Article
Chemistry, Analytical
Jiali Qiang, Zhimin Xu, Yunxia Li, Hongbin Wang, Yaoyang Zhang
Summary: Disulfide bonds play a crucial role in regulating protein oxidation status, structure, and stability. The CADI strategy efficiently identifies disulfide bonds in peptides, although it has limitations in achieving in-depth coverage in complex mammalian cell lysates.
ANALYTICAL CHEMISTRY
(2021)
Editorial Material
Urology & Nephrology
Xiao-juan Yu, Su-xia Wang
Summary: Cryoglobulinemia is a group of diseases characterized by circulating aberrant immunoglobulins, leading to cryoglobulinemic glomerulonephritis. The heterogeneity of cryoglobulinemias due to different types and changing etiologies contributes to the complexities in clinical manifestations and diagnostics.
KIDNEY INTERNATIONAL
(2022)
Article
Biochemistry & Molecular Biology
Le Chang, Bernhard Egger, Thomas Vetter, Doris Y. Tsao
Summary: Understanding how the brain represents complex objects is a central challenge in visual neuroscience. Studies on macaque face patch neurons have shown that they encode axes of a generative model for facial images, but a systematic comparison with other computational models is still lacking. Deep neural networks trained specifically on facial identification did not explain neural responses well due to factors like illumination.
Article
Computer Science, Artificial Intelligence
Peixin Li, Yuru Pei, Yicheng Zhong, Yuke Guo, Hongbin Zha
Summary: This paper presents a deep neural network-based coarse-to-fine framework for 3D face reconstruction and semantic annotation from noisy single-view depth images. The proposed approach leverages 3D morphable model regression and per-vertex geometry refinement to improve performance and enhance local details.
IET COMPUTER VISION
(2021)
Article
Food Science & Technology
Kiana A. West, Robin Schmid, Julia M. Gauglitz, Mingxun Wang, Pieter C. Dorrestein
Summary: There is a growing interest in unraveling the chemical complexity of our diets. To aid in this, researchers have developed a search tool called foodMASST, which allows for the analysis of MS/MS spectra against a metabolomics food and beverage reference database. This tool has the potential to be valuable for nutrition research and the assessment of unique dietary biomarkers.
NPJ SCIENCE OF FOOD
(2022)
Article
Physics, Atomic, Molecular & Chemical
Kai-Fei Wang, Yu-Zhuo Wu, Hao Chi
Summary: This study addresses the challenges posed by large-scale databases in mass spectrometry-based metaproteomic and proteogenomic studies. The researchers developed a database reduction method, DBReducer, which effectively reduces the database, improves peptide identification accuracy and recall, and reduces time consumption. The results show that DBReducer has the potential to be widely used in proteomic analysis with large-scale databases.
INTERNATIONAL JOURNAL OF MASS SPECTROMETRY
(2023)
Review
Public, Environmental & Occupational Health
Rahaf Alturki, Maali Alharbi, Ftoon AlAnzi, Saleh Albahli
Summary: 2020 brought significant changes to people's lives worldwide due to the outbreak of COVID-19. Precautionary measures such as handwashing, social distancing, and mask wearing were implemented to reduce the spread of the disease. However, many people failed to properly adhere to the face mask rule.
FRONTIERS IN PUBLIC HEALTH
(2022)
Article
Multidisciplinary Sciences
Naser Faraji, Seyed Shahriar Arab, Alireza Doustmohammad, Norelle L. Daly, Ahmad Yari Khosroushahi
Summary: ApInAPDB is a database containing 818 apoptosis-inducing anticancer peptides, providing peptide-related information and structural information calculation and presentation. Users can search through three user-friendly tools. This is of great significance for research in peptide design and cancer therapy.
SCIENTIFIC REPORTS
(2022)
Article
Psychology, Multidisciplinary
Emily Brindal, Naomi Kakoschke, Andrew Reeson, David Evans
Summary: Understanding mass behaviors is crucial for tackling major societal events, such as the COVID-19 pandemic. Through case studies and mathematical models, this research reveals common characteristics of crowd behaviors and emphasizes the importance of Social Identity Theory, trust, social connection, and stress.
