Proteomics最新文献

{"title":"Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus larvae","authors":"Tomas Erban,&nbsp;Bruno Sopko","doi":"10.1002/pmic.202300280","DOIUrl":"10.1002/pmic.202300280","url":null,"abstract":"<p>Mass spectrometry proteomics data are typically evaluated against publicly available annotated sequences, but the proteogenomics approach is a useful alternative. A single genome is commonly utilized in custom proteomic and proteogenomic data analysis. We pose the question of whether utilizing numerous different genome assemblies in a search database would be beneficial. We reanalyzed raw data from the exoprotein fraction of four reference Enterobacterial Repetitive Intergenic Consensus (ERIC) I–IV genotypes of the honey bee bacterial pathogen <i>Paenibacillus larvae</i> and evaluated them against three reference databases (from NCBI-protein, RefSeq, and UniProt) together with an array of protein sequences generated by six-frame direct translation of 15 genome assemblies from GenBank. The wide search yielded 453 protein hits/groups, which UpSet analysis categorized into 50 groups based on the success of protein identification by the 18 database components. Nine hits that were not identified by a unique peptide were not considered for marker selection, which discarded the only protein that was not identified by the reference databases. We propose that the variability in successful identifications between genome assemblies is useful for marker mining. The results suggest that various strains of <i>P. larvae</i> can exhibit specific traits that set them apart from the established genotypes ERIC I–V.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300280","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140920261","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contents: Proteomics 10'24","authors":"","doi":"10.1002/pmic.202470073","DOIUrl":"https://doi.org/10.1002/pmic.202470073","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202470073","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140919274","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Board: Proteomics 10'24","authors":"","doi":"10.1002/pmic.202470072","DOIUrl":"https://doi.org/10.1002/pmic.202470072","url":null,"abstract":"","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 10","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202470072","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140919273","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Single-cell proteomics by mass spectrometry: Advances and implications in cancer research","authors":"Yong Chiang Tan,&nbsp;Teck Yew Low,&nbsp;Pey Yee Lee,&nbsp;Lay Cheng Lim","doi":"10.1002/pmic.202300210","DOIUrl":"10.1002/pmic.202300210","url":null,"abstract":"<p>Cancer harbours extensive proteomic heterogeneity. Inspired by the prior success of single-cell RNA sequencing (scRNA-seq) in characterizing minute transcriptomics heterogeneity in cancer, researchers are now actively searching for information regarding the proteomics counterpart. Therefore recently, single-cell proteomics by mass spectrometry (SCP) has rapidly developed into state-of-the-art technology to cater the need. This review aims to summarize application of SCP in cancer research, while revealing current development progress of SCP technology. The review also aims to contribute ideas into research gaps and future directions, ultimately promoting the application of SCP in cancer research.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 12-13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140896365","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative proteomics investigating the intrinsic adaptation mechanism of Aeromonas hydrophila to streptomycin","authors":"Shuangziying Zhang,&nbsp;Wenxiao Yang,&nbsp;Yuyue Xie,&nbsp;Xinrui Zhao,&nbsp;Haoyu Chen,&nbsp;Lishan Zhang,&nbsp;Xiangmin Lin","doi":"10.1002/pmic.202300383","DOIUrl":"10.1002/pmic.202300383","url":null,"abstract":"<p><i>Aeromonas hydrophila</i>, a prevalent pathogen in the aquaculture industry, poses significant challenges due to its drug-resistant strains. Moreover, residues of antibiotics like streptomycin, extensively employed in aquaculture settings, drive selective bacterial evolution, leading to the progressive development of resistance to this agent. However, the underlying mechanism of its intrinsic adaptation to antibiotics remains elusive. Here, we employed a quantitative proteomics approach to investigate the differences in protein expression between <i>A. hydrophila</i> under streptomycin (SM) stress and nonstress conditions. Notably, bioinformatics analysis unveiled the potential involvement of metal pathways, including metal cluster binding, iron-sulfur cluster binding, and transition metal ion binding, in influencing <i>A. hydrophila</i>’<i>s</i> resistance to SM. Furthermore, we evaluated the sensitivity of eight gene deletion strains related to streptomycin and observed the potential roles of petA and AHA_4705 in SM resistance. Collectively, our findings enhance the understanding of <i>A. hydrophila</i>’<i>s</i> response behavior to streptomycin stress and shed light on its intrinsic adaptation mechanism.