J. Proteome Res. [JOURNAL]
Sun
200 papers
Protein Biomarkers as Molecular Tools for Forensic Biofluid Identification.
Chhikara A, Gupta V, Kumari P … +1 more , Dalal J
J Proteome Res · 2026 Apr · PMID 41837722 · Publisher ↗
Forensic proteomics has rapidly established a significant role in forensics, particularly when DNA analysis is insufficient. Proteomics has been frequently recognized for helping reveal useful information about the origi...
Forensic proteomics has rapidly established a significant role in forensics, particularly when DNA analysis is insufficient. Proteomics has been frequently recognized for helping reveal useful information about the origin, state and context of forensic samples. Proteins are considered crucial biomarkers in biological samples because of their ability to elucidate cellular functions and post-mortem alterations. Combining advanced mass spectrometry and bioinformatics has increased the importance of proteomics in forensic sciences. The current study examined the use of proteomic technologies, mass spectrometry, and sophisticated software across the key domains of forensic research. The procedure for Post-Mortem Interval (PMI) estimation and body fluid classification proved to be more precise because of the use of machine learning. Peptide biomarkers have helped identify various species by samples of blood, saliva, and semen, and recognize brain, muscles, and skin tissues. Despite significant advancements, the wide acceptance of forensic proteomics remains problematic due to intricate sample stability, high equipment costs, and strict legal standards. Recent advancements in analytical sensitivity, data interpretation tools, and collaborative efforts toward robust protocols position forensic proteomics as an indispensable component of the forensic toolkit. This review indicates the increasing relevance of proteomics in forensic applications, especially relating to PMI estimation, body fluid differentiation, and disease profiling. It promises to significantly enhance the depth of evidentiary interpretation and contribute to more precise and equitable outcomes in the criminal justice system. Proteomic biomarkers need further validation across a range of environments, and standardized protocols should be developed and tested to ensure that proteomics is suitable for forensic use in the courts.
Combined Quantitative and Qualitative Statistical Analyses Improve Benzodiazepine Target Discovery in Label-free Affinity-Based Protein Profiling Data.
Griggs LH, Kim DN, Leach DT … +9 more , Lomas GX, Stratton KG, Schultz KJ, Sveistyte A, Suazo KF, Callister SJ, Cort JR, Wright AT, Lin VS
J Proteome Res · 2026 Apr · PMID 41830962 · Publisher ↗
Affinity-based protein profiling (AfBPP) allows us to identify target proteins that bind drugs or other small molecules of interest in complex samples. As an enrichment technique, label-free AfBPP often generates data wi...
Affinity-based protein profiling (AfBPP) allows us to identify target proteins that bind drugs or other small molecules of interest in complex samples. As an enrichment technique, label-free AfBPP often generates data with high missingness, particularly in negative control samples. We developed an R package, chemoprotR, which enables both quantitative and qualitative statistical analyses of chemoproteomic data, and applied it to the identification of specific benzodiazepine drug targets in the brain. Benzodiazepines comprise a class of drugs that affect GABA receptors through positive allosteric modulation, but benzodiazepine interactions with other proteins are not fully understood. To this end, we synthesized benzodiazepine affinity-based probes (AfBPs) and applied them to rat brain synaptosomes. Our benzodiazepine AfBPs identified GABA receptor subunits and other proteins with ion channel functions. Across the three probes, there was minimal overlap in protein targets identified by competitive labeling with flurazepam, and FR-DA, the probe based on flurazepam, yielded more significant protein targets than the probes based on flunitrazepam. These results demonstrate the ability of benzodiazepine AfBPs to identify protein targets when used with an authentic benzodiazepine to compete for binding sites and highlight the utility of combined statistical analyses for the interpretation of presence-absence data in AfBPP data sets.
Proteomics and Lipidomics Analysis Reveal That Membrane Remodeling and Extracellular Matrix Alterations Are Crucial for Cisplatin Resistance in Triple-Negative Breast Cancer.
