Article
Biochemical Research Methods
Claudia Gaither, Robert Popp, Sophia P. Borchers, Kjartan Skarphedinsson, Finnur F. Eiriksson, Margret Thorsteinsdottir, Yassene Mohammed, Christoph H. Borchers
Summary: The study demonstrated that leaving a lyophilized peptide mixture at room temperature for up to 20 days does not affect the quantitative performance of mass spectrometry analysis, making it a feasible option for sample transportation. Most peptide concentrations showed minimal fluctuations across different time points, indicating the stability of the peptide mixture under the tested conditions.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Andrea Laguillo-Gomez, Enrique Calvo, Noa Martin-Cofreces, Marta Lozano-Prieto, Francisco Sanchez-Madrid, Jesus Vazquez
Summary: Open-search methods with prior knowledge improve identification performance of protein post-translational modifications by minimizing experimental errors and precursor mass assignation. The introduction of a novel approach enables the study of a wider variety of PTMs, including unknown or unexpected modifications.
JOURNAL OF PROTEOMICS
(2023)
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
Biochemistry & Molecular Biology
Floriane Pailleux, Pauline Maes, Michel Jaquinod, Justine Barthelon, Marion Darnaud, Claire Lacoste, Yves Vandenbrouck, Benoit Gilquin, Mathilde Louwagie, Anne-Marie Hesse, Alexandra Kraut, Jerome Garin, Vincent Leroy, Jean-Pierre Zarski, Christophe Bruley, Yohann Coute, Didier Samuel, Philippe Ichai, Jamila Faivre, Virginie Brun
Summary: By utilizing bioinformatics and proteomics, this study identified alcohol dehydrogenase 1B (ADH1B) as a potential blood biomarker for acetaminophen-induced acute liver injury (ALI). Serum ADH1B concentration increased significantly during the acute phase of the disease and returned to normal levels during recovery.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Medicine, General & Internal
Sarah R. Weber, Yuanjun Zhao, Christopher Gates, Jingqun Ma, Felipe da Veiga Leprevost, Venkatesha Basrur, Alexey I. Nesvizhskii, Thomas W. Gardner, Jeffrey M. Sundstrom
Summary: Vitreous fluid has emerged as a valuable medium for studying retinal diseases, with proteomic analysis providing insights into proliferative diabetic retinopathy. Despite the lack of standardized methodology, there have been numerous studies utilizing mass spectrometry for vitreous proteomic analysis. Moving forward, addressing common pitfalls and proposing next steps is crucial for advancing this field.
JOURNAL OF CLINICAL MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Paleerath Peerapen, Wanida Boonmark, Visith Thongboonkerd
Summary: In this study, the interacting complexes of the apical membrane (ApANXA1) and cytosolic (cyANXA1) forms of ANXA1 in renal epithelial cells under high-calcium condition were characterized using proteomic and bioinformatic approaches. The results showed that the interacting proteins had both common and unique characteristics and properties. This study provides insights into the biochemistry, functions, and pathophysiology of CaOx kidney stone formation induced by high-calcium condition.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Medicine, Research & Experimental
Ankit P. Jain, Janani Sambath, Gajanan Sathe, Irene A. George, Akhilesh Pandey, Erik W. Thompson, Prashant Kumar
Summary: This study developed a targeted proteomics method to accurately measure the abundance of EMT-associated proteins in cancer cell lines, and revealed discrepancies between proteomic and transcriptomic data. The study also found that changes in the EMT proteome may play a role in tumor transformation across different types of cancer.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Devon Kohler, Mateusz Staniak, Tsung-Heng Tsai, Ting Huang, Nicholas Shulman, Oliver M. Bernhardt, Brendan X. MacLean, Alexey I. Nesvizhskii, Lukas Reiter, Eduard Sabido, Meena Choi, Olga Vitek
Summary: The MSstats R-Bioconductor family of packages, particularly the new version MSstats v4.0, is widely used for statistical analyses of quantitative proteomic experiments. It provides improved usability, versatility, and accuracy of statistical methodology, as well as better memory use and computation speed. Empirical comparisons have demonstrated the stronger performance and better usability of MSstats v4.0 compared to existing methods.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Ranjeet S. Bhamber, Andris Jankevics, Eric W. Deutsch, Andrew R. Jones, Andrew W. Dowsey
Summary: The optimized HDF5 file format mzMLb enhances read/write speed and storage efficiency of mass spectrometry data, supporting future versions of mzML and providing easy implementation.
JOURNAL OF PROTEOME RESEARCH
(2021)
Review
Biochemical Research Methods
Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali
Summary: Accurate protein identification is crucial in proteomics, with mass spectrometry being the primary technique used. Understanding data generation and parameters used in computational tools is essential for proper protein identification. Bioinformatics and computational methodologies are also important for validating protein identification in proteomics.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biology
Matthias Fahrner, Melanie Christine Foll, Bjorn Andreas Gruning, Matthias Bernt, Hannes Rost, Oliver Schilling
Summary: The integration of an open-source DIA analysis suite in the web-based and user-friendly Galaxy framework, along with comprehensive training materials, enables a wide community of researchers to perform reproducible and transparent DIA data analysis.
