Article
Chemistry, Analytical
Kenneth Ku, Connor Frey, Maor Arad, Golfam Ghafourifar
Summary: This study compares the digestion efficiency of different immobilized chymotrypsin preparations for bovine serum albumin. A novel immobilization reagent, triethoxysilylbutaraldehyde (TESB), is evaluated and found to provide higher sequence coverage in bottom-up proteomics than traditional immobilization or crosslinking reagents.
ANALYTICAL METHODS
(2022)
Article
Biochemical Research Methods
Ryan M. Riley, Sandra E. Spencer Miko, Ryan D. Morin, Gregg B. Morin, Gian Luca Negri
Summary: PeptideRanger is a tool that efficiently detects and quantifies low abundance proteins by identifying peptides with suitable physiochemical properties for mass spectrometry analysis. It is a flexible and extensively annotated R package that can be customized to prioritize and filter peptides based on selected properties.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Ryan M. Riley, Sandra E. Spencer Miko, Ryan D. Morin, Gregg B. Morin, Gian Luca Negri
Summary: Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins of clinical significance. However, their development is time-consuming and often requires costly libraries of synthetic peptides. To address this, we developed PeptideRanger, an R package that identifies peptides from proteins of interest with physiochemical properties suitable for mass spectrometry analysis.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Food Science & Technology
Kristen Clermont, Charles J. J. Graham, Steven W. W. Lloyd, Casey C. C. Grimm, Jennifer J. J. Randall, Christopher P. P. Mattison
Summary: Proteomic analyses were used to study the protein accumulation during pecan kernel development. Proteins were analyzed through gel-free and label-free mass spectrometry and 2-D gel electrophoresis. Specific proteins related to pecan allergens, histones, and different stages of development were identified. These findings provide a foundation for future research on identifying proteins associated with desirable traits in pecans.
Article
Biochemistry & Molecular Biology
Lona Zeneyedpour, Christoph Stingl, Johan M. Kros, Peter A. E. Sillevis Smitt, Theo M. Luider
Summary: We investigated the feasibility of detecting the presence of specific autoantibodies against potential tumor-associated peptide antigens by enriching these antibody-peptide complexes using Melon Gel resin and mass spectrometry. We successfully detected immunoreactivity against specific phospho-peptides in the plasma of high-grade glioma patients using this method.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Meletia Kallianta, Eftychia Pappa, Heleni Vastardis, Christos Rahiotis
Summary: Mass Spectrometry (MS) is a highly sensitive and universal analytical technique that has rapidly developed in recent decades. It has various applications in dentistry, including research on dental materials and agents, laboratory analysis of biospecimens, and real-time diagnostics in oral surgery and pathology. MS can provide valuable insights into the clinical behavior, toxicity, antimicrobial properties, and biomarkers of dental materials and agents. It is also effective in detecting biomarkers in saliva and providing a comprehensive understanding of cellular functions through metabolite analysis. Additionally, MS shows promising potential for surgical approaches to oral malignant disorders. Overall, MS has revolutionized dental research and has the potential to advance personalized dentistry.
Article
Chemistry, Analytical
Pelin Yildiz, Sureyya Ozcan
Summary: Recent advances in proteomics technologies have allowed for high-throughput analysis of thousands of proteins. In this study, the correlation between protein concentration and corresponding unique peptide responses was investigated under conventional proteolytic digestion conditions. The results indicate that reproducible peptide signals could be misleading in clinical studies and that peptide selection could significantly impact the protein level outcome. This study is the first to explore quantitative protein-peptide correlations in biological samples using all unique peptides representing the same protein, and it opens up a discussion on peptide-based proteomics.
Article
Biochemical Research Methods
Khushman Taunk, Debasish Paul, Raju Dabhi, Chanukuppa Venkatesh, Saikiran Jajula, Venkateshwarlu Naik, Anup Tamhankar, Tufan Naiya, Manas Kumar Santra, Srikanth Rapole
Summary: Proteins play a crucial role in modern biology, and the study of proteomics is important for understanding the protein content in biological samples. This study developed a simple single step method for efficient protein extraction, applicable to a wide range of biological samples.
