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Proteomic characterization of extracellular vesicles in programmed cell death Proteomics (IF 3.4) Pub Date : 2024-03-16 Vivian Weiwen Xue, Sze Chuen Cesar Wong, Huafu Zhao, William Chi Shing Cho
Programmed cell death (PCD) is a fundamental biological process that plays a critical role in cell development, differentiation, and homeostasis. The secretion and uptake of extracellular vesicles (EVs) is one of the important regulatory mechanisms for PCD. EVs are natural membrane structures secreted by cells that contain a variety of proteins, lipids, nucleic acids, and other bioactive molecules
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On the use of tandem mass spectra acquired from samples of evolutionarily distant organisms to validate methods for false discovery rate estimation Proteomics (IF 3.4) Pub Date : 2024-03-16 Dominik Madej, Henry Lam
Estimating the false discovery rate (FDR) of peptide identifications is a key step in proteomics data analysis, and many methods have been proposed for this purpose. Recently, an entrapment‐inspired protocol to validate methods for FDR estimation appeared in articles showcasing new spectral library search tools. That validation approach involves generating incorrect spectral matches by searching spectra
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Characterization of diverse lysine acylations in Bacillus thuringiensis: Substrate profiling and functional exploration Proteomics (IF 3.4) Pub Date : 2024-03-16 Tianxian Liu, Mingya Zhang, Yameng Fan, Lei Zhao, Dan Huang, Liuchang Zhao, Minjia Tan, Bang‐Ce Ye, Jun‐Yu Xu
Lysine acylation has been extensively investigated due to its regulatory role in a diverse range of biological functions across prokaryotic and eukaryotic species. In‐depth acylomic profiles have the potential to enhance comprehension of the biological implications of organisms. However, the extent of research on global acylation profiles in microorganisms is limited. Here, four lysine acylomes were
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Spectral averaging with outlier rejection algorithms to increase identifications in top‐down proteomics Proteomics (IF 3.4) Pub Date : 2024-03-15 Austin V. Carr, Nicholas E. Bollis, John G. Pavek, Michael R. Shortreed, Lloyd M. Smith
The identification of proteoforms by top‐down proteomics requires both high quality fragmentation spectra and the neutral mass of the proteoform from which the fragments derive. Intact proteoform spectra can be highly complex and may include multiple overlapping proteoforms, as well as many isotopic peaks and charge states. The resulting lower signal‐to‐noise ratios for intact proteins complicates
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Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies Proteomics (IF 3.4) Pub Date : 2024-03-13 Anja Alicehajic, Annet Adriana Maria Duivenvoorden, Kaatje Lenaerts
Intestinal ischemia–reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores
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Identification of gravity‐responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data‐independent acquisition mass spectrometry Proteomics (IF 3.4) Pub Date : 2024-03-13 Yayoi Kimura, Yusuke Nakai, Yoko Ino, Tomoko Akiyama, Kayano Moriyama, Takashi Ohira, Tomoyuki Saito, Yutaka Inaba, Ken Kumagai, Akihide Ryo, Hisashi Hirano
Physical inactivity associated with gravity unloading, such as microgravity during spaceflight and hindlimb unloading (HU), can cause various physiological changes. In this study, we attempted to identify serum proteins whose levels fluctuated in response to gravity unloading. First, we quantitatively assessed changes in the serum proteome profiles of spaceflight mice using mass spectrometry with data‐independent
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VPBrowse: Genome‐based representation of MS/MS spectra to quantify 10,000 bovine proteins Proteomics (IF 3.4) Pub Date : 2024-03-12 Selvam Paramasivan, Mohamed Ashick, Kevin J. Dudley, Nana Satake, Paul C. Mills, Pawel Sadowski, Shivashankar H. Nagaraj
SWATH 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
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Transcriptomic analysis and fusion gene identifications of midbody remnants released from colorectal cancer cells reveals they are molecularly distinct from exosomes and microparticles Proteomics (IF 3.4) Pub Date : 2024-03-12 Wittaya Suwakulsiri, Rong Xu, Alin Rai, Maoshan Chen, Adnan Shafiq, David W. Greening, Richard J. Simpson
