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Current Pharmaceutical Design 2023Cancer is an ailment with having a very low survival rate globally. Poor cancer prognosis is primarily caused by the fact that people are found to have the disease when... (Review)
Review
BACKGROUND
Cancer is an ailment with having a very low survival rate globally. Poor cancer prognosis is primarily caused by the fact that people are found to have the disease when it is already well advanced. The goal of this study is to compile information on new avenues of investigation into biomarkers that may facilitate the routine detection of cancer. Proteomic analysis has recently developed into a crucial technique for cancer biology research, working in tandem with genomic analysis. Mass spectrometry techniques are one of several proteome analysis techniques that allow for the highly precise quantitative and qualitative recognition of hundreds of proteins in small quantities from various biological materials. These findings might soon serve as the foundation for better cancer diagnostic techniques.
METHODS
An exhaustive literature survey has been conducted using electronic databases such as Google Scholar, Science Direct, and PubMed with keywords of proteomics, applications of proteomics, the technology of proteomics, biomarkers, and patents related to biomarkers.
RESULT
Studies reported till 2021 focusing on cancer proteomics and the related patents have been included in the present review to obtain concrete findings, highlighting the applications of proteomics in cancer.
CONCLUSION
The present review aims to present the overview and insights into cancer proteomics, recent breakthroughs in proteomics techniques, and applications of proteomics with technological advancements, ranging from searching biomarkers to the characterization of molecular pathways, though the entire process is still in its infancy.
Topics: Humans; Proteomics; Biomarkers; Proteome; Neoplasms; Mass Spectrometry
PubMed: 36927422
DOI: 10.2174/1381612829666230316110932 -
In Vivo (Athens, Greece) 2017Despite the explosive increase in the use of Assisted Reproductive Technologies (ART) over the last 30 years, their success rates remain suboptimal. Proteomics is a... (Review)
Review
Despite the explosive increase in the use of Assisted Reproductive Technologies (ART) over the last 30 years, their success rates remain suboptimal. Proteomics is a rapidly-evolving technology-driven science that has already been widely applied in the exploration of human reproduction and fertility, providing useful insights into its physiology and leading to the identification of numerous proteins that may be potential biomarkers and/or treatment targets of a successful ART pregnancy. Here we present a brief overview of the techniques used in proteomic analyses and attempt a comprehensive presentation of recent data from mass spectrometry-based proteomic studies in humans, regarding all components of ARTs, including the male and female gamete, the derived zygote and embryo, the endometrium and, finally, the ART offspring both pre- and postnatally.
Topics: Animals; Biomarkers; Humans; Proteome; Proteomics; Reproduction; Reproductive Techniques, Assisted
PubMed: 28438852
DOI: 10.21873/invivo.11056 -
Proteomics Mar 2016Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions,... (Review)
Review
Lactobacillus are mainly used for the manufacture of fermented dairy, sourdough, meat, and vegetable foods or used as probiotics. Under optimal processing conditions, Lactobacillus strains contribute to food functionality through their enzyme portfolio and the release of metabolites. An extensive genomic diversity analysis was conducted to elucidate the core features of the genus Lactobacillus, and to provide a better comprehension of niche adaptation of the strains. However, proteomics is an indispensable "omics" science to elucidate the proteome diversity, and the mechanisms of regulation and adaptation of Lactobacillus strains. This review focuses on the novel and comprehensive knowledge of functional proteomics and metaproteomics of Lactobacillus species. A large list of proteomic case studies of different Lactobacillus species is provided to illustrate the adaptability of the main metabolic pathways (e.g., carbohydrate transport and metabolism, pyruvate metabolism, proteolytic system, amino acid metabolism, and protein synthesis) to various life conditions. These investigations have highlighted that lactobacilli modulate the level of a complex panel of proteins to growth/survive in different ecological niches. In addition to the general regulation and stress response, specific metabolic pathways can be switched on and off, modifying the behavior of the strains.
Topics: Bacterial Proteins; Lactobacillus; Metabolic Networks and Pathways; Proteome; Proteomics; Signal Transduction
PubMed: 27001126
DOI: 10.1002/pmic.201500117 -
Methods in Molecular Biology (Clifton,... 2023The plasma and serum proteome has enormous potential as a tool for understanding the health of a number of physiological systems. Despite this potential, the use of...
The plasma and serum proteome has enormous potential as a tool for understanding the health of a number of physiological systems. Despite this potential, the use of plasma and serum proteomics clinically and for research is limited, and there are no strict guidelines on how samples should be collected and prepared for proteomic analysis. Given the sensitivity of proteomic analysis, there are a number of pre-analytical variables that should be considered and determined prior to undertaking proteomics-based methodologies.In this chapter, we provide an example of a blood processing protocol and highlight major considerations for pre-analytical variables involving the collection, processing, and handling of blood samples for plasma and serum proteomics. We provide comprehensive notes on aspects of the protocol that must be considered before commencing sample collections for a proteomic study as well as a thorough checklist to be used when designing new proteomic studies.
Topics: Proteomics; Plasma; Specimen Handling; Serum; Proteome
PubMed: 36781777
DOI: 10.1007/978-1-0716-2978-9_3 -
Methods in Molecular Biology (Clifton,... 2022Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and...
Proteomics plays a pivotal role in systems medicine, in which pharmacoproteomics and toxicoproteomics have been developed to address questions related to efficacy and toxicity of drugs. Mass spectrometry is the core technology for quantitative proteomics, providing the capabilities of identification and quantitation of thousands of proteins. The technology has been applied to biomarker discovery and understanding the mechanisms of drug action. Both stable isotope labeling of proteins or peptides and label-free approaches have been incorporated with multidimensional LC separation and tandem mass spectrometry (LC-MS/MS) to increase the coverage and depth of proteome analysis. A protocol of such an approach exemplified by dimethyl labeling in combination with 2D-LC-MS/MS is described. With further development of novel proteomic tools and increase in sample throughput, the full spectrum of mass spectrometry-based proteomic research will greatly advance systems medicine.