Article
Biochemical Research Methods
Sebastian Dorl, Stephan Winkler, Karl Mechtler, Viktoria Dorfer
Summary: Spectral library search enables more sensitive peptide identification in tandem mass spectrometry experiments, but suffers from limited availability of high-quality libraries and the difficulty of creating decoy spectra for result validation. MS Ana is a new spectral library search engine that addresses these issues by allowing the use of curated or predicted libraries and providing robust false discovery control through its own decoy library generation algorithm. In benchmark tests, MS Ana outperformed database search, achieving 36% more spectrum matches and 4% more proteins identified in single-shot human cell-line data. The quality of result validation was demonstrated through tests on synthetic peptide pools, and the importance of library selection was highlighted by comparing the performance of different publicly available human spectral libraries.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Michael R. Lazear
Summary: Given the complexity and volume of proteomics data, efficient software tools for peptide identification and quantification are necessary. This work introduces Sage, a high-performance, open-source, and freely available proteomics pipeline, which matches the performance of state-of-the-art software tools while running significantly faster.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biology
Ahmed Helal, Davide Tagliazucchi
Summary: The study found that traditional Egyptian cheeses and several cheese varieties consumed worldwide contain bioactive peptides that have the ability to inhibit cardiovascular diseases and type-2 diabetes. Gouda cheese has the highest anti-hypertensive activity, while Edam cheese has the highest amount of peptides for preventing diabetic complications. It is recommended to consume moderate amounts of Gouda, Domiati, and Edam cheeses to lower blood pressure and protect cardiovascular health.
Article
Cell Biology
Matiss Ozols, Alexander Eckersley, Kieran T. Mellody, Venkatesh Mallikarjun, Stacey Warwood, Ronan O'Cualain, David Knight, Rachel E. B. Watson, Christopher E. M. Griffiths, Joe Swift, Michael J. Sherratt
Summary: Peptide location fingerprinting is a proteomic analysis technique that can identify structural modification-associated differences in complex biological samples, such as photoaged and intrinsically aged skin proteomes. This technique has the potential for discovering new biomarker candidates in various pathways, and has been demonstrated to be effective in identifying biomarkers in ageing tendon using published MS data sets.
Article
Chemistry, Applied
Simonetta Caira, Gabriella Pinto, Gianluca Picariello, Paola Vitaglione, Sabrina De Pascale, Andrea Scaloni, Francesco Addeo
Summary: A purification procedure followed by mass spectrometry analysis was used to identify milk-derived peptides in the plasma of healthy volunteers after consuming pasteurized milk. The study revealed individual variability in the presence of peptides from various bovine milk proteins, including caseins and beta-lactoglobulin. The potential bioactivity and immunogenicity of these peptides and their effects on human health require further investigation.
Review
Biochemistry & Molecular Biology
Ekaterina Mikhailovna Stakhneva, Evgeniia Vitalievna Striukova, Yulia Igorevna Ragino
Summary: Proteomic studies play a crucial role in investigating atherosclerotic cardiovascular diseases, identifying potential biomarkers, and offering novel diagnostic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Analytical
Joanna Kruszewska, Joanna Zajda, Magdalena Matczuk
Summary: With the growing interest in the biomedical applications of inorganic nanoparticles (NPs) in recent decades, there is a need for detailed characterization of bio-nano interactions, particularly the protein corona formed on NP surfaces. Analytical methods capable of identifying corona proteins are essential, and bottom-up proteomics is commonly used for this purpose. The experiment's sample preparation, including separation techniques and digestion methods, plays a crucial role in the identification process, with distinct protocols leading to different outcomes. Standardization of protein corona identification protocols is needed to prevent preferential detection of certain proteins with specific digestion procedures.