Proteomics contributions to epigenetic drug discovery
AbstractThe combined activity of epigenetic features, which include histone post-translational modifications, DNA methylation, and nucleosome positioning, regulates gene expression independently from changes in the DNA sequence, defining how the shared genetic information of an organism is used to generate different cell phenotypes. Alterations in epigenetic processes have been linked with a multitude of diseases, including cancer, fueling interest in the discovery of drugs targeting the proteins responsible for writing, erasing, or reading histone and DNA modifications. Mass spectrometry (MS)-based proteomics has emerged ...
Source: Proteomics - September 20, 2023 Category: Biochemistry Authors: Roberta Noberini, Tiziana Bonaldi Tags: REVIEW Source Type: research

Exact p ‐value calculation for XCorr scoring of high‐resolution MS/MS data
AbstractExactp-value (XPV)-based methods for dot product-like score functions —such as the XCorr score implemented in Tide, SEQUEST, Comet or shared peak count-based scoring in MSGF+ and ASPV—provide a fairly good calibration for peptide-spectrum-match (PSM) scoring in database searching-based MS/MS spectrum data identification. Unfortunately, standard XPV methods, in pra ctice, cannot handle high-resolution fragmentation data produced by state-of-the-art mass spectrometers because having smaller bins increases the number of fragment matches that are assigned to incorrect bins and scored improperly. In this article, we...
Source: Proteomics - September 20, 2023 Category: Biochemistry Authors: Kishankumar Bhimani, Arina Peresadina, Dmitrii Vozniuk, Attila Kert ész‐Farkas Tags: RESEARCH ARTICLE Source Type: research

Immune capture and protein profiling of small extracellular vesicles from human plasma
AbstractExtracellular vesicles (EVs), the key players in inter-cellular communication, are produced by all cell types and are present in all body fluids. Analysis of the proteome content is an important approach in structural and functional studies of these vesicles. EVs circulating in human plasma are heterogeneous in size, cellular origin, and functions. This heterogeneity and the potential presence of contamination with plasma components such as lipoprotein particles and soluble plasma proteins represent a challenge in profiling the proteome of EV subsets by mass spectrometry. An immunocapture strategy prior to mass spe...
Source: Proteomics - September 16, 2023 Category: Biochemistry Authors: Łukasz Skoczylas, Marta Gawin, Daniel Fochtman, Piotr Widłak, Theresa L. Whiteside, Monika Pietrowska Tags: REVIEW Source Type: research

Computational tools for inferring transcription factor activity
AbstractTranscription factors (TFs) are essential players in orchestrating the regulatory landscape in cells. Still, their exact modes of action and dependencies on other regulatory aspects remain elusive. Since TFs act cell type-specific and each TF has its own characteristics, untangling their regulatory interactions from an experimental point of view is laborious and convoluted. Thus, there is an ongoing development of computational tools that estimate transcription factor activity (TFA) from a variety of data modalities, either based on a mapping of TFs to their putative target genes or in a genome-wide, gene-unspecifi...
Source: Proteomics - September 15, 2023 Category: Biochemistry Authors: Dennis Hecker, Michael Lauber, Fatemeh Behjati Ardakani, Shamim Ashrafiyan, Quirin Manz, Johannes Kersting, Markus Hoffmann, Marcel H. Schulz, Markus List Tags: REVIEW Source Type: research

Spectral library search for improved TMTpro labelled peptide assignment in human plasma proteomics
In this study, we developed and evaluated a TMTpro-specific spectral library for improved protein identification in human plasma proteomics. The library was constructed by LC-MS/MS analysis of highly fractionated TMTpro-tagged human plasma, human cell lysates, and relevant arterial tissues. The library was curated using several quality filters to ensure reliable peptide identifications. Our results show that spectral library searching using the TMTpro spectral library improves the identification of proteins in plasma samples compared to conventional sequence database searching. Protein identifications made by the spectral ...
Source: Proteomics - September 14, 2023 Category: Biochemistry Authors: Nicolai B. Palstr øm, Amanda J. Campbell, Caroline A. Lindegaard, Samir Cakar, Rune Matthiesen, Hans C. Beck Tags: RESEARCH ARTICLE Source Type: research

Front Cover
Cover Image © Wiley-VCH GmbH. The image is part of a figure in the article DOI:10.1002/pmic.201900203 by Lei Li, Yong Jiang et al. (Source: Proteomics)
Source: Proteomics - September 14, 2023 Category: Biochemistry Tags: FRONT COVER Source Type: research

Contents: Proteomics 18'23
(Source: Proteomics)
Source: Proteomics - September 14, 2023 Category: Biochemistry Tags: CONTENTS Source Type: research

Editorial Board: Proteomics 18'23
(Source: Proteomics)
Source: Proteomics - September 14, 2023 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research

Standard abbreviations
(Source: Proteomics)
Source: Proteomics - September 14, 2023 Category: Biochemistry Tags: STANDARD ABBREVIATIONS Source Type: research