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
Chemistry, Analytical
Jinyi Wu, Shuyi Huang, Lei Tan, Yuling Li, Xiaotong Wu, Yong Liang
Summary: The study suggests an alternative strategy for detecting dengue virus NS1 antigen in clinical serum samples using UHPLC-MS/MS and molecularly imprinted polymers, showing significant promise for early confirmation of infection.
ANALYTICAL CHEMISTRY
(2021)
Article
Polymer Science
Diana-Andreea Blaj, Mihaela Balan-Porcarasu, Brindusa Alina Petre, Valeria Harabagiu, Cristian Peptu
Summary: This paper explores the reaction kinetics and details of the synthesis of beta-cyclodextrin-oligolactide derivatives initiated by beta-cyclodextrin in D,L-lactide through MALDI MS analysis, comparing data with 1H NMR and studying the influence of solvents, revealing a faster reaction in specific solvents due to activation processes.
Article
Biochemical Research Methods
Lev Levitsky, Julia A. Bubis, Mikhail Gorshkov, Irina A. Tarasova
Summary: The study presents the new version of the AA_stat tool, which introduces several new features to aid in the interpretation of open database search results. Through these options, researchers can enhance the interpretation of open search results and demonstrate the utility of AA_stat in the analysis of various amino acid modifications.
JOURNAL OF PROTEOMICS
(2021)
Article
Biochemical Research Methods
Pieter Verschaffelt, James Collier, Alexander Botzki, Lennart Martens, Peter Dawyndt, Bart Mesuere
Summary: The Unipept Visualizations library is a JavaScript package that generates interactive visualizations of both hierarchical and non-hierarchical quantitative data, with support for different visualizations and utilizing the D3.js library.
Article
Biochemical Research Methods
Kay Schallert, Pieter Verschaffelt, Bart Mesuere, Dirk Benndorf, Lennart Martens, Tim Van den Bossche
Summary: In metaproteomics, the protein inference problem is more challenging than in single-species proteomics. To address this issue, we developed a tool called Pout2Prot, which converts Percolator output files into protein group output files that can be used with Prophane.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Multidisciplinary Sciences
Bart Van Puyvelde, Simon Daled, Sander Willems, Ralf Gabriels, Anne Gonzalez de Peredo, Karima Chaoui, Emmanuelle Mouton-Barbosa, David Bouyssie, Kurt Boonen, Christopher J. Hughes, Lee A. Gethings, Yasset Perez-Riverol, Nic Bloomfield, Stephen Tate, Odile Schiltz, Lennart Martens, Dieter Deforce, Maarten Dhaenens
Summary: In the past decade, there has been a revolution in liquid chromatography-mass spectrometry (LC-MS) based proteomics with the introduction of novel instruments and data acquisition methodologies. However, the lack of a benchmark experimental design hampers the development of algorithms to mine publicly available proteomics datasets. To address this, we present a comprehensive dataset acquired using different instrument platforms and data acquisition methods, allowing for algorithm development and performance assessment.
Article
Biochemical Research Methods
Pathmanaban Ramasamy, Elien Vandermarliere, Wim F. Vranken, Lennart Martens
Summary: Protein phosphorylation, the most common reversible post-translational modification of proteins, plays a key role in cellular processes. Using large-scale phospho-proteomics data, we analyze and characterize proteome-wide protein phosphorylation sites (P sites). Differentiating correctly observed P sites from false-positive sites, we explore the context of these P sites in terms of protein structure, solvent accessibility, structural transitions, disorder, and biophysical properties. We also investigate the relative prevalence of disease-linked mutations on and around P sites and assess the structural dynamics of P sites in their phosphorylated and unphosphorylated states. Reprocessing available proteomics experiments enables a more reliable understanding of proteome-wide P sites. Adding the structural context of proteins around P sites uncovers possible conformational switches upon phosphorylation, and by examining different biophysical contexts, we reveal the differential preference in protein dynamics at phosphorylated sites compared to nonphosphorylated counterparts.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Arthur Declercq, Robbin Bouwmeester, Aurelie Hirschler, Christine Carapito, Sven Degroeve, Lennart Martens, Ralf Gabriels
Summary: Immunopeptidomics aims to identify MHC-presented peptides on cells for anti-cancer vaccine development. However, existing data analysis pipelines have difficulty identifying nontryptic peptides. In this study, a retrained (MSPIP)-P-2 model improved predictions for both immuno-peptides and tryptic peptides. The integration of the new models with DeepLC and Percolator in MS(2)Rescore increased spectrum identification rate and unique identified peptides compared to standard Percolator rescoring, and outperformed current immunopeptide-specific identification approaches.