Previously, we reported that human primary (SW480) and metastatic (SW620) colorectal (CRC) cells release three classes of membrane‐encapsulated extracellular vesicles (EVs); midbody remnants (MBRs), exosomes (Exos), and microparticles (MPs). 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
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Dysregulated proteome and N‐glycoproteome in ALG1‐deficient fibroblasts Proteomics (IF 3.4) Pub Date : 2024-03-12 Rohit Budhraja, Neha Joshi, Silvia Radenkovic, Tamas Kozicz, Eva Morava, Akhilesh Pandey
Asparagine‐linked glycosylation 1 protein is a β‐1,4‐mannosyltransferase, is encoded by the ALG1 gene, which catalyzes the first step of mannosylation in N‐glycosylation. Pathogenic variants in ALG1 cause a rare autosomal recessive disorder termed as ALG1‐CDG. We performed a quantitative proteomics and N‐glycoproteomics study in fibroblasts derived from patients with one homozygous and two compound
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Challenges in computational discovery of bioactive peptides in ’omics data Proteomics (IF 3.4) Pub Date : 2024-03-09 Luis Pedro Coelho, Célio Dias Santos‐Júnior, Cesar de la Fuente‐Nunez
Peptides 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
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Varroa destructor parasitism and Deformed wing virus infection in honey bees are linked to peroxisome‐induced pathways Proteomics (IF 3.4) Pub Date : 2024-03-06 Tomas Erban, Dominika Kadleckova, Bruno Sopko, Karel Harant, Pavel Talacko, Martin Markovic, Martina Salakova, Klara Kadlikova, Ruth Tachezy, Jan Tachezy
The ectoparasitic mite Varroa destructor transmits and triggers viral infections that have deleterious effects on honey bee colonies worldwide. We performed a manipulative experiment in which worker bees collected at emergence were exposed to Varroa for 72 h, and their proteomes were compared with those of untreated control bees. Label‐free quantitative proteomics identified 77 differentially expressed
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Computational tools and algorithms for ion mobility spectrometry‐mass spectrometry Proteomics (IF 3.4) Pub Date : 2024-03-05 Dylan H. Ross, Harsh Bhotika, Xueyun Zheng, Richard D. Smith, Kristin E. Burnum‐Johnson, Aivett Bilbao
Ion mobility spectrometry‐mass spectrometry (IMS‐MS or IM‐MS) is a powerful analytical technique that combines the gas‐phase separation capabilities of IM with the identification and quantification capabilities of MS. IM‐MS can differentiate molecules with indistinguishable masses but different structures (e.g., isomers, isobars, molecular classes, and contaminant ions). The importance of this analytical
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Beyond the model organism—Mechanistic analysis of protein post‐translational modifications is ready for all challengers Proteomics (IF 3.4) Pub Date : 2024-03-04 Benjamin C. Orsburn
A historic challenge for shotgun proteomics has been the requirement for high quality, simple, and nonredundant curated protein sequences in small .fasta text files. Due to the intrinsic informatic challenges and time required to assemble these files, proteomics has struggled to expand beyond the confines of a few model organisms. When considering post‐translational modifications that may or may not
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Global acetylome profiling indicates EPA impedes but OA promotes prostate cancer motility through altered acetylation of PFN1 and FLNA Proteomics (IF 3.4) Pub Date : 2024-03-02 Chao He, Xiuyuan Chen, Ying Chen, Jianying Sun, Manting Qi, Sonia Rocha, Mu Wang
Prostate cancer (PCa) is one of the leading causes of cancer morbidity and mortality in men. Metastasis is the main cause of PCa‐associated death. Recent evidence indicated a significant reduction in PCa mortality associated with higher ω‐3 polyunsaturated fatty acids (PUFAs) consumption. However, the underlying mechanisms remained elusive. In this study, we applied global acetylome profiling to study
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Prolonged exposure to dexamethasone alters the proteome and cellular phenotype of human testicular peritubular cells Proteomics (IF 3.4) Pub Date : 2024-02-29 Youli K. Stepanov, Carola Herrmann, Jan B. Stöckl, Frank‐Michael Köhn, Ulrich Pickl, Mathias Trottmann, Thomas Fröhlich, Artur Mayerhofer, Harald Welter
Human testicular peritubular cells (HTPCs) are smooth muscle cells, which in the testis form a small compartment surrounding the seminiferous tubules. Contractions of HTPCs are responsible for sperm transport, HTPCs contribute to spermatogenesis, have immunological roles and are a site of glucocorticoid receptor expression. Importantly, HTPCs maintain their characteristics in vitro, and thus can serve
