Article
Biochemistry & Molecular Biology
Diana Valeria Rossetti, Ilaria Inserra, Alessia Nestico, Federica Vincenzoni, Federica Iavarone, Irene Messana, Massimo Castagnola, Luca Massimi, Gianpiero Tamburrini, Massimo Caldarelli, Claudia Desiderio
Summary: The study aimed to explore the intact proteome of pediatric brain tumors of different WHO grades and localizations to understand the molecular mechanisms underlying the onset and progression of these pathologies. Proteomic analysis revealed statistically significant differences in protein/peptide levels between tumor histotypes, as well as the identification of naturally occurring fragments and post-translational modifications. This study contributes to elucidating the molecular profiles of the most common solid tumors affecting children.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Multidisciplinary Sciences
Lloyd M. Smith, Jeffrey N. Agar, Julia Chamot-Rooke, Paul O. Danis, Ying Ge, Joseph A. Loo, Ljiljana Pasa-Tolic, Yury O. Tsybin, Neil L. Kelleher
Summary: Understanding the structure and properties of proteins is crucial in deciphering biological functions. The concept of defining the human proteome as a reference set of proteoforms is proposed, with a call for improved technologies in a two-pronged strategy.
Review
Plant Sciences
Julia Mergner, Bernhard Kuster
Summary: Proteins play essential roles in cellular processes, and studying protein expression, interactions, and modifications is crucial for understanding the molecular mechanisms underlying plant phenotypes. Mass spectrometry technology allows for the global identification and quantification of thousands of proteins, revealing dynamic changes in the plant proteome.
ANNUAL REVIEW OF PLANT BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Lin Bai, Guojian Yang, Zhaoyu Qin, Jiacheng Lyu, Yunzhi Wang, Jinwen Feng, Mingwei Liu, Tongqing Gong, Xianju Li, Zhengyang Li, Jixi Li, Jun Qin, Wenjun Yang, Chen Ding
Summary: This study used a novel method to analyze the binding activity of transcription factors under DNA modifications and identified potential readers for 5fC-modified DNA. By quantifying the modified DNA-binding activity of 1039 TFs, it revealed the hierarchical networks between the transcriptional protein machinery and modified DNA.
Article
Chemistry, Analytical
Ayako Takemori, Philipp T. Kaulich, Liam Cassidy, Nobuaki Takemori, Andreas Tholey
Summary: The combination of liquid chromatography (LC) and gas-phase separation by field-asymmetric ion mobility spectrometry (FAIMS) is a powerful proteoform separation system for top-down proteomics. In this study, an in-depth top-down proteomics workflow, GeLC-FAIMS-MS, was presented, which utilized a molecular-weight-based proteome fractionation approach using SDS-poly-acrylamide gel electrophoresis. The authors optimized the MS parameters for each gel band and compensating voltage (CV) to improve the identification of proteoforms. They also developed a simple and cost-effective method, combining the PEPPI protocol with an AnExSP method, for stain and SDS removal. Results showed that this method was better suited for low-molecular-weight proteoforms, while a methanol-chloroform-water (MCW)-based protocol showed advantages for higher-molecular-weight proteoforms.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Jonathan G. Van Vranken, Jiaming Li, Dylan C. Mitchell, Jose Navarrete-Perea, Steven P. Gygi
Summary: Recent advances in mass spectrometry have enabled quantitative proteomics to become a powerful tool in drug discovery, with the development of solvent shift assays allowing for the establishment of target engagement and increased efficiency. Using this approach, specific targets of compounds with known mechanisms of action can be readily identified, and combining solvent proteome profiling with other methods can expand the screening capabilities for evidence of ligand binding in the proteome.
Review
Biochemistry & Molecular Biology
Yanmei Chen, Yi Wang, Jun Yang, Wenbin Zhou, Shaojun Dai
Summary: This paper reviews recent breakthroughs and strategies in unraveling the diversity of the plant proteome, focusing on the methods used to analyze posttranslational modifications (PTMs), protein localization, and the organization of proteins into functional modules. It also discusses PTM crosstalk, multiple PTMs temporally regulating protein life cycles, quantitative studies using MS to measure protein turnover rates, and future directions in the study of the plant proteome.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Mahya Bahmani, Angela Juhasz, Utpal Bose, Mitchell G. Nye-Wood, Malcolm Blundell, Crispin A. Howitt, Michelle L. Colgrave
Summary: In this study, the proteome profile of barley grain and malt samples was investigated using SWATH-MS proteomics. The results showed that the C-hordein-reduced lines had a more significant impact on proteome level changes during malting. Upregulated proteins in C-hordein-reduced lines were mainly involved in the tricarboxylic acid cycle and fatty acid peroxidation processes. Proteomics approaches in hordein-reduced barley lines after malting also revealed additional changes in the proteome driven by the genetic background. These findings provide valuable insights for barley breeders and maltsters to optimize gluten-free grains in malt products.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Oncology
Juliana Mueller Bark, Lucas Trevisan Franca de Lima, Xi Zhang, Daniel Broszczak, Paul J. Leo, Rosalind L. Jeffree, Benjamin Chua, Bryan W. Day, Chamindie Punyadeera
Summary: This study demonstrates the feasibility of isolating and characterizing small extracellular vesicles (EVs) from pre- and postoperative saliva samples from glioblastoma (GBM) patients for the first time. Preliminary findings encourage further large cohort validation studies on salivary small EVs to evaluate prognosis in GBM.