MOLECULAR & CELLULAR PROTEOMICS
(2022)
Article
Multidisciplinary Sciences
Rupert L. Mayer, Rein Verbeke, Caroline Asselman, Ilke Aernout, Adillah Gul, Denzel Eggermont, Katie Boucher, Fabien Thery, Teresa M. Maia, Hans Demol, Ralf Gabriels, Lennart Martens, Christophe Becavin, Stefaan C. De Smedt, Bart Vandekerckhove, Ine Lentacker, Francis Impens
Summary: The authors used immunopeptidomics to identify bacterial peptides presented on infected cells and identified antigens that provided protection in mice when used as mRNA vaccine.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Lien Provez, Bart Van Puyvelde, Laura Corveleyn, Nina Demeulemeester, Sigrid Verhelst, Beatrice Lintermans, Simon Daled, Juliette Roels, Lieven Clement, Lennart Martens, Dieter Deforce, Pieter Van Vlierberghe, Maarten Dhaenens
Summary: Omics studies are ideal for generating hypotheses on health and disease. While epigenomics focuses mainly on DNA methylation using sequencing technologies, the study of histone posttranslational modifications (hPTMs) using mass spectrometry is lagging behind. This article presents a comprehensive mass spectrometry-based preprocessed hPTM atlas, providing a valuable resource for exploring histone analysis and epidrug development.
Article
Chemistry, Analytical
Bart Van Puyvelde, Katleen Van Uytfanghe, Laurence Van Oudenhove, Ralf Gabriels, Tessa Van Royen, Arne Matthys, Morteza Razavi, Richard Yip, Terry Pearson, Nicolas Drouin, Jan Claereboudt, Dominic Foley, Robert Wardle, Kevin Wyndham, Thomas Hankemeier, Donald Jones, Xavier Saelens, Geert Martens, Christophe P. Stove, Dieter Deforce, Lennart Martens, Johannes P. C. Vissers, N. Leigh Anderson, Maarten Dhaenens
Summary: A new detection method called Cov2MS is developed using LC-MS and SISCAPA technology to enrich the nucleocapsid protein of SARS-CoV-2 in patient samples. This method shows high sensitivity and multiplexing capability, and can be used with various matrices. It is automatable and can process a large number of samples per day.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemical Research Methods
Elke Debrie, Milan Malfait, Ralf Gabriels, Arthur Declerq, Adriaan Sticker, Lennart Martens, Lieven Clement
Summary: Reliable peptide identification is crucial in MS-based proteomics, and the TDA method is widely used for estimating the FDR. However, the assumptions of TDA are often not verified in practice, which can result in poor FDR control and negatively impact downstream data analysis. To address this issue, the TargetDecoy package is introduced, providing necessary functionality to assess the quality and assumptions of TDA for a given set of PSMs.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: There are various output file formats from proteomics search engines, but the lack of standardized formats makes it difficult to process peptide-spectrum matches (PSMs) and PSM files downstream. This article presents psm_utils, a Python package that can handle various PSM file formats and provides a unified and user-friendly interface. It includes a Python API, a command line interface, and a web application for interconverting PSM files and retrieving basic PSM statistics.
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
Tine Claeys, Maxime Menu, Robbin Bouwmeester, Kris Gevaert, Lennart Martens
Summary: Using data from 183 public human data sets, a machine learning model was trained to identify tissue and cell-type specific protein patterns. The model achieved high accuracy in predicting tissues (98%) and cell types (99%) based on protein abundance. The results provide valuable insights into tissue-specific proteins and can be applied to various downstream applications.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemical Research Methods
Pieter Verschaffelt, Alessandro Tanca, Marcello Abbondio, Tim van den Bossche, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, Bart Mesuere
Summary: Unipept Desktop 2.0 is the latest version of the Unipept Desktop tool, which now supports the analysis of metaproteogenomics datasets. It allows for the automatic construction of targeted protein reference databases for improved taxonomic and functional resolution. By limiting the proteins in the database, (meta)proteogenomic analyses can also be performed with better control and privacy. A case study using human gut metaproteome dataset and matched 16S rRNA gene sequencing data is presented as a proof of concept.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Multidisciplinary Sciences
Tine Claeys, Tim van den Bossche, Yasset Perez-Riverol, Kris Gevaert, Juan Antonio Vizcaino, Lennart Martens
Summary: Public proteomics data often lack essential metadata, but lesSDRF provides a tool to simplify the process of metadata annotation and ensure that the data has lasting impact beyond its initial publication.
NATURE COMMUNICATIONS
(2023)
Article
Biochemical Research Methods
Ralf Gabriels, Arthur Declercq, Robbin Bouwmeester, Sven Degroeve, Lennart Martens
Summary: This study introduces a Python package called psm_utils, which can read and write various proteomics search engine output file formats and handle peptide-spectrum matches (PSMs) and PSM lists in a unified data structure. The package includes a Python API and command line interface, as well as a user-friendly web application for converting PSM files and retrieving basic PSM statistics.
JOURNAL OF PROTEOME RESEARCH
(2023)
