Transcriptomic analysis and fusion gene identifications of midbody remnants released from colorectal cancer cells reveals they are molecularly distinct from exosomes and microparticles
We reported that MBRs were molecularly distinct at the protein level. To gain further biochemical insights into MBRs, Exos, and MPs and their emerging role in CRC, we performed, and report here, for the first time, a comprehensive transcriptome and long noncoding RNA sequencing analysis and fusion gene identification of these three EV classes using the next-generation RNA sequencing technique. Differential transcript expression analysis revealed that MBRs have a distinct transcriptomic profile compared to Exos and MPs with a high enrichment of mitochondrial transcripts lncRNA/pseudogene transcripts that are predicted to bi...
Source: Proteomics - March 12, 2024 Category: Biochemistry Authors: Wittaya Suwakulsiri,
Rong Xu,
Alin Rai,
Maoshan Chen,
Adnan Shafiq,
David W. Greening,
Richard J. Simpson Tags: RESEARCH ARTICLE Source Type: research
VPBrowse: Genome ‐based representation of MS/MS spectra to quantify 10,000 bovine proteins
AbstractSWATH is a data acquisition strategy acclaimed for generating quantitatively accurate and consistent measurements of proteins across multiple samples. Its utility for proteomics studies in nonlaboratory animals, however, is currently compromised by the lack of sufficiently comprehensive and reliable public libraries, either experimental or predicted, and relevant platforms that support their sharing and utilization in an intuitive manner. Here we describe the development of the Veterinary Proteome Browser, VPBrowse (http://browser.proteo.cloud/), an on-line platform for genome-based representation of theBos taurus ...
Source: Proteomics - March 12, 2024 Category: Biochemistry Authors: Selvam Paramasivan,
Mohamed Ashick,
Kevin J. Dudley,
Nana Satake,
Paul C. Mills,
Pawel Sadowski,
Shivashankar H. Nagaraj Tags: TECHNICAL BRIEF 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 - March 11, 2024 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 6'24
(Source: Proteomics)
Source: Proteomics - March 11, 2024 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 6'24
(Source: Proteomics)
Source: Proteomics - March 11, 2024 Category: Biochemistry Tags: EDITORIAL BOARD 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 - March 11, 2024 Category: Biochemistry Tags: FRONT COVER Source Type: research
Contents: Proteomics 6'24
(Source: Proteomics)
Source: Proteomics - March 11, 2024 Category: Biochemistry Tags: CONTENTS Source Type: research
Editorial Board: Proteomics 6'24
(Source: Proteomics)
Source: Proteomics - March 11, 2024 Category: Biochemistry Tags: EDITORIAL BOARD Source Type: research
Challenges in computational discovery of bioactive peptides in ’omics data
AbstractPeptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well as in industry and agriculture. The increase in available ’omics data has recently provided a large opportunity for mining novel enzymes, biosynthetic gene clusters, and molecules. While these data primarily consist of DNA sequences, other types of data provide important complementary information. Due to their size, the approaches proven successful at di scovering novel proteins of canonical size cannot be naïvely applied to the discovery of peptides. Pe...
Source: Proteomics - March 9, 2024 Category: Biochemistry Authors: Luis Pedro Coelho,
C élio Dias Santos‐Júnior,
Cesar de la Fuente‐Nunez Tags: REVIEW Source Type: research
Varroa destructor parasitism and Deformed wing virus infection in honey bees are linked to peroxisome ‐induced pathways
This study complements previous research with different study designs and suggests the importance of the peroxisome, which plays a key role in viral infections. (Source: Proteomics)
Source: Proteomics - March 7, 2024 Category: Biochemistry Authors: Tomas Erban,
Dominika Kadleckova,
Bruno Sopko,
Karel Harant,
Pavel Talacko,
Martin Markovic,
Martina Salakova,
Klara Kadlikova,
Ruth Tachezy,
Jan Tachezy Tags: RESEARCH ARTICLE Source Type: research
Computational tools and algorithms for ion mobility spectrometry ‐mass spectrometry
This article presents an overview of the most recent free and open-source software tools specifically tailored for the analysis and interpretation of data derived from IM-MS instrumentation. This review enumerates these tools and outlines their main algorithmic approaches, while highlighting representative applications across different fields. Finally, a discussion of current limitations and expectable improvements is presented. (Source: Proteomics)
Source: Proteomics - March 5, 2024 Category: Biochemistry Authors: Dylan H. Ross,
Harsh Bhotika,
Xueyun Zheng,
Richard D. Smith,
Kristin E. Burnum ‐Johnson,
Aivett Bilbao Tags: REVIEW Source Type: research
