological fluids generally available including a description of their peculiar properties and the preanalytical challenges inherent to sample collection and storage. Finally, some new insights for biomarker identification and validation challenges are provided.

Use of SELDI-TOF mass spectrometry for identification of new biomarkers: potential and limitations

2007 ◽  
Vol 45 (11) ◽  
Author(s):  
Michael Kiehntopf ◽  
Robert Siegmund ◽  
Thomas Deufel
Keyword(s):  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Clinical Results ◽  
Protein Profiling ◽  
High Throughput Analysis ◽  
Pilot Studies ◽  
Flight Mass Spectrometry ◽  
Analytical Phase ◽  
New Biomarkers ◽  
Tof Ms

AbstractSurface-enhanced laser desorption time of flight mass spectrometry (SELDI-TOF-MS) is an important proteomic technology that is immediately available for the high throughput analysis of complex protein samples. Over the last few years, several studies have demonstrated that comparative protein profiling using SELDI-TOF-MS breaks new ground in diagnostic protein analysis particularly with regard to the identification of novel biomarkers. Importantly, researchers have acquired a better understanding also of the limitations of this technology and various pitfalls in biomarker discovery. Bearing these in mind, great emphasis must be placed on the development of rigorous standards and quality control procedures for the pre-analytical as well as the analytical phase and subsequent bioinformatics applied to analysis of the data. To avoid the risk of false-significant results studies must be designed carefully and control groups accurately selected. In addition, appropriate tools, already established for analysis of highly complex microarray data, need to be applied to protein profiling data. To validate the significance of any candidate biomarker derived from pilot studies in appropriately designed prospective multi-center studies is mandatory; reproducibility of the clinical results must be shown over time and in different diagnostic settings. SELDI-TOF-MS-based studies that are in compliance with these requirements are now required; only a few have been published so far. In the meantime, further evaluation and optimization of both technique and marker validation strategies are called for before MS-based proteomic algorithms can be translated into routine laboratory testing.Clin Chem Lab Med 2007;45:1435–49.

scholarly journals Impact of Freeze-thaw Cycles and Storage Time on Plasma Samples Used in Mass Spectrometry Based Biomarker Discovery Projects

2005 ◽  
Vol 1 ◽  
pp. 117693510500100 ◽  
Author(s):  
Breeana L Mitchell ◽  
Yutaka Yasui ◽  
Christopher I Li ◽  
Annette L. Fitzpatrick ◽  
Paul D Lampe
Keyword(s):  
Mass Spectrometry ◽  
Biomarker Discovery ◽  
Plasma Proteome ◽  
Sample Handling ◽  
Freeze Thaw ◽  
Long Term Storage ◽  
And Storage ◽  
Human Fluids ◽  
Term Storage

Mass spectrometry approaches to biomarker discovery in human fluids have received a great deal of attention in recent years. While mass spectrometry instrumentation and analysis approaches have been widely investigated, little attention has been paid to how sample handling can impact the plasma proteome and therefore influence biomarker discovery. We have investigated the effects of two main aspects of sample handling on MALDI-TOF data: repeated freeze-thaw cycles and the effects of long-term storage of plasma at –70°C. Repeated freeze-thaw cycles resulted in a trend towards increasing changes in peak intensity, particularly after two thaws. However, a 4-year difference in long-term storage appears to have minimal effect on protein in plasma as no differences in peak number, mass distribution, or coefficient of variation were found between samples. Therefore, limiting freeze/thaw cycles seems more important to maintaining the integrity of the plasma proteome than degradation caused by long-term storage at –70°C.

The SELDI-TOF MS Approach to Proteomics: Protein Profiling and Biomarker Identification

2002 ◽  
Vol 292 (3) ◽  
pp. 587-592 ◽  
Author(s):  
Haleem J. Issaq ◽  
Timothy D. Veenstra ◽  
Thomas P. Conrads ◽  
Donna Felschow
Keyword(s):  
Protein Profiling ◽  
Biomarker Identification ◽  
Tof Ms

Nanostructured Affinity Surfaces for MALDI-TOF-MS–Based Protein Profiling and Biomarker Discovery

2009 ◽  
pp. 421-456
Author(s):  
R. M. Vallant ◽  
M. Rainer ◽  
M. Najam-Ul-Haq ◽  
R. Bakry ◽  
C. Petter ◽  
...  
Keyword(s):  
Biomarker Discovery ◽  
Protein Profiling ◽  
Maldi Tof Ms ◽  
Maldi Tof ◽  
Tof Ms