Parihari S, Sarkar S, Vashishtha V … +1 more , Srivastava S
J Proteome Res · 2026 Apr · PMID 41823008 · Publisher ↗
Cisplatin is a widely used chemotherapeutic agent for triple-negative breast cancer (TNBC), but resistance remains a major challenge. Understanding the molecular alterations driving this resistance is essential for ident...
Cisplatin is a widely used chemotherapeutic agent for triple-negative breast cancer (TNBC), but resistance remains a major challenge. Understanding the molecular alterations driving this resistance is essential for identifying therapeutic targets. In this study, we employed an integrated proteomics and lipidomics approach to elucidate key pathways associated with cisplatin resistance. Employing high-resolution mass spectrometry, we conducted a comparative analysis between cisplatin-resistant (cisR) and cisplatin-sensitive (cisS) TNBC cell lines to discover resistance-associated alterations in protein and lipid expression. Proteomic analysis revealed overexpression of extracellular matrix (ECM) remodeling proteins, COL6A1, COL6A2, COL6A3, and VTN, that support epithelial-mesenchymal transition (EMT) and chemoresistance. Membrane-associated proteins such as TIMP2, MMP14, and APP were also elevated, indicating enhanced invasive and pro-survival signaling. Lipidomic alterations, including upregulation of FABP3, FABP4, LPL, and downregulation of PLA2G4A, indicated increased lipid uptake, metabolic rewiring, and membrane restructuring. Notably, elevated long-chain phosphatidylcholines and decreased sphingomyelins suggested increased membrane rigidity and reduced cisplatin permeability. Additionally, dysregulation of CDK activity through CCND2, CCND3, and CCNB2 overexpression indicated accelerated cell cycle progression and evasion of DNA damage checkpoints. Together, this integrative analysis highlights ECM remodeling, cytoskeletal dynamics, and lipid metabolism as major contributors to cisplatin resistance and identifies potential therapeutic markers for TNBC.
Site-Specific and Quantitative O-GlcNAc Proteomics for Hepatocellular Carcinoma.
Hou C, Li P, Pei E … +5 more , Zhang H, Wu C, Deng J, Byers SW, Ma J
J Proteome Res · 2026 Apr · PMID 41811088 · Full text
O-linked β--acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) underlies the pathogenesis of multiple cancers, including hepatocellular carcinoma (HCC). However, comprehensive and quantitative characterization o...
O-linked β--acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) underlies the pathogenesis of multiple cancers, including hepatocellular carcinoma (HCC). However, comprehensive and quantitative characterization of site-specific O-GlcNAcylation at the proteome scale remains technically challenging. Here, we employed an integrated workflow for the quantitative O-GlcNAc proteomics of HCC and controls. Proteins from liver samples were subjected to chemoenzymatic labeling, photocleavable alkyne-biotin-based enrichment, proteolytic digestion, and isotopic labeling with tandem mass tags. The O-GlcNAc peptides were analyzed by a nanoUPLC-MS/MS system in HCD product-dependent EThcD (HCD-pd-EThcD) mode for site mapping and quantification. A total of 440 O-GlcNAc peptides, representing 305 sites on 196 proteins, were confidently identified. Differential analysis revealed 190 O-GlcNAc peptides from 121 proteins significantly upregulated in HCC after normalization to their corresponding protein abundance. Functional enrichment and protein-protein interaction analyses indicate that proteins with increased levels of O-GlcNAcylation are involved in nuclear transport, transcriptional regulation, and ATP-dependent chromatin remodeling. Our work provides quantitative proteomic insights into O-GlcNAcylation in HCC, revealing global upregulation and functional clustering of O-GlcNAc-modified proteins. These findings will help elucidate the functional roles of O-GlcNAcylation in liver cancer, facilitating the development of novel therapeutics and sensitive biomarkers.
Untargeted Metabolomic and Lipidomic Profiling in Cystic Fibrosis Patients Using UPLC-QTOF-MS.
