25 papers · ranked by Valyu relevance
Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang + 2 more
Metabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using ^15^N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the ^15^N stable-isotope labeled protein…
Ruben Shrestha, Andres V. Reyes, Peter R. Baker, Zhi-Yong Wang + 2 more
'Robert J. Chalkley' 'Shou-Ling Xu'] Metabolic labeling using stable isotopes is widely used for the relative quantification of proteins in proteomic studies. In plants, metabolic labeling using 15N has great potential, but the associated complexity of data analysis has limited its usage. Here, we present the 15N…
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…
Muhammad Afzaal, Farhan Saeed, Muzzamal Hussain, Farheen Shahid + 2 more
'Azhari Siddeeg' 'Ammar Al‐Farga'] Title: ABSTRACT Adulteration and mislabeling have become a very common global malpractice in food industry. Especially foods of animal origin are prepared from plant sources and intentionally mislabeled. This type of mislabeling is an important concern in food safety as the replaced…
Stanislav Naryzhny, Alfredo Budillon
The number and identity of proteins and proteoforms presented in a single human cell (a cellular proteome) are fundamental biological questions. The answers can be found with sophisticated and sensitive proteomics methods, including advanced mass spectrometry (MS) coupled with separation by gel electrophoresis and…
Constantin Ammar, Marvin Thielert, Caroline A. M. Weiss, Edwin H. Rodriguez + 4 more
Quantitative readout is essential in proteomics, yet current bioinformatics methods lack a framework to handle the inherent multi-level nature of the data (fragments, MS1 isotopes, charge states, modifications, peptides and genes). We present AlphaQuant, which introduces tree-based quantification. This approach…
Ting Huang, Jian Wang, Alexey Stukalov, Margaret K. R. Donovan + 18 more
The wide dynamic range of circulating proteins coupled with the diversity of proteoforms present in plasma has historically impeded comprehensive and quantitative characterization of the plasma proteome at scale. Automated nanoparticle (NP) protein corona-based proteomics workflows can efficiently compress the dynamic…
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…
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…
Slavov, Nikolai
Over the last decade, proteomic analysis of single cells by mass spectrometry transitioned from an uncertain possibility to a set of robust and rapidly advancing technologies supporting the accurate quantification of thousands of proteins. We review the major drivers of this progress, from establishing feasibility to…
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…
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.…
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…
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…
Yifan Yao, Xuemei Wen, Hongjuan Pan, Ziwei Chen
Host cell proteins (HCPs) are process-related impurities derived from host organisms used for recombinant protein production in biopharmaceutical manufacturing. The generation of HCPs may lead to potential safety risks, such as immunogenicity, reduced drug efficacy and long-term side effects. Therefore, in the…
Huang Tang, Shuting Liu, Kang, Chenyue + 7 more
In the past 40 years, single-molecule techniques have been rapidly developed and widely applied in numerous fields of biology researches, offering new insights that conventional biochemical assays cannot discover. In this review, to help fully appreciate the powerfulness of single-molecule methods, we systemically…
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.…
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…