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Advancing rare cancer research by MALDI mass spectrometry imaging: Applications, challenges, and future perspectives in sarcoma Proteomics (IF 3.4) Pub Date : 2024-02-25 Maren Nicole Stillger, Mujia Jenny Li, Pia Hönscheid, Cläre von Neubeck, Melanie Christine Föll
MALDI mass spectrometry imaging (MALDI imaging) uniquely advances cancer research, by measuring spatial distribution of endogenous and exogenous molecules directly from tissue sections. These molecular maps provide valuable insights into basic and translational cancer research, including tumor biology, tumor microenvironment, biomarker identification, drug treatment, and patient stratification. Despite
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Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri) Proteomics (IF 3.4) Pub Date : 2024-02-24 Dietmar Kültz, Alison M. Gardell, Anthony DeTomaso, Greg Stoney, Baruch Rinkevich, Yuval Rinkevich, Andy Qarri, Weizhen Dong, Brenda Luu, Mandy Lin
Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress‐induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep‐coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low‐quality transitions, and only
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Target‐decoy false discovery rate estimation using Crema Proteomics (IF 3.4) Pub Date : 2024-02-21 Andy Lin, Donavan See, William E. Fondrie, Uri Keich, William Stafford Noble
Assigning statistical confidence estimates to discoveries produced by a tandem mass spectrometry proteomics experiment is critical to enabling principled interpretation of the results and assessing the cost/benefit ratio of experimental follow‐up. The most common technique for computing such estimates is to use target‐decoy competition (TDC), in which observed spectra are searched against a database
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Top-down proteomics and proteoforms – special issue Proteomics (IF 3.4) Pub Date : 2024-02-13 Andreas Tholey, Hartmut Schlüter
Proteins are involved in almost all biological processes and for this reason, the ensemble of all proteins in a biology entity, the proteome, represents THE central functional level within the different – omes. While we still speak about proteins in our daily work with proteomes, we have to take into account that proteins are not simply the product of the transcription and translation of genetic information
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Analysis of secreted small extracellular vesicles from activated human microglial cell lines reveals distinct pro- and anti-inflammatory proteomic profiles Proteomics (IF 3.4) Pub Date : 2024-02-11 Xueming Niu, Zhen Zhang, Quan Zhou, Alain Wuethrich, Richard Lobb, Matt Trau
Microglia are a specialized population of innate immune cells located in the central nervous system. In response to physiological and pathological changes in their microenvironment, microglia can polarize into pro-inflammatory or anti-inflammatory phenotypes. A dysregulation in the pro-/anti-inflammatory balance is associated with many pathophysiological changes in the brain and nervous system. Therefore
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An AI-generated proteome-scale dataset of predicted protein structures for the ctenophore Mnemiopsis leidyi Proteomics (IF 3.4) Pub Date : 2024-02-08 R. Travis Moreland, Suiyuan Zhang, Sofia N. Barreira, Joseph F. Ryan, Andreas D. Baxevanis
This Dataset Brief describes the computational prediction of protein structures for the ctenophore Mnemiopsis leidyi. Here, we report the proteome-scale generation of 15,333 protein structure predictions using AlphaFold, as well as an updated implementation of publicly available search, manipulation, and visualization tools for these protein structure predictions through the Mnemiopsis Genome Project
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Pharmaco-phosphoproteomic analysis of cancer-associated KIT mutations D816V and V560G Proteomics (IF 3.4) Pub Date : 2024-02-09 Heather C. Murray, Kasey Miller, Matthew D. Dun, Nicole M. Verrills
The CD117 mast/stem cell growth factor receptor tyrosine kinase (KIT) is critical for haematopoiesis, melanogenesis and stem cell maintenance. KIT is commonly activated by mutation in cancers including acute myeloid leukaemia, melanoma and gastrointestinal stromal tumours (GISTs). The kinase and the juxtamembrane domains of KIT are mutation hotspots; with the kinase domain mutation D816V common in
