ProteomicsPub Date : 2026-04-23Epub Date: 2026-02-13DOI: 10.1002/pmic.70109
Loay J. Jabre, Elden Rowland, J. Scott P. McCain, Erin M. Bertrand
{"title":"Deep Proteomic Profiles of the Antarctic Diatom Fragilariopsis Cylindrus Under Varying Iron and Manganese Conditions","authors":"Loay J. Jabre, Elden Rowland, J. Scott P. McCain, Erin M. Bertrand","doi":"10.1002/pmic.70109","DOIUrl":"10.1002/pmic.70109","url":null,"abstract":"<p><i>Fragilariopsis cylindrus</i> is a key diatom in the Southern Ocean, where low iron and manganese availability constrain primary production and biogeochemical activity. The molecular mechanisms used by polar diatoms, including <i>F. cylindrus</i>, to cope with trace metal limitations remain largely unexplored. Here we present phenotypic characterizations and proteomic profiles of <i>F. cylindrus</i> grown under controlled iron (low, medium, high) and manganese (low, high) conditions that reflect those observed in the Southern Ocean. Using data-independent acquisition mass spectrometry, we measured over 8000 unique proteins capturing diverse metabolic responses, including those related to photosynthesis, elemental transport, and intracellular trafficking. We confirm consistent expression of canonical iron stress proteins (e.g., phytotransferrin) under low iron, and identify additional candidate biomarkers for iron and manganese stress that could be explored in future laboratory and field experiments. Our data also support the notion that one flavodoxin isoform in <i>F. cylindrus</i> is iron responsive and one is not, and show that PsaE, a protein associated with the iron-rich photosystem-I, is upregulated under low iron. Altogether, this dataset is among the most comprehensive proteomic characterizations of trace metal physiology in polar diatoms to date, providing a foundation for connecting molecular responses to trace metal availability and ocean biogeochemistry.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"112-119"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106929/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146176885","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":"Quantitative Proteomics Reveals the Adaptive Mechanisms of Aeromonas hydrophila Under Cobalt Stress","authors":"Xiaowei Zhang, Chenghao Shen, Zhen Qiu, Linbin Chen, Binghui Zhang, Chunyan Jia, Jinting Guo, Feiliao Lai, Xiangmin Lin","doi":"10.1002/pmic.70106","DOIUrl":"10.1002/pmic.70106","url":null,"abstract":"<div>\u0000 \u0000 <p>Cobalt is an essential micronutrient but becomes toxic at elevated concentrations, requiring microorganisms to balance acquisition and detoxification. <i>Aeromonas hydrophila</i>, an opportunistic aquatic pathogen, is often encountered in metal-contaminated aquatic environments; however, its adaptive responses to cobalt stress have not been systematically characterized. Here, we applied quantitative proteomics to characterize the global protein response of <i>A. hydrophila</i> under cobalt stress. A total of 2767 proteins were identified, of which 724 were differentially abundant. Enrichment analyses indicated that cobalt exposure was associated with alterations in energy metabolism, oxidative phosphorylation, and ribosome-related pathways. Gene set enrichment analysis suggested an overall upregulation of ribosome-associated functions, accompanied by down regulation of carbon metabolism and the tricarboxylic acid cycle. Protein–protein interaction network mapping identified 15 functional clusters, with core modules linked to oxidative phosphorylation, ABC transport, carbohydrate metabolism, and Fe–S cluster biogenesis. Ten hub proteins associated with respiratory and transport systems were identified based on network topology. Functional validation using seven deletion mutants indicated that genes encoding shikimate kinase, glutaminase, and arsenate reductase contribute to cobalt tolerance. Together, these findings provide a systems-level view of how <i>A. hydrophila</i> adapts to cobalt stress, reveal candidate factors mediating metal resistance, and suggest potential targets for antimicrobial development and bioremediation strategies.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"37-47"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146008002","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-03-27DOI: 10.1002/pmic.70118
Asia Saorin, Alberto Martinez-Serra, Michael Henry, Paula Meleady, Marco P. Monopoli
{"title":"Mass Spectrometry Proteomics of the Nanoparticle Corona Is Highly Dependent on Sample Preparation Protocol","authors":"Asia Saorin, Alberto Martinez-Serra, Michael Henry, Paula Meleady, Marco P. Monopoli","doi":"10.1002/pmic.70118","DOIUrl":"10.1002/pmic.70118","url":null,"abstract":"<p>It is widely established that the layers of proteins bound to the surface of nanoparticles (NPs), also known as the protein corona, critically influence their behavior in biological environments. Despite numerous proteomics studies performed in different NP-corona systems, the impact of proteomic sample preparation methods on corona profiling remains poorly understood. In this study, we systematically compared five digestion protocols, namely S-Trap<sup>TM</sup>, iST<sup>TM</sup>, ProteaseMAX<sup>TM</sup>, RapiGest<sup>TM</sup>, and a routine in-gel digestion protocol commonly used in several laboratories. Protein corona samples were isolated from silica NPs incubated in 80% human plasma in phosphate-buffered saline. Protocol performance was assessed in terms of digestion efficiency, protein and peptide yield, reproducibility, and identification bias. Proteomic characterization revealed marked differences across protocols, highlighting the influence of protocol on protein digestion, recovery, and representation. Our findings emphasize the need for method standardization and tailored protocol selection in corona studies to ensure accurate and reproducible proteomic profiling.