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 19","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluation of proteome dynamics: Implications for statistical confidence in mass spectrometric determination","authors":"Inga Popova,&nbsp;Ekaterina Savelyeva,&nbsp;Tatyana Degtyarevskaya,&nbsp;Dmitrii Babaskin,&nbsp;Andrei Vokhmintsev","doi":"10.1002/pmic.202300351","DOIUrl":"10.1002/pmic.202300351","url":null,"abstract":"<p>Single-cell proteomics is currently far less productive than other approaches. Still, the proteomic community is having trouble adapting to the limitation of having to examine fewer cells than they would like. Studies on a small number of cells should be carefully planned to maximize the chances of success in this situation. This study aims to determine how sample size and measurement speed (slope)/variation affect the accuracy of a protein proteome mass spectrometric determination. The determination accuracy was shown to increase, and the false positive rate was shown to decrease as the sample size increased from 7 to 100 cells and the measurement slope/variation (S/V) ratio increased from 1 to 6. Furthermore, it was discovered that the number of cells in the sample increased the accuracy of this estimate. Thus, for 100 cells, the measurement S/V ratio was typically estimated to be very close to the real-world value, with a standard deviation of 0.35. For sample sizes from 7 to 100 cells, this accuracy was seen when calculating the measurement S/V ratio. The findings can help researchers plan experiments for mass spectroscopic protein proteome determination and other research purposes.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of effective, simple, and low-cost precipitation methods for depleting abundant plasma proteins to enhance the depth and breadth of plasma proteomics","authors":"Shawn J. Rice,&nbsp;Chandra P. Belani","doi":"10.1002/pmic.202400071","DOIUrl":"10.1002/pmic.202400071","url":null,"abstract":"<p>Plasma is an abundant source of proteins and potential biomarkers to aid in the detection, diagnosis, and prognosis of human diseases. These proteins are often present at low levels in the blood and difficult to identify and measure due to the large dynamic range of proteins. The goal of this work was to characterize and compare various protein precipitation methods related to how they affect the depth and breadth of plasma proteomic studies. Abundant protein precipitation with perchloric acid (PerCA) can increase protein identifications and depth of plasma proteomic studies. Three acid- and four solvent-based precipitation methods were evaluated. All methods tested provided excellent plasma proteomic coverage (&gt;600 identified protein groups) and detected protein in the low pg/mL range. Functional enrichment analysis revealed subtle differences within and larger changes between the precipitant groups. Methanol-based precipitation outperformed the other methods based on identifications and reproducibility. The methods’ performance was verified using eight lung cancer patient samples, where &gt;700 protein groups were measured and proteins with an estimated plasma concentration of ∼10 pg/mL were detected. Various protein precipitation agents are amenable to extending the depth and breadth of plasma proteomes. These data can guide investigators to implement inexpensive, high-throughput methods for their plasma proteomic workflows.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 15","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400071","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828388","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"From flesh to bones: Multi-omics approaches in forensic science","authors":"Noemi Procopio,&nbsp;Andrea Bonicelli","doi":"10.1002/pmic.202200335","DOIUrl":"10.1002/pmic.202200335","url":null,"abstract":"<p>Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 12-13","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202200335","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140828579","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The cuticle proteome of a planktonic crustacean","authors":"Kathrin A. Otte,&nbsp;Maridel Fredericksen,&nbsp;Peter Fields,&nbsp;Thomas Fröhlich,&nbsp;Christian Laforsch,&nbsp;Dieter Ebert","doi":"10.1002/pmic.202300292","DOIUrl":"10.1002/pmic.202300292","url":null,"abstract":"<p>The cuticles of arthropods provide an interface between the organism and its environment. Thus, the