27 papers · ranked by Valyu relevance
Jacques Colinge, Keiryn L Bennett, Fran Lewitter
Proteomics is defined as the protein complement of the genome and involves the complete analysis of all the proteins in a given sample . Several technologies are involved, and numerous questions concerning the proteins are addressed. What proteins are contained in a biological sample? At what concentration do the…
Lukas Käll, Olga Vitek, Fran Lewitter
Despite the challenges, mass spectrometry-based proteomics continues to bring high promise for basic science and clinical research . Several studies recently demonstrated that with appropriate care and training, it is now possible to accurately and reproducibly identify and quantify proteins across laboratories and…
Lotta J. Happonen, Markku Varjosalo
Structural proteomics has undergone a profound transformation, driven by the convergence of advanced experimental methodologies and computational innovations. Cutting-edge mass spectrometry (MS)-based approaches, including cross-linking MS (XL-MS), hydrogen-deuterium exchange MS (HDX-MS), and limited proteolysis MS…
Maggie P. Y. Lam, Edward Lau, Dominic C. M. Ng, Ding Wang + 1 more
'Peipei Ping'] Proteomics plays an increasingly important role in our quest to understand cardiovascular biology. Fueled by analytical and computational advances in the past decade, proteomics applications can now go beyond merely inventorying protein species, and address sophisticated questions on cardiac physiology.…
Anna Marabotti, Paolo Romano, Angelo Facchiano
The variety of topics covered in the articles present in the Research Topic (and even more in the contributions presented during the meeting) confirms the vast possibility of application of computational methods in proteomics. The panel discussion in the Conference Program highlighted the importance of making…
Jan Rudolph, Jürgen Cox
Proteomics data analysis strongly benefits from not studying single proteins in isolation but taking their multivariate interdependence into account. We introduce PerseusNet, the new Perseus network module for the biological analysis of proteomics data. Proteomics is commonly used to generate networks, e.g. with…
Authors not listed
Mass spectrometry (MS) is a cornerstone technology in modern molecular biology, powering diverse applications across proteomics, metabolomics, lipidomics, glycomics, and beyond. As the field continues to evolve, rapid advancements in instrumentation, acquisition strategies, machine learning, and scalable computing have…
Mamoun Ahram, Emanuel F. Petricoin
Recent technological developments in proteomics have shown promising initiatives in identifying novel biomarkers of various diseases. Such technologies are capable of investigating multiple samples and generating large amount of data end-points. Examples of two promising proteomics technologies are mass spectrometry…
Yasset Perez-Riverol, Pablo Moreno
The recent improvements in mass spectrometry instruments and new analytical methods are increasing the intersection between proteomics and big data science. In addition, the bioinformatics analysis is becoming an increasingly complex and convoluted process involving multiple algorithms and tools. A wide variety of…
Authors not listed
Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms…
Zhiqiang Gao, Cheng Chang, Yunping Zhu, Yan Fu
The selection of proteotypic peptides, i.e., detectable unique representatives of proteins of interest, is a key step in targeted shotgun proteomics. To date, much effort has been made to understand the mechanisms underlying peptide detection via mass spectrometry (MS) and to predict proteotypic peptides in the absence…
Amol Prakash, Shadab Ahmad, Swetaketu Majumder, Conor Jenkins + 1 more
The standard platform for proteomics experiments today is mass spectrometry, particularly for samples derived from complex matrices. Recent increases in mass spectrometry sequencing speed, sensitivity and resolution now permit comprehensive coverage of even the most precious and limited samples, particularly when…
Yuming Jiang, Rex Devasahayam Arokia Balaya, Dina Schuster, Benjamin A. Neely + 15 more
'Benjamin A. Neely' 'Germán L. Rosano' 'Norbert Volkmar' 'Amanda Momenzadeh' 'Trenton M. Peters-Clarke' 'Susan Egbert' 'Simion Kreimer' 'Emma H. Doud' 'Oliver M. Crook' 'Amit Kumar Yadav' 'Muralidharan Vanuopadath' 'Martín L. Mayta' 'Anna G. Duboff' 'Nicholas M. Riley' 'Robert L. Moritz' 'Jesse G. Meyer'] Proteomics is…