</p>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"98-111"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106918/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147519502","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-02-18DOI: 10.1002/pmic.70111
Charis Gonidaki, Agnieszka Latosinska, Antonia Vlahou, Rafael Stroggilos, Harald Mischak
{"title":"Practical Impact of Imputation and Batch-Effect Correction for Proteomics/Peptidomics Differential-Abundance Analysis","authors":"Charis Gonidaki, Agnieszka Latosinska, Antonia Vlahou, Rafael Stroggilos, Harald Mischak","doi":"10.1002/pmic.70111","DOIUrl":"10.1002/pmic.70111","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>MS-based proteomics offers powerful opportunities for biomarker discovery; nevertheless, it is associated with technical challenges, including missing values and batch effects. Although imputation and batch-correction methods are well established in proteomics, their impact remains incompletely characterized in large-scale clinical proteomics datasets. Here, we examine the practical impact and interaction of three popular imputation methods (Gaussian, ½ LOD, KNN) in combination with three batch-effect correction approaches (ComBat, ComBat with disease covariate, MNN) on differential abundance analysis in a CE-MS urine peptidomics dataset of 1,050 samples across 13 batches from chronic kidney disease (CKD) patients and controls. Downstream effects were assessed based on peptide validation between discovery and validation sets. Imputation method choice had minimal impact on the final list of disease-associated peptides (DAPs), given the missingness structure and normalization strategy. In contrast, batch-effect correction largely affected the results: MNN and especially unadjusted ComBat removed a large proportion of DAPs (<span></span><math>\u0000 <semantics>\u0000 <mo>∼</mo>\u0000 <annotation>$sim $</annotation>\u0000 </semantics></math>50% and >90%, respectively), whereas inclusion of disease status in the ComBat model largely preserved biological signal. This study highlights how popular preprocessing choices can affect biological signal, showing that imputation and batch-effect correction interact and jointly influence downstream results, underscoring the need for caution when applying batch-effect correction.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Statement of Significance of the Study</h3>\u0000 \u0000 <p>Finding reliable biomarkers in clinical proteomics requires addressing the technical noise that can hide true biological signals. In this work, we examine the practical impact and interaction of commonly used imputation and batch correction methods on the list of peptides that emerge as differentially abundant. Instead of relying on simulations or small datasets, we examine a large, real-world urine-peptidomics cohort of more than 1,000 samples screened for chronic kidney disease. The results demonstrate that, in datasets such as the one used here, different preprocessing strategies can lead to substantially different outcomes. Imputation and batch-effect correction were found to be interdependent, and batch effect removal can lead to loss of meaningful biological differences, highlighting the importance of applying such corrections with caution.</p>\u0000 </section>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"48-58"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106926/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146217946","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-01-06DOI: 10.1002/pmic.70094
Adrien Brown, Alexandre Burel, Sarah Cianférani, Christine Carapito, Fabrice Bertile
{"title":"Brownotate, a Comprehensive Solution to Generate Protein Sequence Databases for Any Species","authors":"Adrien Brown, Alexandre Burel, Sarah Cianférani, Christine Carapito, Fabrice Bertile","doi":"10.1002/pmic.70094","DOIUrl":"10.1002/pmic.70094","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Proteomics is strengthening research in biology and the diversification of the model organisms studied is very promising for fully understanding the complexity of biological principles. However, the lack of protein sequence databases for many species is a major bottleneck. Existing computational solutions are usually incomplete and/or only usable by bioinformaticians. We have built an open-source, user-friendly pipeline, called Brownotate, which allows anyone to generate protein sequence databases for any species as long as sequencing information