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
Environmental Sciences
Charlotte Mappa, Olivier Pible, Jean Armengaud, Beatrice Alpha-Bazin
Summary: The use of mass spectrometry for rapid identification of microorganisms has been expanding in recent years due to its efficiency. This methodology is crucial in combating bioterrorism by providing quick and versatile pathogen identification, including subtyping for confirmation of widespread attacks. The study presented a new methodology based on next-generation proteomics and tandem mass spectrometry to discover protein biomarkers for discriminating spores and vegetative cells, with a focus on Bacillus atrophaeus, a biowarfare simulant. The researchers proposed a global quantitative evaluation of discriminant biomarkers for these two groups based on normalized spectral abundance factors.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(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
Ophthalmology
Maite Lopez-Lopez, Uxia Regueiro, Susana Belen Bravo, Maria del Pilar Chantada-Vazquez, Carmen Pena, Elio Diez-Feijoo, Pablo Hervella, Isabel Lema
Summary: This study utilized a qualitative approach to explore the tear proteome of patients with keratoconus (KC), finding that the expression of certain proteins in tears of KC patients differed from the control group. These differences were linked to processes such as cell death, oxidative damage, and inflammation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2022)
Article
Microbiology
Charlotte Mappa, Beatrice Alpha-Bazin, Olivier Pible, Jean Armengaud
Summary: Shotgun proteomics is a promising alternative technique for identifying pathogens and characterizing their antimicrobial resistance genes. Proteotyping microorganisms through tandem mass spectrometry is expected to be essential in modern healthcare, and it also plays a crucial role in developing new biotechnological applications through culturomics. Phylopeptidomics is a new strategy that improves the quantification of microbial contributions by estimating phylogenetic distances and calculating the ratio of shared peptides. The study established the limit of detection for tandem mass spectrometry proteotyping and demonstrated the independence of bacterial identification by phylopeptidomics from their growth stage and the robustness of the method in the presence of additional bacteria.
Article
Chemistry, Medicinal
Md Abdus Shukur Imran, Monica Carrera, Sara Perez-Polo, Jaime Perez, Lorena Barros, Sonia Dios, Camino Gestal
Summary: The common octopus (Octopus vulgaris) is highly sought after for human consumption and has also been considered for aquaculture diversification. The octopus ink, a by-product in seafood processing, has been found to have antimicrobial and antioxidant properties. In this study, advanced proteomics techniques were used to create a reference dataset of peptides from octopus ink and investigate its bioactive potential. Various immune functioning proteins and bioactive peptides with potential health benefits, such as antimicrobial and antioxidant properties, were identified. These findings contribute to the development of pharmacological and functional food products.
Article
Engineering, Environmental
Montserrat Carrascal, Ester Sanchez-Jimenez, Jie Fang, Carlos Perez-Lopez, Antoni Ginebreda, Damia Barcelo, Joaquin Abian
Summary: A large-scale proteomics approach was used to investigate the protein composition of wastewater from 10 different municipalities in Catalonia. The study revealed that excreta from humans and residues from livestock were the main sources of proteins in wastewater. These findings provide new insights into wastewater proteomics and propose specific bioindicators for wastewater-based environmental monitoring.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2023)
Review
Biochemical Research Methods
Stephan Fuchs, Susanne Engelmann
Summary: Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry have greatly improved the detection and characterization of proteins with up to 100 amino acids. These proteins play crucial roles in cellular processes and their systematic identification and characterization have emerged as an important field of microbial research. This review provides an overview of strategies for predicting and identifying these proteins on a large scale, and discusses future developments in this field.
Article
Food Science & Technology
Bruna Cavecci-Mendonca, Karen Monique Luciano, Tauane Vaccas, Laudiceia Alves de Oliveira, Eloisa Fornaro Clemente, Bruno Cesar Rossini, Jose Cavalcante Souza Vieira, Luciana Curtolo de Barros, Ilka Biondi, Pedro de Magalhaes Padilha, Lucilene Delazari dos Santos
Summary: Snakebite envenoming, a neglected tropical disease, has been studied to understand the protein and metallic ion composition of Brazilian snake venoms. The findings provide insights for potential diagnostic device development.
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)
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
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
Jingrong Ma, Chuang Pan, Haiming Chen, Weijun Chen, Wenxue Chen, Ming Zhang, Qiuping Zhong
Summary: This study investigated the proteome of coconut meat using shotgun proteomics and protein-based bioinformatic analysis. A total of 1686 proteins were identified, including antioxidant proteins and globulins. Network analysis revealed the associations of globulins with Cupin and Oleosin sub-networks, and antioxidant proteins with glutathione metabolism and peroxisome sub-networks. The study also discovered that bioactive peptides, with antioxidant and emulsifying properties, can be obtained through in-silico digestion.