Matthew Waas, Jack Littrell, Rebekah L. Gundry
Cell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry…
Tobias Rehfeldt, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat + 6 more
Dataset acquisition and curation are often the hardest and most time-consuming parts of a machine learning endeavor. This is especially true for proteomics-based LC-IM-MS datasets, due to the high-throughput data structure with high levels of noise and complexity between raw and machine learning-ready formats. While…
Conor Jenkins, Alexis L. Norris, Maura O’Neill, Sudipto Das + 2 more
Isobaric labeling-based relative quantification techniques such as iTRAQ and TMT were introduced 15 years ago and are now nearly ubiquitous in shotgun proteomics labs around the world. The methods for data processing in these experiments has changed little since inception, with peptide database searching of all MS/MS…
Sugandima Vidanagamachchi, S. D. Dewasurendra, Roshan Ragel, Mahesan Niranjan
'Mahesan Niranjan'] Abstract—The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing throughputs, rapid processing rates and reliability of…
Fettah Erdogan, Raiyan Chowdhury, Serap Beldar, Tom Bobby Chandy + 3 more
The landscape of drug discovery is undergoing a transformative phase with the influx of structural biology and omics data. Identifying optimal drug targets amid this data surge presents a multifaceted challenge. Covalent inhibitors, once undervalued, now hold substantial promise, especially targeted covalent inhibitors…
Sugandima Vidanagamachchi, S. D. Dewasurendra, Roshan Ragel, Mahesan Niranjan
'Mahesan Niranjan'] Abstract— The problem of inferring proteins from complex peptide samples in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing throughputs, rapid processing rates and reliability of results. This is exacerbated by the fact that…
Wajdi Dhifli, Abdoulaye Baniré Diallo
Motivation: Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a protein structure remains a difficult, costly, and time consuming…
Christophe Vanderaa, Laurent Gatto
Sound data analysis is essential to retrieve meaningful biological information from singlecell proteomics experiments. This analysis is carried out by computational methods that are assembled into workflows, and their implementations influence the conclusions that can be drawn from the data. In this work, we explore…
Authors not listed
The rapid advancements in computational methods have revolutionized drug discovery and development. These methods, ranging from molecular modelling to machine learning algorithms, have drastically increased in number and sophistication. However, a comprehensive understanding of these diverse approaches is essential for…
Edgar López-López, Oscar Robles, Fabien Plisson, José L. Medina-Franco
Peptides are a re-emerged strategy to fight a plethora of diseases and their utility has been expanded to new areas. Now sequence-based peptide design opens up new possibilities to develop peptidic molecular entities. However, its methodological limitations (e.g., its inefficiency in designing large peptides and that…
Mahmood A. Rashid, Firas Khatib, Abdul Sattar
—Protein structure prediction is a challenging and unsolved problem in computer science. Proteins are the sequence of amino acids connected together by single peptide bond. The combinations of the twenty primary amino acids are the constituents of all proteins. In-vitro laboratory methods used in this problem are very…
Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones, Pierre-Alain Binz + 25 more
The Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) has been successfully developing guidelines, data formats, and controlled vocabularies (CVs) for the proteomics community and other fields supported by mass spectrometry since its inception twenty years ago. Here we describe the general…
Samuel Hoff, Maximilian Zinke, Nadia Izadi‐Pruneyre, Massimiliano Bonomi
'Massimiliano Bonomi'] Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of Structural Biology, no single method comprehensively reveals the behavior of biological systems…
Rodrigo Ochoa
The in silico design of peptides and proteins as binders is useful for diagnosis and therapeutics due to their low adverse effects and major specificity. To select the most promising candidates, a key matter is to understand their interactions with protein targets. In this work, we present PARCE, an open source…