is available. The pipeline can extract already existing protein sequences, but also automatically annotate any genome assembly or assemble and annotate any DNA sequence dataset. By testing the pipeline with numerous sequencing and assembly datasets covering a large part of the phylogenetic tree, we show that Brownotate generates fragmented but good quality assemblies and good quality annotations when compared to reference data. By comparing the use of protein databases generated by Brownotate or downloaded from NCBI to interpret proteomic data, we show very comparable results. The Brownotate pipeline is, therefore, an important new addition to the proteomics toolbox. The pipeline and its web interface are freely available at https://github.com/LSMBO/Brownotate and https://github.com/LSMBO/brownotate-app, respectively.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Summary</h3>\u0000 \u0000 <div>\u0000 <ul>\u0000 \u0000 <li>\u0000 <p>This study evaluated the performance of a newly developed pipeline, Brownotate, for the assembly and annotation of sequencing data for multiple species, from prokaryotes to eukaryotes. We compared their fragmentation level (assembly) and completeness based on evolutionary expectations of gene content, and we evaluated their overlap. Brownotate generated fragmented, slightly less complete assemblies. However, the overlap of proteins predicted was very good, despite an excess of predicted sequences of small size with Brownotate. In addition, the interpretation of proteomics data downloaded from PRIDE repository for 27 species was found to lead to very similar results regardless of the origin of the protein sequencing database used, whether it was generated by Brownotate or downloaded from NCBI. Brownotate, made available to the community, will, therefore, be a tool of choice to mitigate the lack of an appropriate protein sequence database for many species, and allow proteomists to analyse without delay samples from species for which only sequencing data are available.</p>\u0000 </li>\u0000 </ul>\u0000 </div>\u0000 </section>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"13-26"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106930/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145909824","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-02-26DOI: 10.1002/pmic.70110
Kiran K. Mangalaparthi, Daigo Gunji, Olajide E. Olaleye, Amy J. French, Gunveen S. Sachdeva, Shilpa Venkataraman, Neha Joshi, Tianqi Gao, Sumankalai Ramachandran, Julie A. Vrana, Kenneth J. Rothschild, Mark J. Lim, Gargey Yagnik, Saba Yasir, Michael Keeney, Akhilesh Pandey
{"title":"Imaging Mass Spectrometry-Based Assessment of ER, PR, and HER2 Protein Expression in Breast Cancer","authors":"Kiran K. Mangalaparthi, Daigo Gunji, Olajide E. Olaleye, Amy J. French, Gunveen S. Sachdeva, Shilpa Venkataraman, Neha Joshi, Tianqi Gao, Sumankalai Ramachandran, Julie A. Vrana, Kenneth J. Rothschild, Mark J. Lim, Gargey Yagnik, Saba Yasir, Michael Keeney, Akhilesh Pandey","doi":"10.1002/pmic.70110","DOIUrl":"10.1002/pmic.70110","url":null,"abstract":"<div>\u0000 \u0000 <p>Imaging mass spectrometry has made significant advancements in recent years owing to its ability to study the spatial localization and abundance of proteins, peptides, lipids, glycans, metabolites, and drugs. In this study, we employed an imaging mass spectrometry-based workflow called MALDI-IHC, which uses antibodies conjugated with photocleavable mass-tags, to investigate the detection of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) along with pan-cytokeratin in formalin-fixed paraffin-embedded (FFPE) sections from cases with breast cancer. The expression of ER, PR, and HER2 was consistent with the clinical diagnosis based on conventional immunohistochemistry, lacking signal in triple-negative cases and concordant signals in the cases that were classified as ER+/PR+/HER2+, ER+/PR+/HER2−, and ER−/PR−/HER2+ groups, respectively. In addition, the potential utility of a seconday antibody-based MALDI-IHC approach for HER2 expression was evaluated. In agreement with immunohistochemistry results, HER2 expression co-localized within tumor regions in a HER2+ breast cancer case, while no expression was observed in a HER2− case. Collectively, these results highlight the potential of imaging mass spectrometry-based MALDI-IHC workflow for multiplexed detection of proteins in clinically relevant tissue sections.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"6-12"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147288996","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-02-25DOI: 10.1002/pmic.70112
Ashley N. Ives, James M. Fulcher, Alex R. Bautista, Reta Birhanu Kitata, Sarah M. Williams, David A. Bennett, Philip L. De Jager, Vladislav A. Petyuk
