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The tumour‐derived extracellular vesicle proteome varies by endometrial cancer histology and is confounded by an obesogenic environment Proteomics (IF 3.4) Pub Date : 2024-04-22 Anastasiia Artuyants, George Guo, Marcella Flinterman, Martin Middleditch, Bincy Jacob, Kate Lee, Laura Vella, Huaqi Su, Michelle Wilson, Lois Eva, Andrew N. Shelling, Cherie Blenkiron
Endometrial cancer, the most common gynaecological cancer worldwide, is closely linked to obesity and metabolic diseases, particularly in younger women. New circulating biomarkers have the potential to improve diagnosis and treatment selections, which could significantly improve outcomes. Our approach focuses on extracellular vesicle (EV) biomarker discovery by directly profiling the proteome of EVs
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Proteomic profiling of antibiotic‐resistant Escherichia coli GW‐AmxH19 isolated from hospital wastewater treated with physical plasma Proteomics (IF 3.4) Pub Date : 2024-04-22 Veronika Hahn, Daniela Zühlke, Hauke Winter, Annchristin Landskron, Jörg Bernhardt, Susanne Sievers, Michael Schmidt, Thomas von Woedtke, Katharina Riedel, Juergen F. Kolb
Microorganisms which are resistant to antibiotics are a global threat to the health of humans and animals. Wastewater treatment plants are known hotspots for the dissemination of antibiotic resistances. Therefore, novel methods for the inactivation of pathogens, and in particular antibiotic‐resistant microorganisms (ARM), are of increasing interest. An especially promising method could be a water treatment
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Model fusion for predicting unconventional proteins secreted by exosomes using deep learning Proteomics (IF 3.4) Pub Date : 2024-04-21 Yonglin Zhang, Lezheng Yu, Ming Yang, Bin Han, Jiesi Luo, Runyu Jing
Unconventional secretory proteins (USPs) are vital for cell‐to‐cell communication and are necessary for proper physiological processes. Unlike classical proteins that follow the conventional secretory pathway via the Golgi apparatus, these proteins are released using unconventional pathways. The primary modes of secretion for USPs are exosomes and ectosomes, which originate from the endoplasmic reticulum
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Review of predicting protein stability changes upon variations Proteomics (IF 3.4) Pub Date : 2024-04-21 Yiling Qiu, Tao Huang, Yu‐Dong Cai
Forecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently
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From data to discovery: The essential role of computational tools in proteomics Proteomics (IF 3.4) Pub Date : 2024-04-17 Wout Bittremieux
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Characterization of a chromatin‐associated TCF7L1 complex in human embryonic stem cells Proteomics (IF 3.4) Pub Date : 2024-04-17 Linh M. Vuong, Songqin Pan, Robert A. Sierra, Marian L. Waterman, Paul D. Gershon, Peter J. Donovan
Human embryonic stem cells (hESCs) resemble the pluripotent epiblast cells found in the early postimplantation human embryo and represent the “primed” state of pluripotency. One factor that helps primed pluripotent cells retain pluripotency and prepare genes for differentiation is the transcription factor TCF7L1, a member of a small family of proteins known as T cell factors/Lymphoid enhancer factors
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Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links Proteomics (IF 3.4) Pub Date : 2024-04-17 Arslan Siraj, Robbin Bouwmeester, Arthur Declercq, Luisa Welp, Aleksandar Chernev, Alexander Wulf, Henning Urlaub, Lennart Martens, Sven Degroeve, Oliver Kohlbacher, Timo Sachsenberg
In protein‐RNA cross‐linking mass spectrometry, UV or chemical cross‐linking introduces stable bonds between amino acids and nucleic acids in protein‐RNA complexes that are then analyzed and detected in mass spectra. This analytical tool delivers valuable information about RNA‐protein interactions and RNA docking sites in proteins, both in vitro and in vivo. The identification of cross‐linked peptides
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DREAMweb: An online tool for graph‐based modeling of NMR protein structure Proteomics (IF 3.4) Pub Date : 2024-04-17 Niladri Ranajan Das, Kunal Narayan Chaudhury, Debnath Pal
The value of accurate protein structural models closely conforming to the experimental data is indisputable. DREAMweb deploys an improved DREAM algorithm, DREAMv2, that incorporates a tighter bound in the constraint set of the underlying optimization approach. This reduces the artifacts while modeling the protein structure by solving the distance‐geometry problem. DREAMv2 follows a bottom‐up strategy
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Polyglutamine disease proteins: Commonalities and differences in interaction profiles and pathological effects Proteomics (IF 3.4) Pub Date : 2024-04-14 Megan Bonsor, Orchid Ammar, Sigrid Schnoegl, Erich E. Wanker, Eduardo Silva Ramos
Currently, nine polyglutamine (polyQ) expansion diseases are known. They include spinocerebellar ataxias (SCA1, 2, 3, 6, 7, 17), spinal and bulbar muscular atrophy (SBMA), dentatorubral‐pallidoluysian atrophy (DRPLA), and Huntington's disease (HD). At the root of these neurodegenerative diseases are trinucleotide repeat mutations in coding regions of different genes, which lead to the production of
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Imputation of missing values in lipidomic datasets Proteomics (IF 3.4) Pub Date : 2024-04-11 Nicolas Frölich, Christian Klose, Elisabeth Widén, Samuli Ripatti, Mathias J. Gerl
