28 papers · ranked by Valyu relevance
Valerie C. Wasinger, Ming Zeng, Yunki Yau
The accurate quantitation of proteins and peptides in complex biological systems is one of the most challenging areas of proteomics. Mass spectrometry-based approaches have forged significant in-roads allowing accurate and sensitive quantitation and the ability to multiplex vastly complex samples through the…
Barbara Deracinois, Christophe Flahaut, Sophie Duban-Deweer, Yannis Karamanos
'Yannis Karamanos'] Proteomics became a key tool for the study of biological systems. The comparison between two different physiological states allows unravelling the cellular and molecular mechanisms involved in a biological process. Proteomics can confirm the presence of proteins suggested by their mRNA content and…
Florence Arsène-Ploetze, Philippe N. Bertin, Christine Carapito
Recent advances in microbial ecology allow studying microorganisms in their environment, without laboratory cultivation, in order to get access to the large uncultivable microbial community. With this aim, environmental proteomics has emerged as an appropriate complementary approach to metagenomics providing…
Huiyan Li, Robert Popp, Christoph H. Borchers
Proteins are the functional molecules in organisms and are therefore excellent biomarker candidates for a diversity of diseases. Immunoassays and mass spectrometry (MS) are two major technologies being used in proteomics; however, they either lack specificity or sensitivity. An emerging trend is to combine immunoassays…
Paolo Cifani, Alex Kentsis
Data Dependent Acquisition Data Independent Acquisition Parallel Reaction Monitoring post-translational modification strong anion exchange (chromatography) Strong cation exchange (chromatography) Despite superior analytical features, mass spectrometry proteomics remains seldom used for the basic investigation and…
John E. Hale
Quantitative protein measurements by mass spectrometry have gained wide acceptance in research settings. However, clinical uptake of mass spectrometric protein assays has not followed suit. In part, this is due to the long-standing acceptance by regulatory agencies of immunological assays such as ELISA assays. In most…
Salvatore Cappadona, Peter R. Baker, Pedro R. Cutillas, Albert J. R. Heck + 1 more
'Albert J. R. Heck' 'Bas van Breukelen'] Mass spectrometry-based proteomics has evolved as a high-throughput research field over the past decade. Significant advances in instrumentation, and the ability to produce huge volumes of data, have emphasized the need for adequate data analysis tools, which are nowadays often…
Brandon Ho, Anastasia Baryshnikova, Grant W. Brown
Global gene expression and proteomics tools have allowed large-scale analyses of the transcriptome and proteome in eukaryotic cells. These tools have enabled studies of protein abundance changes that occur in cells under stress conditions, providing insight into regulatory programs required for cellular adaptation.…
Ting Huang, Peijun Zhu, Zengyou He
Motivation: In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the sample. Then the relative or absolute protein abundance is estimated with…
Karina Dome, Zoya Akimenko, Aleksey Bychkov, Yuri Kalambet + 3 more
'Oleg Lomovsky' 'Giulio Malucelli' 'Xavier Colom'] Polyacrylamide gel electrophoresis is widely used for studying proteins and protein-containing objects. However, it is employed most frequently as a qualitative method rather than a quantitative one. This paper shows the feasibility of routine digital image acquisition…
Andrew M Frey, Frances Sidgwick, Andrew Porter, Pawel Palmowski + 1 more
Advances in mass spectrometry and associated computational tools have resulted in the wide-spread adoption of Data-Independent Acquisition (DIA) for proteomics. Experiments using state-of-the-art instrumentation and specialised modes of acquisition report ever increasing throughput and protein identification rates.…
Aleksandra A. Petelski, Nikolai Slavov
Increasing evidence suggests that ribosomes actively regulate protein synthesis. However, much of this evidence is indirect, leaving this layer of gene regulation largely unexplored, in part due to methodological limitations. Indeed, we review evidence demonstrating that commonly used methods, such as transcriptomics…
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…
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…
Bryson C. Gibbons, Thomas L. Fillmore, Yuqian Gao, Ronald J. Moore + 4 more
Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in clinical biomarker, cellular modeling and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant…
Michael J. MacCoss, Javier A. Alfaro, Meni Wanunu, Danielle A. Faivre + 1 more
'Danielle A. Faivre' 'Nikolai Slavov'] - 1. Department of Genome Sciences, University of Washington, Seattle, WA 98117, USA 0000-0003-1853- 0256 maccoss@uw.edu - 2. International Centre for Cancer Vaccine Science, University of Gdańsk, Gdańsk, Poland. javier.alfaro@proteogenomics.ca - 3. Department of Biochemistry and…
Deanna L Plubell, Philip M. Remes, Christine C. Wu, Cristina C. Jacob + 8 more
The development of targeted assays that monitor biomedically relevant proteins is an important step in bridging discovery experiments to large scale clinical studies. Targeted assays are currently unable to scale to hundreds or thousands of targets. We demonstrate the generation of large-scale assays using a novel…
Thierry Rabilloud
Two dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when multiple quantitative comparisons of samples must be made, and even for large samples…
Mahsa Babaei, Soheila Kashanian, Huang‐Teck Lee, Frances Harding
Protein biomarkers represent specific biological activities and processes, so they have had a critical role in cancer diagnosis and medical care for more than 50 years. With the recent improvement in proteomics technologies, thousands of protein biomarker candidates have been developed for diverse disease states.…
Authors not listed
Wheat contributes 19% of the protein in the global human diet. Mid-infrared spectroscopy (MIR) combined with attenuated total reflection (ATR) is an excellent analytical method for assessing the chemical composition of complex biological samples. In contrast to established techniques used for wheat protein analysis, we…
Authors not listed
Plasma proteomics has regained attention in recent years through advancements in mass spectrometry instrumentation and sample preparation, as well as new high-throughput affinity-based technologies. Here, we evaluate the analytical performance of the new Olink Reveal platform, a proximity extension assay (PEA)-based…
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…
Sarah Döring, Michael G. Weller, Yvonne Reinders, Zoltán Konthur + 2 more
'Carsten Jaeger' 'Ohad Mazor'] This review describes mass spectrometry (MS)-based approaches for the absolute quantification of therapeutic monoclonal antibodies (mAbs), focusing on technical challenges in sample treatment and calibration. Therapeutic mAbs are crucial for treating cancer and inflammatory, infectious…
Zhaowei Meng, Amir Ata Saei, Xuepei Zhang, Hezheng Lyu + 5 more
Here we present a high-throughput virtual top-down proteomics approach that restores the molecular weight (MW) information in shotgun proteomics, and demonstrate its utility in studying proteolytic events in programmed cell death. With Gel-Assisted Proteome Position Integral Shift (GAPPIS), we quantified over 7000…
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
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…
Bryon Drown, Kevin Jooß, Rafael Melani, Cameron Lloyd-Jones + 2 more
A functional understanding of the human body requires structure-function studies of proteins at scale. The chemical structure of proteins is controlled at the transcriptional, translational, and post-translational levels, creating a variety of products with modulated functions within the cell. The term “proteoform”…
Ulrich Pabst
The idea of peptide mass fingerprinting (PMF) was first introduced in 1989, when protein research was facing a serious issue with automated Edman-degradation taking nearly one hour per reaction cycle. There was a dire need for more streamlined and fast ways to analyse proteins and peptides. Since the first steps…