Article
Biochemical Research Methods
Laurent Gatto, Ruedi Aebersold, Juergen Cox, Vadim Demichev, Jason Derks, Edward Emmott, Alexander M. Franks, Alexander R. Ivanov, Ryan T. Kelly, Luke Khoury, Andrew Leduc, Michael J. MacCoss, Peter Nemes, David H. Perlman, Aleksandra A. Petelski, Christopher M. Rose, Erwin M. Schoof, Jennifer Van Eyk, Christophe Vanderaa, John R. R. Yates III, Nikolai Slavov
Summary: Analyzing proteins from single cells by tandem mass spectrometry (MS) has the potential to accurately quantify thousands of proteins across thousands of single cells. However, various factors affecting experimental design, sample preparation, data acquisition and analysis may undermine the accuracy and reproducibility of the results. Best practices, quality controls, and data-reporting recommendations are proposed to enhance the reliability of quantitative workflows for single-cell proteomics.
Article
Engineering, Biomedical
Amish Asthana, Riccardo Tamburrini, Deborah Chaimov, Carlo Gazia, Stephen J. Walker, Mark Van Dyke, Alice Tomei, Sandrine Lablanche, John Robertson, Emmanuel C. Opara, Shay Soker, Giuseppe Orlando
Summary: Interactions between pancreatic ECM and islet cells play a crucial role in islet physiology, and combining engineering approaches with mass spectrometry techniques can provide a more comprehensive analysis of the proteome for creating physiologically relevant pancreatic microenvironments.
Article
Cell Biology
Charles Banliat, Coline Mahe, Regis Lavigne, Emmanuelle Com, Charles Pineau, Valerie Labas, Benoit Guyonnet, Pascal Mermillod, Marie Saint-Dizier
Summary: A comprehensive study of proteome dynamics in non-rodent mammalian embryos developed in vivo was conducted. Proteomic changes in bovine embryos at different developmental stages were analyzed, and distinct patterns were observed. Proteins that increased in abundance during development were associated with RNA metabolism, protein translation, and ribosome biogenesis, while proteins that decreased in abundance were involved in Golgi vesicle transport and protein processing in endoplasmic reticulum. The results provide valuable insights into the molecular mechanisms underlying early embryo development.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Environmental Sciences
Benjamin Trotter, Magdalena Wilde, Julian Brehm, Evdokia Dafni, Arlinda Aliu, Georg J. Arnold, Thomas Froehlich, Christian Laforsch
Summary: Research on the effects of microplastics on freshwater organisms, particularly Daphnia, has shown that chronic exposure to polystyrene microplastics can lead to decreased body length and offspring numbers in Daphnia magna. Proteomic analysis revealed changes in protein abundance, including alterations in enzymes and important physiological pathways. This study highlights the potential impact of long-term exposure to microplastics on the fitness of aquatic organisms.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biochemical Research Methods
Sergio Ciordia, Gloria Alvarez-Sola, Maria Rullan, Jesus M. Urman, Matias A. Avila, Fernando J. Corrales
Summary: The analysis of biological fluids for disease-related proteins is an important field of research. However, challenges exist, especially in complex matrices like bile. A new procedure described in this study significantly improves protein recovery from rat bile, providing valuable resources for further understanding disease molecular markers.
JOURNAL OF PROTEOMICS
(2021)
Review
Biochemical Research Methods
Gilbert S. Omenn
Summary: The HUPO Human Proteome Project celebrates its 10th anniversary by achieving the milestone of confident detection of proteins from 90% of predicted protein-coding genes. This global project has influenced data-sharing, quality assurance, and issued stringent guidelines for detecting missing proteins. The project's impact is highlighted in special issues of Nature Communications and Journal of Proteome Research.
MOLECULAR & CELLULAR PROTEOMICS
(2021)
Article
Biochemical Research Methods
Anton Kalyuzhnyy, Patrick A. Eyers, Claire E. Eyers, Emily Bowler-Barnett, Maria J. Martin, Zhi Sun, Eric W. Deutsch, Andrew R. Jones
Summary: This study profiles the human phosphoproteome to estimate the false discovery rate of phosphosites and predict a more realistic count of true identifications. It highlights significant potential of false-positive data in phosphorylation databases and emphasizes the importance of quality control for such data.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Kerry A. Ramsbottom, Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaino, Eric W. Deutsch, Andrew R. Jones
Summary: Phosphoproteomic methods are used to identify and quantify phosphorylation sites on proteins. This study introduces the concept of scoring modifications on a decoy amino acid to estimate the global false localization rate (FLR) independently.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Xiyang Luo, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev Levitsky, Mark Ivanov, Julia A. Bubis, Ralf Gabriels, Henry Webel, Aniel Sanchez, Mingze Bai, Lukas Kall, Yasset Perez-Riverol
Summary: Spectrum clustering is a powerful strategy for minimizing redundant mass spectra and generating consensus spectra. This study evaluates the impact of the consensus spectrum generation step on downstream peptide identification and identifies the most reliable methods. The results provide valuable insights for future research in this field.