cuticle's structure influences how the organism responds to and interacts with its surroundings. Here, we used label-free quantification proteomics to provide a proteome of the moulted cuticle of the aquatic crustacean <i>Daphnia magna</i>, which has long been a prominent subject of studies on ecology, evolution, and developmental biology. We detected a total of 278 high-confidence proteins. Using protein sequence domain and functional enrichment analyses, we identified chitin-binding structural proteins and chitin-modifying enzymes as the most abundant protein groups in the cuticle proteome. Structural cuticular protein families showed a similar distribution to those found in other arthropods and indicated proteins responsible for the soft and flexible structure of the <i>Daphnia</i> cuticle. Finally, cuticle protein genes were also clustered as tandem gene arrays in the <i>D. magna</i> genome. The cuticle proteome presented here will be a valuable resource to the <i>Daphnia</i> research community, informing genome annotations and investigations on diverse topics such as the genetic basis of interactions with predators and parasites.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 14","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202300292","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812762","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular vesicles—An omics view","authors":"David W. Greening,&nbsp;Alin Rai,&nbsp;Richard J. Simpson","doi":"10.1002/pmic.202400128","DOIUrl":"10.1002/pmic.202400128","url":null,"abstract":"<p>Extracellular vesicles (EVs) are taking a central stage in intercellular communication, as conserved signaling mediators across species and kingdoms. In fact, there has been an emergence in the understanding and expansion of EVs in diverse fields including cell biology, biomedical sciences, immune regulation and vaccine development, biomarker discovery, and disease diagnosis/monitoring. To enhance and modify their form, function, and therapeutic utility, the field has expanded to modify EVs using various bioengineering strategies, which collectively have garnered significant clinical interest given their potential for drug delivery and therapeutic intervention. As heterogeneous, phospholipid membrane-enclosed structures. EVs affect the functions of other cells through their surface proteins, complex encapsulated cargo molecules (including proteins and RNAs), and select lipids and glycans. Moreover, EVs are a potential source of disease-associated biomarkers for diagnosis, composed of a molecular fingerprint of the releasing cell type (i.e., tumor-specific molecules), enabling a molecular analysis of practically all organs in the body.</p><p>The form and function of EVs is marked by their proteome. Proteomic studies have generated new knowledge in the EV field, with exceptional insights into cargo sorting mechanisms [<span>1, 2</span>], EV heterogeneity and the subtypes and sub-populations of EVs and particles [<span>3-7</span>], genesis [<span>8</span>], surfaceome [<span>9, 10</span>], interaction network [<span>11</span>], intracellular trafficking pathways [<span>12</span>], release (including organs [<span>13, 14</span>]/tissues [<span>15</span>]), targeting/localization [<span>16</span>], uptake [<span>17</span>] and function [<span>18, 19</span>], to identifying specific marker proteins [<span>20</span>]. Their interrogation of EVs in biofluids has also highlighted their diagnostic potential [<span>21-23</span>] and therapeutic targets [<span>24</span>], establishing the role of EVs in health and disease.</p><p><i>This issue reveals a new understanding of EVs that influences their diverse signaling functions. The studies outlined in this issue (26 articles, covering 16 research studies) shed light on new potential players in intercellular signaling, from cells, tissues, bacteria, and even platelets, and uncovers the functional tasks and diagnostic potential accomplished by the cargo of these extracellular membranous structures</i>.</p><p>Platelet-derived EVs (pEVs) represent the most abundant EV type in the circulation in healthy humans. Moon et al., [<span>25</span>] examined the proteome dynamic of pEVs in the context of different physiological platelet agonist to induce platelet activation, uncovering the mode of platelet activation as a direct impact on the proteome landscape. Using agonists representative of the varied activation states of platelets within a thrombus, the correlation study revealed an upregulation of various classes","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"24 11","pages":""},"PeriodicalIF":3.4,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/pmic.202400128","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140812760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}