Farjallah A, Bergeron C, Cliche D … +2 more , Cantin AM, Auray-Blais C
J Proteome Res · 2026 Apr · PMID 41808657 · Publisher ↗
Cystic fibrosis (CF), also known as mucoviscidosis, is a rare, autosomal recessive genetic disease. It is caused by various mutations in the (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which disrupt the...
Cystic fibrosis (CF), also known as mucoviscidosis, is a rare, autosomal recessive genetic disease. It is caused by various mutations in the (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which disrupt the normal function of the chloride ion channel. Clinical manifestations of CF typically include recurrent respiratory infections, chronic airway inflammation, a progressive decline in lung function, and intermittent pulmonary exacerbations. The primary aim of our study is to identify plasma biomarkers in patients with cystic fibrosis through untargeted metabolomic and lipidomic analyses, with the goal of enabling early detection, accurate diagnosis, and effective monitoring of the disease. Liquid chromatography (LC) coupled with time-of-flight mass spectrometry (TOF-MS) was employed to discriminate the 24 cystic fibrosis patients from the 26 age- and gender-matched healthy controls. Multivariate statistical and pathway enrichment analyses revealed dysregulation in galactose metabolism, glycolysis/gluconeogenesis, bile acid metabolism, fatty acid metabolism, steroid hormone biosynthesis, and amino acid catabolism. The quantification of the targeted cystic fibrosis biomarkers identified by combined lipidomic and metabolomic analyses will be valuable for early diagnosis and treatment.
Correction to "Integrated Single-Tip IMAC-HILIC Enables Simultaneous Analysis of Plant Phosphoproteomics and N-Glycoproteomics".
Chen CW, Chen TA, Lin PY … +2 more , Lin SY, Hsu CC
J Proteome Res · 2026 Apr · PMID 41807308 · Full text
Abstract loading — click title to view on PubMed.
A Sensitive, Specific, and Cost-Effective Lauroylation-Assisted Workflow for Profiling Peptide-Level Protease Specificity Using Proteomic Identification of Cleavage Sites (PICS), with Applicability to Protein-Level N-Terminomics.
Okanishi H, Uno I, Nishimura SI … +2 more , Kanai Y, Masui R
J Proteome Res · 2026 Apr · PMID 41805451 · Publisher ↗
Proteases play crucial roles in numerous biological processes through specific protein cleavage, and their dysregulation has been implicated in various diseases. To better understand protease specificity, we developed a...
Proteases play crucial roles in numerous biological processes through specific protein cleavage, and their dysregulation has been implicated in various diseases. To better understand protease specificity, we developed a lauroylation-assisted proteomic identification of protease cleavage sites (PICS) workflow that labels and enriches targeted protease-generated neo-N-termini using economical reagents and standard laboratory equipment. The lauroylation enables both discrimination of the neo-N-termini in LC-MS/MS and efficient enrichment on a C18 StageTip by exploiting its hydrophobicity. Among tested acylations, we found lauroylation to be optimal for PICS and improved enrichment and fractionation conditions. We demonstrated that this method can profile specificities of multiple proteases with high sensitivity. Furthermore, we extended this concept to N-terminomics to examine proteolysis at the protein level. Protein N-terminal dimethylation is used for labeling, and tryptic internal peptides are lauroylated for removal. This approach identified over 1500 cleavages induced by etoposide, including 912 Asp-cleaved sites consistent with caspase-3 motifs and sensitive to inhibition by Z-DEVD-FMK. Additionally, 2286 protein N-termini were identified in untreated cells, including 1794 non-ORF N-termini with 665 previously annotated processing sites. These results demonstrate that our workflow provides a simple, economical, and widely applicable method for characterizing protease cleavage at both peptide and protein levels.
Glucocorticoid-Induced Proteome and Phosphoproteome Changes in Breast Cancer Cell Lines.