{"title":"Single-Cell Nanodroplet Processing Proteomics Pipeline for Analysis of Human-Derived Microglia","authors":"Ashley N. Ives, James M. Fulcher, Alex R. Bautista, Reta Birhanu Kitata, Sarah M. Williams, David A. Bennett, Philip L. De Jager, Vladislav A. Petyuk","doi":"10.1002/pmic.70112","DOIUrl":"10.1002/pmic.70112","url":null,"abstract":"<div>\u0000 \u0000 \u0000 <section>\u0000 \u0000 <p>Single-cell omics tools provide unique insights into heterogeneous cell populations and their responses to stimuli. For example, single-cell RNA sequencing has identified several transcriptionally distinct populations of microglia, which are resident immune cells of the central nervous system (CNS) that are responsive to CNS injury, infection, and neurodegeneration. To date, single-cell studies of microglia have focused on RNA-sequencing or cytometry by time of flight (CyTOF), which provide indirect readouts of protein abundance or quantification of a limited number of targets. Herein, we present a workflow based on FACS-assisted isolation, cryopreservation, and nanodroplet-based processing for single-cell mass spectrometry proteomics analysis of the postmortem human brain cortex-derived microglia. From a single microglial cell, 1039 proteins could be identified on average. As a proof-of-principle, we applied single-cell proteomics for exploring the heterogeneity of brain microglia at the cellular level. This pilot proteomics data partially recapitulates the prior microglia subtypes. Specifically, we determined that mitochondrial proteins, in particular members of NADH dehydrogenase (Complex I), cytochrome b-c1 (Complex III), cytochrome c oxidase (Complex IV), F1-ATPase (Complex V), and Na+/K+-ATPase complex, drive variation across microglia. This pipeline offers the potential for identifying functionally and analytically relevant protein targets for microglia in Alzheimer's disease and other neurological disorders.</p>\u0000 </section>\u0000 \u0000 <section>\u0000 \u0000 <h3> Significance of the Study</h3>\u0000 \u0000 <p>Microglia are a key brain cell type that may contribute to pathogenesis in neurodegenerative disease. Transcriptomic profiling of microglia from the central nervous system of humans and animal models has identified several subtypes of microglia, and complementary proteomic profiling of microglia is likely to provide functionally and therapeutically relevant targets. Single-cell proteomics studies of human-derived microglia are lacking. This work describes a label-free, single-cell proteomics approach for microglia isolated by fluorescence-activated cell sorting from a human donor that yields comparable numbers of identifications in comparison to prior single-cell RNA sequencing studies of microglia. This approach holds promise for enabling large-scale proteomics-based subtyping of microglia and studying their roles in neurodegenerative diseases.</p>\u0000 </section>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"59-68"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13106911/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147300575","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}
ProteomicsPub Date : 2026-04-23Epub Date: 2026-03-29DOI: 10.1002/pmic.70116
Junjun Yan, Yong Long, Jing Ren, Bei Han, Tong Zhou, Guodong Ge, Qing Li, Guili Song, Zongbin Cui
{"title":"Dynamic Phosphoproteomic Profiling Captured Early Signaling Events for Cold Acclimation in Larval Zebrafish","authors":"Junjun Yan, Yong Long, Jing Ren, Bei Han, Tong Zhou, Guodong Ge, Qing Li, Guili Song, Zongbin Cui","doi":"10.1002/pmic.70116","DOIUrl":"10.1002/pmic.70116","url":null,"abstract":"<div>\u0000 \u0000 <p>The acclimation at mild low temperature can improve the ability of cold tolerance and protect tissues from stress-induced injury in many species, but mechanisms triggering the signal transduction of cold acclimation remain largely unknown. Here, we deciphered the early signaling events associated with immediate temperature drops in zebrafish larvae. Early alternations in the phosphoproteome of larval zebrafish were captured during cold exposure by using an optimized sampling protocol of denaturing with trichloroacetic acid and a tandem mass tagging-based quantitative phosphoproteomic approach. A total of 12,916 phosphosites on 4931 proteins were identified in the phosphoproteome and 7329 phosphosites on 3391 proteins were quantified with 1490 phosphosites on 1098 proteins differentially regulated by cold exposure. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of upregulated phosphosites identified immediate early phosphorylation events on transmembrane proteins, MAPK and transcription factors, and signal pathways that are essential for cold acclimation in larval zebrafish. Moreover, key kinases activated during cold acclimation of larval zebrafish including Ca<sup>2+</sup>/calmodulin-dependent protein kinase-II, protein kinase C, and protein kinase A were experimentally confirmed. Furthermore, a scaffolding protein AHNAK and many other proteins in AHNAK-mediated signaling pathways were robustly phosphorylated, suggesting their key roles in coordinating cold signal perception and transduction. Together, these findings provide a solid foundation for systematically understanding the signaling events of cold acclimation and a valuable phosphoproteome resource for functional studies of stress responses.</p>\u0000 </div>","PeriodicalId":224,"journal":{"name":"Proteomics","volume":"26 5","pages":"69-85"},"PeriodicalIF":3.9,"publicationDate":"2026-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147571494","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}