Recognition Pattern, Functional Mechanism and Application of Chitin and Chitosan Oligosaccharides in Sustainable Agriculture

2020 ◽  
Vol 26 (29) ◽  
pp. 3508-3521 ◽  
Author(s):  
Xiaochen Jia ◽  
Mijanur R. Rajib ◽  
Heng Yin
Keyword(s):  
Agricultural Production ◽  
Growth And Yield ◽  
Biotic Stresses ◽  
The Past ◽  
Chitosan Oligosaccharides ◽  
Recognition Pattern ◽  
Functional Mechanism ◽  
Chitin And Chitosan ◽  
And Storage ◽  
Further Development

Background: Application of chitin attracts much attention in the past decades as the second abundant polysaccharides in the world after cellulose. Chitin oligosaccharides (CTOS) and its deacetylated derivative chitosan oligosaccharides (COS) were shown great potentiality in agriculture by enhancing plant resistance to abiotic or biotic stresses, promoting plant growth and yield, improving fruits quality and storage, etc. Those applications have already served huge economic and social benefits for many years. However, the recognition mode and functional mechanism of CTOS and COS on plants have gradually revealed just in recent years. Objective: Recognition pattern and functional mechanism of CTOS and COS in plant together with application status of COS in agricultural production will be well described in this review. By which we wish to promote further development and application of CTOS and COS–related products in the field.

Nanotechnology Based Delivery Systems of Drugs Currently Used to Treat Alzheimer’s Disease

2020 ◽  
Vol 10 (3) ◽  
pp. 228-247
Author(s):  
Niloufar Choubdar ◽  
Sara Avizheh
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Polymeric Nanoparticles ◽  
Biological Fluids ◽  
Delivery Systems ◽  
Original Research ◽  
Sustained Drug Release ◽  
The Past ◽  
Site Of Action ◽  
Therapeutic Compound

Alzheimer’s Disease (AD) is one of the most common forms of dementia affecting over 46 million people, according to AD International. Over the past few decades, there has been considerable interest in developing nanomedicines. Using nanocarriers, the therapeutic compound could be delivered to the site of action where it gets accumulated. This accumulation, therefore, reduces the required doses for therapy. Alternatively, using nanocarriers decreases the side effects. Nanotechnology has had a great contribution in developing Drug Delivery Systems (DDS). These DDS could function as reservoirs for sustained drug release or control the pharmacokinetics and biodistribution of the drugs. In the current review, we have collected 38 original research articles using nanotechnology as DDS for the clinically used cholinesterase inhibitor drugs donepezil (DPZ), Rivastigmine (Riv), and galantamine (Gal) used for AD treatment from 2002 to 2017 from Scopus and PubMed databases. Regarding DDS used for DPZ, most of the research in recent years dealt with polymeric nanoparticles (NPs) including Poly-D, L-Lactide-Co-Glycolide (PLGA), and chitosans (CHs), then Liposomes (LPs), nanogels, and natural products, respectively. In terms of Riv most of the research performed was focused on polymeric NPs including PLGA, polylactic acid (PLA), Poly-Ε-Caprolactone (PCL), poly-alkyl-cyanoacrylates, CH, gelatin and then LPs. The highest application of NPs in regard to Gal was related to modified LPs and polymeric NPs. Polymeric NPs demonstrate safety, higher stability in biological fluids and against enzymatic metabolism, biocompatibility, bioavailability, and improved encapsulation efficacy. LPs, another major delivery system used, demonstrate biocompatibility, ease of surface modification, and amphiphilic nature.

scholarly journals Metabolic Evaluation of Urine from Patients Diagnosed with High Grade (HG) Bladder Cancer by SPME-LC-MS Method

Molecules ◽  
2021 ◽  
Vol 26 (8) ◽  
pp. 2194
Author(s):  
Kamil Łuczykowski ◽  
Natalia Warmuzińska ◽  
Sylwia Operacz ◽  
Iga Stryjak ◽  
Joanna Bogusiewicz ◽  
...  
Keyword(s):  
Thin Film ◽  
Bladder Cancer ◽  
High Performance ◽  
Biomarker Discovery ◽  
Solid Phase ◽  
Biological Fluids ◽  
Reversed Phase ◽  
Control Group ◽  
Metabolic Evaluation ◽  
Metabolomic Profiling