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Assessing the precision of a detergent-assisted cartridge precipitation workflow for non-targeted quantitative proteomics Proteomics (IF 3.4) Pub Date : 2024-02-01 Jessica L. Nickerson, Hugo Gagnon, Peter D. Wentzell, Alan A. Doucette
Detergent-based workflows incorporating sodium dodecyl sulfate (SDS) necessitate additional steps for detergent removal ahead of mass spectrometry (MS). These steps may lead to variable protein recovery, inconsistent enzyme digestion efficiency, and unreliable MS signals. To validate a detergent-based workflow for quantitative proteomics, we herein evaluate the precision of a bottom-up sample preparation
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Top-down ion mobility/mass spectrometry reveals enzyme specificity: Separation and sequencing of isomeric proteoforms Proteomics (IF 3.4) Pub Date : 2024-01-28 Francis Berthias, Nurgül Bilgin, Jasmin Mecinović, Ole N. Jensen
Enzymatic catalysis is one of the fundamental processes that drives the dynamic landscape of post-translational modifications (PTMs), expanding the structural and functional diversity of proteins. Here, we assessed enzyme specificity using a top-down ion mobility spectrometry (IMS) and tandem mass spectrometry (MS/MS) workflow. We successfully applied trapped IMS (TIMS) to investigate site-specific
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iDVEIP: A computer-aided approach for the prediction of viral entry inhibitory peptides Proteomics (IF 3.4) Pub Date : 2024-01-23 Hui-Ju Kao, Tzu-Hsiang Weng, Chia-Hung Chen, Yu-Chi Chen, Kai-Yao Huang, Shun-Long Weng
With the notable surge in therapeutic peptide development, various peptides have emerged as potential agents against virus-induced diseases. Viral entry inhibitory peptides (VEIPs), a subset of antiviral peptides (AVPs), offer a promising avenue as entry inhibitors (EIs) with distinct advantages over chemical counterparts. Despite this, a comprehensive analytical platform for characterizing these peptides
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Analyzing domain features of small proteins using a machine-learning method Proteomics (IF 3.4) Pub Date : 2024-01-22 ShiJian Ding, HuiPing Liao, FeiMing Huang, Lei Chen, Wei Guo, KaiYan Feng, Tao Huang, Yu-Dong Cai
Small proteins (SPs) are a unique group of proteins that play crucial roles in many important biological processes. Exploring the biological function of SPs is necessary. In this study, the InterPro tool and the maximum correlation method were utilized to analyze functional domains of SPs. The purpose was to identify important functional domains that can indicate the essential differences between small
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Mycobacterium abscessus extracellular vesicles increase mycobacterial resistance to clarithromycin in vitro Proteomics (IF 3.4) Pub Date : 2024-01-18 Charlie A. Vermeire, Xuejuan Tan, Yurong Liang, Stephen K. Kotey, Janet Rogers, Steven D. Hartson, Lin Liu, Yong Cheng
Nontuberculous Mycobacteria (NTM) are a group of emerging bacterial pathogens that have been identified in cystic fibrosis (CF) patients with microbial lung infections. The treatment of NTM infection in CF patients is challenging due to the natural resistance of NTM species to many antibiotics. Mycobacterium abscessus is one of the most common NTM species found in the airways of CF patients. In this
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Secretome processing for proteomics: A methods comparison Proteomics (IF 3.4) Pub Date : 2024-01-14 Catarina Almeida-Marques, Frank Rolfs, Sander R. Piersma, Irene V. Bijnsdorp, Thang V. Pham, Jaco C. Knol, Connie R. Jimenez
The cancer cell secretome comprises a treasure-trove for biomarkers since it reflects cross-talk between tumor cells and their surrounding environment with high detectability in biofluids. In this study, we evaluated six secretome sample processing workflows coupled to single-shot mass spectrometry: (1) Protein concentration by ultrafiltration with a molecular weight cut-off (MWCO) filter and sample
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HB-EGF-loaded nanovesicles enhance trophectodermal spheroid attachment and invasion Proteomics (IF 3.4) Pub Date : 2024-01-12 Qi Hui Poh, Alin Rai, Jonathon Cross, David W. Greening
The ability of trophectodermal cells (outer layer of the embryo) to attach to the endometrial cells and subsequently invade the underlying matrix are critical stages of embryo implantation during successful pregnancy establishment. Extracellular vesicles (EVs) have been implicated in embryo-maternal crosstalk, capable of reprogramming endometrial cells towards a pro-implantation signature and phenotype