FRONTIERS IN PSYCHOLOGY
(2022)
Article
Neurosciences
Jeremy C. Simon, Jennifer N. Gutsell
Summary: Dehumanization affects our ability to neurally simulate, cooperate, and empathize with others. Individual differences in recognizing the humanity of people we interact with have been shown to have a direct impact on our neural processing and behavior in face-to-face interactions.
SOCIAL COGNITIVE AND AFFECTIVE NEUROSCIENCE
(2021)
Review
Computer Science, Interdisciplinary Applications
Sahil Sharma, Vijay Kumar
Summary: This paper thoroughly explores the topic of 3D face reconstruction, covering various techniques such as deep learning, epipolar geometry, one-shot learning, 3D morphable model, and shape from shading methods. It provides a performance analysis of different techniques and discusses the challenges and future scope of 3D face reconstruction.
ARCHIVES OF COMPUTATIONAL METHODS IN ENGINEERING
(2022)
Article
Computer Science, Artificial Intelligence
Usman Cheema, Seungbin Moon
Summary: This paper introduces a multi-modal disguised face dataset to facilitate research in disguised face recognition and performs qualitative and quantitative analysis to evaluate the challenging nature of disguise add-ons. The dataset will be publicly available.
COMPUTER VISION AND IMAGE UNDERSTANDING
(2021)
Article
Microbiology
Allister Irvine, Darrin Mckenzie, Ciaran J. McCoy, Robert L. J. Graham, Ciaren Graham, Sharon A. Huws, Louise E. Atkinson, Angela Mousley
Summary: In contrast to nematodes, flatworms do not possess traditional antimicrobial peptides (AMPs), but they have a unique repertoire of cysteine-rich AMP-like peptides. In addition, a computational prediction approach identified eight novel helminth AMP-like peptides with antibacterial activities.
Article
Biochemical Research Methods
Viswajit Mulpuru, Rahul Semwal, Pritish Kumar Varadwaj, Nidhi Mishra
Summary: This study aims to develop a database containing antimicrobial peptides from the human microbiome to combat drug-resistant strains. Through modeling the sequence and structure of 1087 unique AMPs, valuable information and visualization tools are provided for discovering novel antimicrobial drugs to fight drug-resistant bacteria.
CURRENT BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Jens Fritsche, Daniel J. Kowalewski, Linus Backert, Frederik Gwinner, Sonja Dorner, Martin Priemer, Chih-Chiang Tsou, Franziska Hoffgaard, Michael Romer, Heiko Schuster, Oliver Schoor, Toni Weinschenk
Summary: Knowledge about the peptide repertoire presented by human leukocyte antigens (HLA) is crucial for unlocking target-specific cancer immunotherapies, but with increasing immunopeptidomics datasets, the risk of misidentification and false annotation of HLA ligands is rising. This study introduces computational and experimental methods to identify fake ligands and emphasizes the importance of system suitability and detection of source fragmentation events. By focusing on high-throughput sequence verification and quality control, the study aims to uncover limitations and pitfalls in existing datasets to identify true HLA ligands.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Endocrinology & Metabolism
Kiara Boodhoo, Mare Vlok, David L. Tabb, Kathryn H. Myburgh, Mari van de Vyver
Summary: This study showed that chronic wounds in obese diabetic individuals have delayed healing processes and dysregulated protein expression compared to acute wounds. Early intervention in the healing process may be crucial for effective outcomes.
JOURNAL OF MOLECULAR ENDOCRINOLOGY
(2021)
Article
Astronomy & Astrophysics
S. W. Ndiritu, A. M. M. Scaife, D. L. Tabb, M. Carcamo, J. Hanson
Summary: The incomplete sampling of data in complex polarization measurements negatively affects RM transfer function and Faraday depth spectra. The novel method presented in this paper, based on Gaussian processes, improves the resolution of reconstructed Faraday depth spectra by inferring missing polarization data.
MONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY
(2021)
Article
Biochemical Research Methods
Damien B. Wilburn, Alicia L. Richards, Danielle L. Swaney, Brian C. Searle
Summary: Library searching is a powerful technique for detecting peptides, and the authors have developed a software tool CIDer to convert libraries between HCD and CID fragmentation methods. Using simple linear models and basic principles of peptide fragmentation, they can explain up to 43% of the variation between ions fragmented by HCD and CID. They also found that in some cases, searching converted CID libraries can detect more peptides.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Neurosciences
F. A. Concepcion, M. N. Khan, J-D Ju Wang, A. D. Wei, J. G. Ojemann, A. L. Ko, Y. Shi, J. K. Eng, J-M Ramirez, N. P. Poolos
Summary: Phosphorylation changes occur at individual HCN channel amino acid residues during epileptogenesis, leading to altered HCN1 channel phosphorylation in epilepsy. The novel phosphosite S791 may be of pathogenic importance in epilepsy.
Article
Plant Sciences
Ashwil Klein, Lizex H. H. Husselmann, Achmat Williams, Liam Bell, Bret Cooper, Brent Ragar, David L. Tabb
Summary: Proteomics has been more valuable in model organisms with genome sequence annotations than in nonmodel organisms lacking such annotations. This study aimed to establish a protein sequence set for the nonmodel organism chia using RNA-Seq experiments. The results showed that assembling RNA-Seq datasets for chia resulted in high completeness of transcript sequences, though the number of sequences and genes varied. After six-frame translation, orthologs were detected among other species within the same taxonomic order.
Article
Virology
Brian McEllin, Brian C. Searle, Lisa DePledge, George Sun, Charles Cobbs, Mohsen Karimi
Summary: HPV-positive head and neck squamous cell carcinoma (HNSCC) can metastasize to rare sites such as the brain, with specific risk factors for this phenotype needing further study. Analysis of tumors from two patients revealed HPV genome integration into host genome at known hotspots, providing potential targets for future research on biomarkers for metastasis prediction and novel therapeutic options.
Article
Chemistry, Analytical
Ian R. Smith, Jimmy K. Eng, Anthony S. Barente, Alexander Hogrebe, Ariadna Llovet, Ricard A. Rodriguez-Mias, Judit Villen
Summary: Stable-isotope labeling with amino acids in cell culture (SILAC)-based metabolic labeling is a widely used proteomics approach for quantitative comparisons. In this study, a new strategy was developed to coisolate and fragment SILAC peptide pairs for relative quantification. The modified database search engine and developed tool facilitated the analysis and quantification of SILAC peptide pairs. The coisolation approach improved the expectation scores and achieved more quantifications compared to traditional methods.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Eric W. Deutsch, Juan Antonio Vizcaino, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, Yasset Perez-Riverol, David L. Tabb, Mathias Walzer, Sylvie Ricard-Blum, Henning Hermjakob, Steffen Neumann, Tytus D. Mak, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, Nuno Bandeira, Jeremy Carver, Benjamin Pullman, Zhi Sun, Nils Hoffmann, Jim Shofstahl, Yunping Zhu, Luana Licata, Federica Quaglia, Silvio C. E. Tosatto, Sandra E. Orchard
Summary: The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been developing guidelines and standards for the proteomics community for 20 years. The organization describes its operation, the current state of existing standards, and the proposals currently being developed. They emphasize the importance of community participation and collaboration with other organizations to promote data sharing and accelerate progress in proteomics.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Attila Kertesz-Farkas, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles Grant, Michael R. Hoopmann, Andy Lin, Yang Y. Lu, Robert L. Moritz, Michael J. MacCoss, William Stafford Noble
Summary: The Crux tandem mass spectrometry data analysis toolkit is a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Although many publications have described the individual components of Crux, a comprehensive summary has not been published since 2014. The goal of this work is to provide a summary of Crux's functionality, focusing on developments since 2014. Recent developments include speed improvements to the Tide search engine, a new score function, two new confidence estimation procedures, and three new tools.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Eric W. Deutsch, Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, Robert L. Moritz