Topics: Biomarkers; Chromatography, Liquid; Proteome; Proteomics; Tandem Mass Spectrometry
PubMed: 35437715
DOI: 10.1007/978-1-0716-2265-0_1 -
Methods in Molecular Biology (Clifton,... 2022Top-down proteomics methods have a distinct advantage over bottom-up methods in that they analyze intact proteins rather than digested peptides which can result in loss...
Top-down proteomics methods have a distinct advantage over bottom-up methods in that they analyze intact proteins rather than digested peptides which can result in loss of information regarding the intact protein. However, the analysis of intact proteins using top-down proteomics methods has been impeded by the low resolution of typical separation approaches applied in bottom-up proteomics studies. To increase the coverage of intact proteomes, orthogonal, two-dimensional separation techniques have been developed to improve the separation efficiency; in this chapter, we describe a two-dimensional HPLC separation technique that utilizes a high-pH mobile phase in the first dimension followed by a low-pH mobile phase in the second dimension. This two-dimensional pH-based HPLC approach demonstrates increased separation efficiency of intact proteins and increased proteome coverage when compared to one-dimensional HPLC in the analysis of larger and lower abundance proteoforms.
Topics: Chromatography, High Pressure Liquid; Peptides; Proteome; Proteomics; Tandem Mass Spectrometry
PubMed: 35657585
DOI: 10.1007/978-1-0716-2325-1_4 -
Current Opinion in Chemical Biology Feb 2015Advances in mass spectrometry (MS) have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple... (Review)
Review
Advances in mass spectrometry (MS) have transformed the scope and impact of protein characterization efforts. Identifying hundreds of proteins from rather simple biological matrices, such as yeast, was a daunting task just a few decades ago. Now, expression of more than half of the estimated ā¼20,000 human protein coding genes can be confirmed in record time and from minute sample quantities. Access to proteomic information at such unprecedented depths has been fueled by strides in every stage of the shotgun proteomics workflow-from sample processing to data analysis-and promises to revolutionize our understanding of the causes and consequences of proteome variation.
Topics: Humans; Mass Spectrometry; Peptides; Proteome; Proteomics
PubMed: 25461719
DOI: 10.1016/j.cbpa.2014.10.017 -
Briefings in Bioinformatics Jan 2023The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced...
The label-free quantification (LFQ) has emerged as an exceptional technique in proteomics owing to its broad proteome coverage, great dynamic ranges and enhanced analytical reproducibility. Due to the extreme difficulty lying in an in-depth quantification, the LFQ chains incorporating a variety of transformation, pretreatment and imputation methods are required and constructed. However, it remains challenging to determine the well-performing chain, owing to its strong dependence on the studied data and the diverse possibility of integrated chains. In this study, an R package EVALFQ was therefore constructed to enable a performance evaluation on >3000 LFQ chains. This package is unique in (a) automatically evaluating the performance using multiple criteria, (b) exploring the quantification accuracy based on spiking proteins and (c) discovering the well-performing chains by comprehensive assessment. All in all, because of its superiority in assessing from multiple perspectives and scanning among over 3000 chains, this package is expected to attract broad interests from the fields of proteomic quantification. The package is available at https://github.com/idrblab/EVALFQ.
Topics: Proteome; Proteomics; Reproducibility of Results
PubMed: 36403090
DOI: 10.1093/bib/bbac477 -
FEMS Microbiology Letters Sep 2014Endospores are metabolically dormant, multi-layered cellular structures formed by Gram-positive bacteria belonging to the genera Bacillus, Clostridium and related... (Review)
Review
Endospores are metabolically dormant, multi-layered cellular structures formed by Gram-positive bacteria belonging to the genera Bacillus, Clostridium and related organisms. Their external layers are composed of proteins which in part play a role in the resistance behaviour of spores to varied chemical and environmental assaults. Thus, protein analysis is of major interest in spore biology. Spore proteomic studies have been carried out previously but these studies have focused on the soluble coat protein fraction. Using gel-based techniques, protein identification and analysis were performed. Mass spectrometry-driven proteomics has opened new avenues to resolve in particular the insoluble part of the spore layer proteomes. Mass spectrometry-based qualitative and quantitative proteomics methods expand the knowledge about both the actual composition and the amount of proteins in their various layers. The techniques can also be used to study the integrity of the layers as well as spore biology in general. This notion is explored concisely in this mini-review.
Topics: Bacillus; Bacterial Proteins; Clostridium; Mass Spectrometry; Proteome; Proteomics; Spores, Bacterial
PubMed: 25110127
DOI: 10.1111/1574-6968.12568 -
Current Opinion in Chemical Biology Feb 2020Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational... (Review)
Review
Small molecule metabolites play important roles in regulating protein functions, which are acted through either covalent non-enzymatic post-translational modificationsĀ or non-covalent binding interactions. Chemical proteomic strategies can help delineate global landscapes of cellular protein-metabolite interactions and provide molecular insights about their mechanisms of action. In this review, we summarized the recent progress in developments and applications of chemoproteomic strategies to profile protein-metabolite interactions.
Topics: Animals; Humans; Metabolome; Metabolomics; Proteins; Proteome; Proteomics
PubMed: 31812894
DOI: 10.1016/j.cbpa.2019.11.003