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Proteomics of urinary small extracellular vesicles in early diagnosis of kidney diseases in children-expectations and limitations Proteomics (IF 3.4) Pub Date : 2024-01-11 Klaudia Korecka, Marta Gawin, Agnieszka Pastuszka, Mirosław Partyka, Tomasz Koszutski, Monika Pietrowska, Lidia Hyla-Klekot
The primary function of the kidneys is to maintain systemic homeostasis (disruption of renal structure and function results in multilevel impairment of body function). Kidney diseases are characterized by a chronic, progressive course and may result in the development of chronic kidney disease (CKD). Evaluation of the composition of the proteome of urinary small extracellular vesicles (sEVs) as a so-called
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Identification of a rare [Gγ(Aγδβ)0] -thalassemia using tandem mass spectrometry Proteomics (IF 3.4) Pub Date : 2024-01-11 Anikha Bellad, Kannan Rangiah, Gajanan Sathe, Gourav Dey, Pragalatha Kumar Appadorai, Hemalatha Lokanatha, Pradeep Rudra Murthy, Aruna Gowdra, Akhilesh Pandey
Thalassemias are a group of inherited monogenic disorders characterized by defects in the synthesis of one or more of the globin chain subunits of the hemoglobin tetramer. Delta-beta (δβ-) thalassemia has large deletions in the β globin gene cluster involving δ- and β-globin genes, leading to absent or reduced synthesis of both δ- and β-globin chains. Here, we used direct globin-chain analysis using
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Four sides to the story: A proteomic comparison of liquid-phase and matrix-bound extracellular vesicles in 2D and 3D cell cultures Proteomics (IF 3.4) Pub Date : 2024-01-10 Maria Peshkova, Alexander Korneev, Daria Revokatova, Olga Smirnova, Timofey Klyucherev, Victoria Shender, Georgij Arapidi, Nastasia Kosheleva, Peter Timashev
Multipotent mesenchymal stromal cells (MSCs)-derived extracellular vesicles (EVs) play important roles in cellular communication and are extensively studied as promising therapeutic agents. While there is a substantial pool of studies on liquid-phase EVs, data on EVs bound to the extracellular matrix (ECM) is lacking. There is also an emerging trend of accumulating and comparing data on characteristics
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Effects of genetic variation on the structure of RNA and protein Proteomics (IF 3.4) Pub Date : 2024-01-10 Jingxuan Kang, Siyu Wei, Zhe Jia, Yingnan Ma, Haiyan Chen, Chen Sun, Jing Xu, Junxian Tao, Yu Dong, Wenhua Lv, Hongsheng Tian, Xuying Guo, Shuo Bi, Chen Zhang, Yongshuai Jiang, Hongchao Lv, Mingming Zhang
Changes in the structure of RNA and protein, have an important impact on biological functions and are even important determinants of disease pathogenesis and treatment. Some genetic variations, including copy number variation, single nucleotide variation, and so on, can lead to changes in biological function and increased susceptibility to certain diseases by changing the structure of RNA or protein
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Changes in the astronaut serum proteome during prolonged spaceflight Proteomics (IF 3.4) Pub Date : 2024-01-07 Yayoi Kimura, Yusuke Nakai, Yoko Ino, Tomoko Akiyama, Kayano Moriyama, Tatsuya Aiba, Takashi Ohira, Kenji Egashira, Yu Yamamoto, Yuriko Takeda, Yutaka Inaba, Akihide Ryo, Tomoyuki Saito, Ken Kumagai, Hisashi Hirano
The molecular mechanisms associated with spaceflight-induced biological adaptations that may affect many healthy tissue functions remain poorly understood. In this study, we analyzed temporal changes in the serum proteome of six astronauts during prolonged spaceflight missions using quantitative comprehensive proteome analysis performed with the data-independent acquisition method of mass spectrometry
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Proteome profile of the cerebellum from α7 nicotinic acetylcholine receptor deficient mice Proteomics (IF 3.4) Pub Date : 2024-01-07 Karolina Magdalena Caban, Pia Seßenhausen, Jan Bernard Stöckl, Bastian Popper, Artur Mayerhofer, Thomas Fröhlich
The alpha7 nicotinic acetylcholine receptor (α7 nAChR; CHRNA7) is expressed in the nervous system and in non-neuronal tissues. Within the central nervous system, it is involved in various cognitive and sensory processes such as learning, attention, and memory. It is also expressed in the cerebellum, where its roles are; however, not as well understood as in the other brain regions. To investigate the
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Defining the relationship between cellular and extracellular vesicle (EV) content in breast cancer via an integrative multi-omic analysis Proteomics (IF 3.4) Pub Date : 2024-01-03 Rebecca E. Lane, Darren Korbie, Kum Kum Khanna, Ahmed Mohamed, Michelle M. Hill, Matt Trau