Summary: The Trans-Proteomic Pipeline (TPP) mass spectrometry data analysis suite has undergone continuous development and refinement since the publication of its first tools, PeptideProphet and ProteinProphet, 20 years ago. The latest release offers a wide range of tools for spectrum processing, spectrum searching, search validation, abundance computation, protein inference, and more. These tools incorporate machine-learning modeling to maximize information extraction and establish robust statistical models for accurate information derivation. This article presents an overview of the latest TPP tools, their deployment on different platforms, tutorials for their usage, and synergistic projects leveraging TPP. The article concludes with outlined plans for future TPP development.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Oncology
Noor Jailkhani, Karl R. Clauser, Howard H. Mak, Steffen Rickelt, Chenxi Tian, Charles A. Whittaker, Kenneth K. Tanabe, Stephen R. Purdy, Steven A. Carr, Richard O. Hynes
Summary: Metastases, which are difficult to detect and treat, are the leading cause of cancer-related deaths. There is a clinical need for therapies specifically targeting metastases. This study focuses on developing nanobodies against extracellular matrix (ECM) proteins expressed in human metastases as potential vehicles for targeted delivery of imaging and therapeutic agents. By using phage-display libraries and proteomics, the researchers identified a conserved set of ECM proteins that are abundantly expressed in metastases from TNBC and colorectal cancer. They successfully isolated nanobodies against one of these proteins, tenascin-C (TNC), and demonstrated their specificity in binding TNBC tumors and metastases. The study suggests that generic nanobodies against tumors and metastases have great potential as cancer-agnostic tools for delivering therapeutics to the tumor microenvironment.
Article
Biochemical Research Methods
David L. Tabb, Kyowon Jeong, Karen Druart, Megan S. Gant, Kyle A. Brown, Carrie Nicora, Mowei Zhou, Sneha Couvillion, Ernesto Nakayasu, Janet E. Williams, Haley K. Peterson, Michelle K. McGuire, Mark A. McGuire, Thomas O. Metz, Julia Chamot-Rooke
Summary: This study evaluates four top algorithms for top-down identification in their yield of PrSMs while controlling false discovery rate. The study finds that these algorithms perform well in generating PrSMs, but approximately half of the identified proteoforms are specific to only one algorithm. Deconvolution algorithms show inconsistency in precursor charges and mass determinations, contributing to identification variability. Detection of post-translational modifications is also inconsistent among algorithms. Applying multiple search engines provides more comprehensive assessments of experiments, and there is a need for greater interoperability of top-down algorithms.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Matthys J. Potgieter, Andrew J. M. M. Nel, Suereta Fortuin, Shaun Garnett, Jerome Wendoh, David Tabb, Nicola Mulder, Jonathan Blackburn
Summary: MetaNovo is an open-source software pipeline that integrates existing tools with a custom algorithm to produce targeted protein sequence databases for mass spectrometry metaproteomic analysis as an intermediate filtering step prior to standard sequence database search approaches. The software uses open-source tools to match peptide mass spectrometry spectra to sequence database entries and can be installed in a cluster or run standalone on a Linux machine. It is relevant for analyzing protein data from multiple organisms, where the exact species composition is unknown, and provides an avenue for analysis when accurate taxonomic characterization is not available.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Mathias Walzer, Kyowon Jeong, David L. Tabb, Juan Antonio Vizcaino
Summary: Although Top-down (TD) proteomics techniques are gaining popularity in intact protein and proteoform analysis, efforts are required to promote their adoption at different levels. Open science practices, including data sharing and open data analysis workflows, need to be improved and implemented.
Article
Biochemistry & Molecular Biology
Frederic Fischer, Egor Vorontsov, Evelyne Turlin, Christian Malosse, Camille Garcia, David L. Tabb, Julia Chamot-Rooke, Riccardo Percudani, Daniel Vinella, Hilde De Reuse
Summary: Acquisition and homeostasis of essential metals during host colonization by bacterial pathogens rely on metal uptake, trafficking, and storage proteins. How these factors have evolved within bacterial pathogens is poorly defined. In this study, the researchers analyzed histidine-rich proteins (HRPs) among 39 Epsilonproteobacteria to investigate their role in gastric colonization by Helicobacter spp. They found that gastric Helicobacter spp. have an expanded repertoire of HRPs, particularly those with C-terminal histidine-rich domains, which may be associated with the presence of the essential nickel enzyme urease. This HRP expansion is believed to be associated with the unique properties of these organisms that require large amounts of intracellular nickel for survival.