Lipidomic data often exhibit missing data points, which can be categorized as missing completely at random (MCAR), missing at random, or missing not at random (MNAR). In order to utilize statistical methods that require complete datasets or to improve the identification of potential effects in statistical comparisons, imputation techniques can be employed. In this study, we investigate commonly used
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Differential expression of N‐glycopeptides derived from serum glycoproteins in mild cognitive impairment (MCI) patients Proteomics (IF 3.4) Pub Date : 2024-04-11 Cristian D. Gutierrez Reyes, Mojgan Atashi, Mojibola Fowowe, Sherifdeen Onigbinde, Oluwatosin Daramola, David M. Lubman, Yehia Mechref
Mild cognitive impairment (MCI) is an early stage of memory loss that affects cognitive abilities with the aging of individuals, such as language or visual/spatial comprehension. MCI is considered a prodromal phase of more complicated neurodegenerative diseases such as Alzheimer's. Therefore, accurate diagnosis and better understanding of the disease prognosis will facilitate prevention of neurodegeneration
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Functional proteomics reveals that Slr0237 is a SigE‐regulated glycogen debranching enzyme pivotal for glycogen breakdown Proteomics (IF 3.4) Pub Date : 2024-04-06 Ye Liu, Haitao Ge, Dandan Lu
The group 2 σ factor for RNA polymerase SigE plays important role in regulating central carbon metabolism in cyanobacteria. However, the regulation of SigE for these pathways at a proteome level remains unknown. Using a sigE‐deficient strain (ΔsigE) of Synechocystis sp. PCC 6803 and quantitative proteomics, we found that SigE depletion induces differential protein expression for sugar catabolic pathways
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Proteomic profiling of small extracellular vesicles derived from mouse pancreatic cancer and stellate cells: Role in pancreatic cancer Proteomics (IF 3.4) Pub Date : 2024-04-04 Chamini J. Perera, SM Zahid Hosen, Tanzila Khan, Haoyun Fang, Alpha Raj Mekapogu, Zhihong Xu, Marco Falasca, Suresh T. Chari, Jeremy S. Wilson, Ron Pirola, David W. Greening, Minoti V. Apte
Small extracellular vesicles (sEVs) are cell‐derived vesicles evolving as important elements involved in all stages of cancers. sEVs bear unique protein signatures that may serve as biomarkers. Pancreatic cancer (PC) records a very poor survival rate owing to its late diagnosis and several cancer cell‐derived proteins have been reported as candidate biomarkers. However, given the pivotal role played
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Open‐source large language models in action: A bioinformatics chatbot for PRIDE database Proteomics (IF 3.4) Pub Date : 2024-04-01 Jingwen Bai, Selvakumar Kamatchinathan, Deepti J. Kundu, Chakradhar Bandla, Juan Antonio Vizcaíno, Yasset Perez‐Riverol
We here present a chatbot assistant infrastructure (https://www.ebi.ac.uk/pride/chatbot/) that simplifies user interactions with the PRIDE database's documentation and dataset search functionality. The framework utilizes multiple Large Language Models (LLM): llama2, chatglm, mixtral (mistral), and openhermes. It also includes a web service API (Application Programming Interface), web interface, and
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Differential effects of physiological agonists on the proteome of platelet‐derived extracellular vesicles Proteomics (IF 3.4) Pub Date : 2024-04-01 Mitchell J. Moon, Alin Rai, Prerna Sharma, Haoyun Fang, James D. McFadyen, David W. Greening, Karlheinz Peter
Arterial thrombosis manifesting as heart attack and stroke is the leading cause of death worldwide. Platelets are central mediators of thrombosis that can be activated through multiple activation pathways. Platelet‐derived extracellular vesicles (pEVs), also known as platelet‐derived microparticles, are granular mixtures of membrane structures produced by platelets in response to various activating
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The temporal protein signature analyses of developing human deciduous molar tooth germ Proteomics (IF 3.4) Pub Date : 2024-03-24 Xiaohang Chen, Gaochi Li, Jian Zhang, Liang Hu, Guoqiang Zhao, Buling Wu, Fengxiang Wei, Fu Xiong
The tooth serves as an exemplary model for developmental studies, encompassing epithelial‐mesenchymal transition and cell differentiation. The essential factors and pathways identified in tooth development will help understand the natural development process and the malformations of mineralized tissues such as skeleton. The time‐dependent proteomic changes were investigated through the proteomics of
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A review of disease risk prediction methods and applications in the omics era Proteomics (IF 3.4) Pub Date : 2024-03-24 Chen Sun, Xiangshu Cheng, Jing Xu, Haiyan Chen, Junxian Tao, Yu Dong, Siyu Wei, Rui Chen, Xin Meng, Yingnan Ma, Hongsheng Tian, Xuying Guo, Shuo Bi, Chen Zhang, Jingxuan Kang, Mingming Zhang, Hongchao Lv, Zhenwei Shang, Wenhua Lv, Ruijie Zhang, Yongshuai Jiang
Risk prediction and disease prevention are the innovative care challenges of the 21st century. Apart from freeing the individual from the pain of disease, it will lead to low medical costs for society. Until very recently, risk assessments have ushered in a new era with the emergence of omics technologies, including genomics, transcriptomics, epigenomics, proteomics, and so on, which potentially advance
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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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