26 papers · ranked by Valyu relevance
Cosette Abdallah, Eliane Dumas-Gaudot, Jenny Renaut, Kjell Sergeant
Two-dimensional gel electrophoresis (2-DE) is widely applied and remains the method of choice in proteomics; however, pervasive 2-DE-related concerns undermine its prospects as a dominant separation technique in proteome research. Consequently, the state-of-the-art shotgun techniques are slowly taking over and…
Jakob Vowinckel, Floriana Capuano, Kate Campbell, Michael J. Deery + 2 more
The combination of qualitative analysis with label-free quantification has greatly facilitated the throughput and flexibility of novel proteomic techniques. However, such methods rely heavily on robust and reproducible sample preparation procedures. Here, we benchmark a selection of in gel, on filter, and in solution…
Ankita Punetha, Deepak Kotiya, Masaru Miyagi, Costel C. Darie
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset…
David Hartlmayr, Claudia Ctortecka, Anjali Seth, Sasha Mendjan + 2 more
The analysis of single cell proteomes has recently become a viable complement to transcript and genomics studies. Proteins are the main driver of cellular functionality and mRNA levels are often an unreliable proxy of such. Therefore, the global analysis of the proteome is essential to study cellular identities. Both…
Noelia Dasilva, Paula Díez, Sergio Matarraz, María González-González + 3 more
'Sara Paradinas' 'Alberto Orfao' 'Manuel Fuentes'] During the last years, proteomics has facilitated biomarker discovery by coupling high-throughput techniques with novel nanosensors. In the present review, we focus on the study of label-based and label-free detection systems, as well as nanotechnology approaches…
Joseph E Lucas, J Will Thompson, Laura G Dubois, Jeanette McCarthy + 10 more
'Hans Tillmann' 'Alexander Thompson' 'Norah Shire' 'Ron Hendrickson' 'Francisco Dieguez' 'Phyllis Goldman' 'Kathleen Schwarz' 'Keyur Patel' 'John McHutchison' 'M Arthur Moseley'] Background Label-free quantitative proteomics holds a great deal of promise for the future study of both medicine and biology. However, the…
Katrina Carbonara, Martin Andonovski, Jens R. Coorssen, Julian Whitelegge
'Julian Whitelegge'] Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To…
Mingze Bai, Jingwen Deng, Chengxin Dai, Julianus Pfeuffer + 1 more
Testing for significant differences in quantities on protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a fixed proteomics quantification software, there exists a multitude of tools and R packages to perform the…
Maria del Pilar Chantada-Vázquez, Susana B. Bravo, Sofía Barbosa-Gouveia, José V. Alvarez + 2 more
'Sofía Barbosa-Gouveia' 'José V. Alvarez' 'María L. Couce' 'Antonio Lucacchini'] Inherited metabolic disorders (IMD) are rare medical conditions caused by genetic defects that interfere with the body’s metabolism. The clinical phenotype is highly variable and can present at any age, although it more often manifests in…
Yumi Kwon, Jongmin Woo, Fengchao Yu, Sarah M. Williams + 9 more
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has…
Daniel H.J. Ng, Jonathan D. Humphries, Julian N. Selley, Stacey Warwood + 3 more
The ability to provide an unbiased qualitative and quantitative description of the global changes to proteins in a cell or an organism would permit the systems-wide study of complex biological systems. Label-free quantitative shotgun proteomic strategies (including LC-MS ion intensity quantification and spectral…
Laurent Gatto, Andy Christoforou
This review presents how R, the popular statistical environment and programming language, can be used in the frame of proteomics data analysis. A short introduction to R is given, with special emphasis on some of the features that make R and its add-on packages a premium software for sound and reproducible data…
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…
Nikolai Slavov
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made such analysis feasible for nucleic acids, but single-cell protein analysis…
Karl K. Krull, Syed A. Ali, Jeroen Krijgsveld
Proteome analysis by data-independent acquisition (DIA) has become a powerful approach to obtain deep proteome coverage, and has gained recent traction for label-free analysis of single cells. However, optimal experimental design for DIA-based single-cell proteomics has not been fully explored, and performance metrics…
Matthew Sonnett, Eyan Yeung, Martin Wühr
Quantitative analysis of proteomes across multiple time points, organelles, and perturbations is essential for understanding both fundamental biology and disease states. The development of isobaric tags (e.g. TMT) have enabled the simultaneous measurement of peptide abundances across several different conditions. These…
Shankar Dutt, Hancheng Shao, Buddini I. Karawdeniya, Y. M. Nuwan D. Y. Bandara + 3 more
'Y. M. Nuwan D. Y. Bandara' 'Elena Daskalaki' 'Hanna Suominen' 'P. Kluth'] Proteins are arguably one of the most important class of biomarkers for health diagnostic purposes. Label-free solid-state nanopore sensing is a versatile technique for sensing and analysing biomolecules such as proteins at single-molecule…
Jian‐An Huang, Mansoureh Z. Mousavi, Giorgia Giovannini, Yingqi Zhao + 3 more
'Aliaksandr Hubarevich' 'Denis Garoli' 'Francesco De Angelis'] Surface-enhanced Raman spectroscopy (SERS) is a sensitive label-free optical method that can provide fingerprint Raman spectra of biomolecules such as DNA, amino acids and proteins. While SERS of single DNA molecule has been recently demonstrated, Raman…
Yuewen Zhang, Maya A. Wright, Pavan K. Challa, Kadi-Liis Saar + 3 more
'Sean R. A. Devenish' 'Quentin Peter' 'Tuomas P. J. Knowles'] Protein identification and profiling is critical for the advancement of cell and molecular biology as well as medical diagnostics. Although mass spectrometry and protein microarrays are commonly used for protein identification, both methods require extensive…
Authors not listed
The process of label selection holds significant importance in the field of electrochemical biosensors, as it directly impacts the achievement of low detection limits and a wide dynamic range. To attain these objectives, it is necessary to take into account several aspects, including low electroactive potential, high…
Authors not listed
The analysis of macromolecules - such as proteins - pose a significant bottleneck in analytical science. We have developed surface treatment techniques utilising direct and radiofrequency current argon plasmas, able to quickly digest condensed-phase macromolecules while maintaining spatial resolution of analytes. We…
Manoj M. Varma
Immunoassay formats applicable for clinical or point-of-care diagnostics fall into two broad classes. One which uses labeled secondary antibodies for signal transduction and the other which does not require the use of any labels. Comparison of the limits of detection (LoD) reported by these two sensing approaches over…
Benjamin Neely, Yasset Perez-Riverol, Magnus Palmblad
The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite the fundamental importance of QC, it typically falls behind learning new techniques, instruments, or software.…
Authors not listed
Machine learning holds significant promise for accelerating biomarker discovery in clinical proteomics, yet its real-world impact remains limited by widespread methodological pitfalls and unrealistic expectations. In this perspective, we critically examine the integration of machine learning into clinical proteomics…
Eric Deutsch, Luis Mendoza, David Shteynberg, Michael Hoopmann + 3 more
The Trans-Proteomic Pipeline mass spectrometry data analysis suite has been in continual development and refinement since its first tools PeptideProphet and ProteinProphet were published twenty years ago. The current release provides a large complement of tools for spectrum processing, spectrum searching, search…
Lisa Alcock, Bruno Oliveira, Michael Deery, Tara Pukala + 3 more
Norbornene derivatives were validated as probes for cysteine sulfenic acid on proteins and in live cells. Trapping sulfenic acids with norbornene probes is highly selective and revealed a different reactivity profile than the traditional dimedone reagent. The norbornene probe also revealed a superior chemoselectivity…