JOURNAL OF PROTEOME RESEARCH
(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
Tobias G. Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaino, Eric W. Deutsch
Summary: Data set acquisition and curation are challenging in machine learning, particularly for proteomics-based LC-MS data sets due to data reduction. ProteomicsML is introduced as an online resource for accessing proteomics-based data sets and tutorials. It simplifies data access and provides tutorials for interacting with advanced algorithms. ProteomicsML enables comparison of machine learning algorithms and offers introductory material for newcomers in the field. The platform is freely available at https://www.proteomicsml.org/, and contributions are welcome at https://github.com/ProteomicsML/ProteomicsML.
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
Biochemical Research Methods
Benjamin A. Neely, Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, Siegfried Gessulat, Lukas Kaell, Pawel Palczynski, Samuel H. Payne, Tobias Greisager Rehfeldt, Tobias Schmidt, Veit Schwaemmle, Julian Uszkoreit, Juan Antonio Vizcaino, Mathias Wilhelm, Magnus Palmblad
Summary: In recent years, machine learning has made significant progress in modeling mass spectrometry data for proteomics analysis. A workshop was conducted to evaluate and explore machine learning applications in multidimensional mass spectrometry-based proteomics analysis. The workshop helped identify knowledge gaps, define needs, and discuss the possibilities, challenges, and future opportunities. The summary of the discussions conveys excitement about the potential of machine learning in proteomics and aims to inspire future research.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Mukul K. Midha, Charu Kapil, Michal Maes, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, Robert L. Moritz
Summary: The efficient generation of peptide molecular ions by the electrospray source is the major contribution to ion detectability in liquid chromatography-driven mass spectrometry-based proteomics. The newly designed vacuum insulated probe heated electrospray ionization (VIP-HESI) source coupled with a Bruker timsTOF PRO mass spectrometer in microspray mode demonstrates superior performance. VIP-HESI significantly improves chromatography signals compared to electrospray ionization (ESI) and nanospray ionization, providing increased protein detection with higher quantitative precision and enhancing reproducibility of sample injection amounts.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Klaas J. van Wijk, Tami Leppert, Zhi Sun, Eric W. Deutsch
Summary: A recent paper in Science Advances suggests that intrachloroplast proteins in Arabidopsis can be polyubiquitinated and transferred to the cytosol for degradation, challenging the existing belief that chloroplast organelles lack polyubiquitination mechanisms. However, a reanalysis of the raw mass spectrometry data revealed discrepancies and issues with the results, including extensive artifactual modifications caused by the use of alkylating agent iodoacetamide. As a result, the conclusions regarding intra-chloroplast polyubiquitination cannot be supported by these data. Recommendations for future research are provided to avoid similar pitfalls.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Microbiology
Alan P. R. Lorenzetti, Ulrike Kusebauch, Livia S. Zaramela, Wei-Ju Wu, Joao P. P. de Almeida, Serdar Turkarslan, Adrian L. G. de Lomana, Jose V. Gomes-Filho, Ricardo Z. N. Vencio, Robert L. Moritz, Tie Koide, Nitin S. Baliga
Summary: In this study, we investigated the scale of post-transcriptional regulation in the halophilic archaeon Halobacterium salinarum NRC-1. Our integrated analysis revealed that a large number of protein-coding genes in the genome of this haloarchaeon are likely targeted by multiple mechanisms for post-transcriptional processing and regulation. Additionally, we found evidence for the conditional post-transcriptional regulation of a subset of genes involved in stressful environment acclimation. These findings provide valuable insights into the role of post-transcriptional regulation in environmental adaptation and are made available as an interactive atlas for further research.
Article
Plant Sciences
Klaas J. van Wijk, Stephane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, Eric W. Deutsch
Summary: This study investigates the impact of RNA editing on the protein accumulation of organelle-encoded proteins in Arabidopsis. It identifies the nonredundant set of protein identifiers and predicted editing sites, and determines the accumulation of edited and unedited proteoforms at the protein level. The results show that major RNA editing sites are required for stable protein accumulation.
Article
Multidisciplinary Sciences
Ulrike Kusebauch, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrian Lopez Garcia de Lomana, Nitin S. Baliga, Robert L. Moritz
Summary: Researchers have reported a comprehensive spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, which enables the measurement of a large fraction of its proteome. This library provides a valuable resource for confidently measuring and quantifying any protein of this archaeon.