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
Biochemistry & Molecular Biology
Dany Dominguez-Perez, Daniela Almeida, Josef Wissing, Andre M. Machado, Lothar Jansch, Agostinho Antunes, Luis Filipe Castro, Vitor Vasconcelos, Alexandre Campos, Isabel Cunha
Summary: This study focused on the adhesive system of the stalked goose barnacle L. anatifera, identifying a variety of proteins including cement specific adhesive proteins, proteases, protease inhibitors, and other structural proteins. Through shotgun proteomic analysis, the researchers identified and quantified peptide sequences in the adhesive gland and cement, providing insight into the composition of the adhesive proteins. The study also identified unannotated proteins with similar properties to known CPs and demonstrated the importance of Principal Components Analysis in identifying non-conserved adhesive proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Cardiac & Cardiovascular Systems
J. Manuel Pioner, Xuan Guan, Jordan M. Klaiman, Alice W. Racca, Lil Pabon, Veronica Muskheli, Jesse Macadangdang, Cecilia Ferrantini, Michael R. Hoopmann, Robert L. Moritz, Deok-Ho Kim, Chiara Tesi, Corrado Poggesi, Charles E. Murry, Martin K. Childers, David L. Mack, Michael Regnier
CARDIOVASCULAR RESEARCH
(2020)
Article
Multidisciplinary Sciences
Matthew The, Lukas Kall
NATURE COMMUNICATIONS
(2020)
Article
Biochemical Research Methods
Kyle Lucke, Jake Pennington, Patrick Kreitzberg, Lukas Kall, Oliver Serang
Summary: Nonparametric statistical tests are essential in scientific experiments, but sorting becomes a bottleneck in computation. Selection and partitioning are usually performed on transformed statistical significance values due to the unknown threshold, necessitating data sorting. Layer-ordered heaps provide a solution by partially sorting values efficiently.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Vidur Kailash, Luis Mendoza, Robert L. Moritz, Michael R. Hoopmann
Summary: SPACEPro is a tool developed to evaluate the efficiency and reproducibility of protein cleavage in peptide samples, providing comprehensive information on sample processing to peptides at the PSM, peptide, and protein levels. It helps users understand the quality of sample processing efficiency and develop protocols for improvement with minimal effort.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Matthew The, Lukas Kall
Summary: Error estimation for differential protein quantification is challenging due to multiple error sources, but Triqler model combines them into one quantification error. The interface with MaxQuant allows quick reanalysis of processed data, showing superior performance in various data sets. Triqler and its interface are available as a Python module under Apache 2.0 license.
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Microbiology
David W. Cobb, Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, Vasant Muralidharan
Summary: The study revealed the essential role of Thioredoxin (Trx) superfamily proteins in the endoplasmic reticulum (ER) of Plasmodium falciparum for parasite survival. By identifying a small molecule inhibitor targeting the redox activities of Trx-domain proteins, the study provides a new direction for future antimalarial drug development.
Editorial Material
Biochemical Research Methods
Susan T. Weintraub, Michael R. Hoopmann, Magnus Palmblad
JOURNAL OF PROTEOME RESEARCH
(2021)
Article
Biochemical Research Methods
Magnus Palmblad, Sebastian Boecker, Sven Degroeve, Oliver Kohlbacher, Lukas Kall, William Stafford Noble, Mathias Wilhelm
Summary: This article discusses the specific guidelines for conducting and reporting machine learning in proteomics and metabolomics, emphasizing the importance of describing molecular structure, function, and physicochemical properties.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Deanna L. Plubell, Lukas Kall, Bobbie-Jo Webb-Robertson, Lisa M. Bramer, Ashley Ives, Neil L. Kelleher, Lloyd M. Smith, Thomas J. Montine, Christine C. Wu, Michael J. MacCoss
Summary: Traditional proteomics methods aggregate peptide quantities into protein groups, potentially overlooking important biological differences between different components. Therefore, it is necessary to reconsider the practice of aggregating protein values to a single quantity in order to capture the contributions of existing proteoforms.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Markus Ekvall, Patrick Truong, Wassim Gabriel, Mathias Wilhelm, Lukas Kall
Summary: Machine learning has long been essential in interpreting proteomics data from mass spectrometry. Recently, the Transformer model, successful in other fields of bioinformatics, has been applied with the convenience of transfer learning. In this study, a Transformer based on the TAPE model was implemented to predict MS2 intensities, outperforming the traditional recurrent neural network-based predictor Prosit.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Gustavo S. Jeuken, Nicholas P. Tobin, Lukas Kall
Summary: High throughput biology allows for the measurement of relative concentrations of biomolecules from tissue samples, but interpreting the resulting differences between samples remains a challenge. Pathway analysis provides a way to study these differences in terms of altered pathway activity. In this study, we demonstrate the use of a method for pathway-based survival analysis, using the METABRIC dataset. Our findings show that pathway activities can serve as better prognostic markers for survival than individual transcripts.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Patrick Truong, Matthew The, Lukas Kall
Summary: A common goal in quantitative shotgun proteomics experiments is to identify proteins that show differential abundance under specific experimental conditions. However, this is challenging as mass spectrometry analyzes protein fragments rather than intact proteins. In this study, we demonstrate that a Bayesian hierarchical probabilistic model called Triqler can be adapted for data-independent acquisition (DIA) data after making minor changes to account for missing values. Furthermore, we show that Triqler outperforms other state-of-the-art protein summarization tools when evaluated on DIA data.
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
Microbiology
Susana Martinez Arbas, Shaman Narayanasamy, Malte Herold, Laura A. Lebrun, Michael R. Hoopmann, Sujun Li, Tony J. Lam, Benoit J. Kunath, Nathan D. Hicks, Cindy M. Liu, Lance B. Price, Cedric C. Laczny, John D. Gillece, James M. Schupp, Paul S. Keim, Robert L. Moritz, Karoline Faust, Haixu Tang, Yuzhen Ye, Alexander Skupin, Patrick May, Emilie E. L. Muller, Paul Wilmes
Summary: The study found that CRISPR plays a more important role in defense against plasmids than phages, and the variability in plasmid abundance over time has a greater impact on community dynamics than phages. In addition, the enrichment of protospacers targeting genes involved in the transmission of iMGEs helps understand population fitness and devise control strategies.
NATURE MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Michael R. Hoopmann, Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David D. Shteynberg, Lingjie He, Bin Xia, Stoyan H. Stoychev, Gilbert S. Omenn, Susan T. Weintraub, Robert L. Moritz
JOURNAL OF PROTEOME RESEARCH
(2020)