Bladder cancer (BC) is a common malignancy of the urinary system and a leading cause of death worldwide. In this work, untargeted metabolomic profiling of biological fluids is presented as a non-invasive tool for bladder cancer biomarker discovery as a first step towards developing superior methods for detection, treatment, and prevention well as to further our current understanding of this disease. In this study, urine samples from 24 healthy volunteers and 24 BC patients were subjected to metabolomic profiling using high throughput solid-phase microextraction (SPME) in thin-film format and reversed-phase high-performance liquid chromatography coupled with a Q Exactive Focus Orbitrap mass spectrometer. The chemometric analysis enabled the selection of metabolites contributing to the observed separation of BC patients from the control group. Relevant differences were demonstrated for phenylalanine metabolism compounds, i.e., benzoic acid, hippuric acid, and 4-hydroxycinnamic acid. Furthermore, compounds involved in the metabolism of histidine, beta-alanine, and glycerophospholipids were also identified. Thin-film SPME can be efficiently used as an alternative approach to other traditional urine sample preparation methods, demonstrating the SPME technique as a simple and efficient tool for urinary metabolomics research. Moreover, this study’s results may support a better understanding of bladder cancer development and progression mechanisms.

scholarly journals Lung adenocarcinoma and lung squamous cell carcinoma cancer classification, biomarker identification, and gene expression analysis using overlapping feature selection methods

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Joe W. Chen ◽  
Joseph Dhahbi
Keyword(s):  
Gene Expression ◽  
Feature Selection ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Biomarker Discovery ◽  
Lung Squamous Cell Carcinoma ◽  
Cancer Classification ◽  
Selection Methods ◽  
Biomarker Identification ◽  
Overlapping Method

AbstractLung cancer is one of the deadliest cancers in the world. Two of the most common subtypes, lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), have drastically different biological signatures, yet they are often treated similarly and classified together as non-small cell lung cancer (NSCLC). LUAD and LUSC biomarkers are scarce, and their distinct biological mechanisms have yet to be elucidated. To detect biologically relevant markers, many studies have attempted to improve traditional machine learning algorithms or develop novel algorithms for biomarker discovery. However, few have used overlapping machine learning or feature selection methods for cancer classification, biomarker identification, or gene expression analysis. This study proposes to use overlapping traditional feature selection or feature reduction techniques for cancer classification and biomarker discovery. The genes selected by the overlapping method were then verified using random forest. The classification statistics of the overlapping method were compared to those of the traditional feature selection methods. The identified biomarkers were validated in an external dataset using AUC and ROC analysis. Gene expression analysis was then performed to further investigate biological differences between LUAD and LUSC. Overall, our method achieved classification results comparable to, if not better than, the traditional algorithms. It also identified multiple known biomarkers, and five potentially novel biomarkers with high discriminating values between LUAD and LUSC. Many of the biomarkers also exhibit significant prognostic potential, particularly in LUAD. Our study also unraveled distinct biological pathways between LUAD and LUSC.

scholarly journals Personal Carbon Trading—Lost in the Policy Primeval Soup?

2021 ◽  
Vol 13 (8) ◽  
pp. 4592
Author(s):  
Fabio Bothner
Keyword(s):  
Ghg Emissions ◽  
Emission Trading ◽  
Political Agenda ◽  
Carbon Trading ◽  
Multiple Streams ◽  
Policy Proposal ◽  
The Past ◽  
Multiple Streams Approach ◽  
Carbon Taxation ◽  
Set Up

The number of emission trading and carbon taxation schemes implemented has grown rapidly over the past decade. Together, they cover approximately 16% of global greenhouse gas (GHG) emissions. Although more than two-thirds of global GHG emissions are related to household consumption, approaches that directly target households, such as personal carbon trading (PCT), do not play a role in the fight against climate change. This is especially puzzling as measures taken so far are not sufficient to reach the 2 °C target. One clue to solving this puzzle comes from political science in the form of the multiple streams approach, which defines criteria that a policy proposal must meet to become part of the political agenda. Based on these criteria, this article conducts a systematic review on PCT to clarify why PCT does not play a role in the reduction of GHG emissions. The results show that there are three main problems with the PCT proposal. First, scholars often criticize the set-up costs as well as the running costs of such a system. Second, there is no clear consensus within the research community on public acceptance of PCT. Third, it is still unclear whether politicians are receptive to PCT or not.

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