Much recent research has been dedicated to exploring the utility of extracellular vesicles (EVs) as circulating disease biomarkers. Underpinning this work is the assumption that the molecular cargo of EVs directly reflects the originating cell. Few attempts have been made, however, to empirically validate this on the -omic level. To this end, we have performed an integrative multi-omic analysis of
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A crustacean neuropeptide spectral library for data-independent acquisition (DIA) mass spectrometry applications Proteomics (IF 3.4) Pub Date : 2024-01-03 Lauren Fields, Min Ma, Kellen DeLaney, Ashley Phetsanthad, Lingjun Li
Neuropeptides have tremendous potential for application in modern medicine, including utility as biomarkers and therapeutics. To overcome the inherent challenges associated with neuropeptide identification and characterization, data-independent acquisition (DIA) is a fitting mass spectrometry (MS) method of choice to achieve sensitive and accurate analysis. It is advantageous for preliminary neuropeptidomic
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Analysis of N- and O-linked site-specific glycosylation by ion mobility mass spectrometry: State of the art and future directions Proteomics (IF 3.4) Pub Date : 2024-01-03 Michael Girgis, Gregory Petruncio, Paul Russo, Steven Peyton, Mikell Paige, Diana Campos, Miloslav Sanda
Glycosylation, the major post-translational modification of proteins, significantly increases the diversity of proteoforms. Glycans are involved in a variety of pivotal structural and functional roles of proteins, and changes in glycosylation are profoundly connected to the progression of numerous diseases. Mass spectrometry (MS) has emerged as the gold standard for glycan and glycopeptide analysis
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The multifaceted roles of small extracellular vesicles in metabolic reprogramming in the tumor microenvironments Proteomics (IF 3.4) Pub Date : 2024-01-03 Zhixian Chen, Judy Wai Ping Yam, Xiaowen Mao
The link between metabolism and tumor progression has been extensively researched for a long time. With the increasing number of studies uncovering the multiple functions of metabolic reprogramming in tumor microenvironments, the regulatory network seems to become even more intricate at the same time. Small extracellular vesicles (sEV), as crucial mediators facilitating intercellular communications
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Flash MS/MS proteotyping allows identifying microbial isolates in 36 s of mass spectrometry signal Proteomics (IF 3.4) Pub Date : 2024-01-02 Madisson Chabas, Jean-Charles Gaillard, Béatrice Alpha-Bazin, Jean Armengaud
Rapid identification of microorganisms is essential for medical diagnostics, sanitary controls, and food safety. High-throughput analytical platforms currently rely on whole-cell MALDI-TOF mass spectrometry to process hundreds of samples per day. Although this technology has become a reference method, it is unable to process most environmental isolates and opportunistic pathogens due to an incomplete
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Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy Proteomics (IF 3.4) Pub Date : 2024-01-03 Liang Yue, Tingting Gong, Wenhao Jiang, Liujia Qian, Wangang Gong, Yaoting Sun, Xue Cai, Heli Xu, Fanghua Liu, He Wang, Sainan Li, Yi Zhu, Zhiguo Zheng, Qijun Wu, Tiannan Guo
Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32
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Mechanism of action of pseudopteroxazole and pseudopterosin G: Diterpenes from marine origin Proteomics (IF 3.4) Pub Date : 2023-12-29 Niklas B. M. Janzing, Christoph H. R. Senges, Pascal Dietze, Bradley Haltli, Douglas H. Marchbank, Russell G. Kerr, Julia E. Bandow
Pseudopteroxazole (Ptx) and the pseudopterosins are marine natural products with promising antibacterial potential. While Ptx has attracted interest for its antimycobacterial activity, pseudopterosins are active against several clinically relevant pathogens. Both compound classes exhibit low cytotoxicity and accessibility to targeted synthesis, yet their antibacterial mechanisms remain elusive. In
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Integration of proteomics in the molecular tumor board Proteomics (IF 3.4) Pub Date : 2023-12-24 Johanna Thiery, Matthias Fahrner
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics
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Integration of single-cell proteomic datasets through distinctive proteins in cell clusters Proteomics (IF 3.4) Pub Date : 2023-12-22 Mehmet Burak Koca, Fatih Erdoğan Sevilgen
The use of mass spectrometry and antibody-based sequencing technologies at the single-cell level has led to an increase in single-cell proteomic datasets. Integrating these datasets is crucial to eliminate the batch effect that often arises due to their limited sequencing molecules. Although methods for horizontally integrating high-dimensional single-cell transcriptomic datasets can also be applied
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Global quantitative proteomic analysis of aged mouse hippocampus Proteomics (IF 3.4) Pub Date : 2023-12-19 He Huang, Ashley J. van Waardenberg, Mark E. Graham, Victor Anggono, Jocelyn Widagdo
Understanding the molecular changes associated with the aged brain forms the basis for developing potential strategies for slowing cognitive decline associated with normal aging. Focusing on the hippocampus, a critical brain region involved in learning and memory, we employed tandem mass tag methodology to investigate global proteomic changes that occur in advanced-aged (20-month) versus young (3-month)
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The need for open and FAIR data in top-down proteomics Proteomics (IF 3.4) Pub Date : 2023-12-13 Frederik Lermyte
In recent years, there has been a tremendous evolution in the high-throughput, tandem mass spectrometry-based analysis of intact proteins, also known as top-down proteomics (TDP). Both hardware and software have developed to the point that the technique has largely entered the mainstream, and large-scale, ambitious, multi-laboratory initiatives have started to make their appearance in the literature
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Characterization of outer membrane vesicles released by clinical isolates of Neisseria gonorrhoeae Proteomics (IF 3.4) Pub Date : 2023-12-07 Subhash Dhital, Pankaj Deo, Isabella Stuart, Cheng Huang, Lauren Zavan, Mei-Ling Han, Maria Kaparakis-Liaskos, Georg Ramm, Ralf B. Schittenhelm, Benjamin Howden, Thomas Naderer
The sexually transmitted pathogen Neisseria gonorrhoeae releases membrane vesicles including outer membrane vesicles (OMVs) during infections. OMVs traffic outer membrane molecules, such as the porin PorB and lipo-oligosaccharide (LOS), into host innate immune cells, eliciting programmed cell death pathways, and inflammation. Little is known, however, about the proteome and LOS content of OMVs released
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Proteome of spores from biological indicators in sterilization processes: Bacillus pumilus and Bacillus atrophaeus Proteomics (IF 3.4) Pub Date : 2023-12-07 Imed Dorbani, Jean Armengaud, Frédéric Carlin, Catherine Duport
Bacillus atrophaeus and Bacillus pumilus spores are widely used as biological indicators to assess the effectiveness of decontamination procedures. Spores are intricate, multi-layered cellular structures primarily composed of proteins, which significantly contribute to their extreme resistance. Therefore, conducting a comprehensive proteome analysis of spores is crucial to identify the specific proteins
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Human cord plasma proteomic analysis reveals sexually dimorphic proteins associated with intrauterine growth restriction Proteomics (IF 3.4) Pub Date : 2023-12-07 Ayodele Jacob Akinyemi, Xiu Quan Du, Jennifer Aguilan, Simone Sidoli, David Hirsch, Tao Wang, Sandra Reznik, Mamta Fuloria, Maureen J. Charron
Intrauterine growth restriction (IUGR) is associated with increased risk of cardiometabolic disease later in life and has been shown to affect female and male offspring differently, but the mechanisms remain unclear. The purpose of this study was to identify proteomic differences and metabolic risk markers in IUGR male and female neonates when compared to appropriate for gestational age (AGA) babies
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A compositional data model to predict the isotope distribution for average peptides using a compositional spline model Proteomics (IF 3.4) Pub Date : 2023-12-03 Agten Annelies, Vilenne Frédérique, Prostko Piotr, Valkenborg Dirk
We propose an updated approach for approximating the isotope distribution of average peptides given their monoisotopic mass. Our methodology involves in-silico cleavage of the entire UNIPROT database of human-reviewed proteins using Trypsin, generating a theoretical peptide dataset. The isotope distribution is computed using BRAIN. We apply a compositional data modelling strategy that utilizes an additive