Cho H, Olsen JV
J Proteome Res · 2026 Apr · PMID 41801802 · Full text
Glucocorticoids (GCs) are steroid hormones that bind to the glucocorticoid receptor (GR) as ligands to initiate systemic anti-inflammatory effects. GCs are commonly administered alongside chemotherapy to reduce treatment...
Glucocorticoids (GCs) are steroid hormones that bind to the glucocorticoid receptor (GR) as ligands to initiate systemic anti-inflammatory effects. GCs are commonly administered alongside chemotherapy to reduce treatment-related side effects in breast cancer patients. However, GC administration has been shown to promote metastasis in breast cancer. In this study, we used quantitative mass-spectrometry-based approaches to analyze proteome and phosphoproteome of three breast cancer cell lines following treatment of a clinically approved synthetic GC, dexamethasone (Dex). By comparing MCF7, MDA-MB-231, and MDA-MB-436 cells, we suggest that the level of GR significantly affects Dex-mediated responses. Additionally, we identify noncanonical transcription factors (TFs) and kinases that are regulated by GR in different cell lines. Together, our data present Dex-induced protein modulations and modifications involving several TFs and kinases that regulate cytoskeletal remodeling and migration in breast cancer cell lines. These findings highlight the need for careful consideration of GC use in breast cancer therapy and identify potential molecular targets for mitigating adverse effects.
Salivary Proteomics Reveals Oxidative Markers in E-Cigarette Users.
de Carvalho Faria N, Carvalho BFDC, Alves MGO … +5 more , Feitosa Lima I, Iwai LK, Salardani M, Zelanis A, Almeida JD
J Proteome Res · 2026 Apr · PMID 41801104 · Full text
Electronic cigarettes (e-cigs) have become increasingly popular, particularly among younger populations. This study aimed to evaluate the salivary proteome of e-cig users and identify potential alterations in saliva comp...
Electronic cigarettes (e-cigs) have become increasingly popular, particularly among younger populations. This study aimed to evaluate the salivary proteome of e-cig users and identify potential alterations in saliva composition. Participants were divided into the Electronic Cigarette Group (EG, = 25 regular exclusive users) and the Control Group (CG, = 25 nonsmokers/nonusers), matched by sex and age. Clinical examination and unstimulated saliva collection were performed for proteomic analysis. A total of 1,773 proteins were identified, of which 92 had consistent quantitative values between groups. Comparison using the Wilcoxon-Mann-Whitney test revealed 22 proteins with differential abundance ( ≤ 0.05), most of them up-regulated in EG, notably Peroxiredoxin-1, while few showed decreased abundance. Functional enrichment analysis highlighted pathways related to keratinization, keratinocyte differentiation, and stress response, suggesting activation of cellular defense and adaptation mechanisms. These results indicate that e-cig aerosol exposure induces biological alterations in the oral environment, including modulation of proteins linked to oxidative stress and epithelial integrity. Overall, the findings emphasize the need for long-term monitoring of e-cig users and reinforce the importance of educational strategies to counter the perception of low risk associated with electronic cigarettes.
Comprehensive Lysine Ubiquitome Profiling Reveals Diverse Functions of Lysine Ubiquitination in .
Qu Z, Gong Z, Olajide JS … +3 more , Wang J, Yin H, Cai J
J Proteome Res · 2026 Apr · PMID 41800604 · Publisher ↗
is a parasitic protozoan with a direct lifecycle in a single host, but with diverse intermediate stages while developing in the host. Each developmental stage has distinct structural, pathogenic, genetic, and protein ex...
is a parasitic protozoan with a direct lifecycle in a single host, but with diverse intermediate stages while developing in the host. Each developmental stage has distinct structural, pathogenic, genetic, and protein expression, emerging from gene modifications and post-translational modifications (PTMs) of proteins. Ubiquitination regulates diverse cellular functions and activities. Until now, however, there have been sparse data on ubiquitination except on some ubiquitin-related enzymes. It is pertinent to unveil the mechanism through which developmental stages convert ubiquitin to its development. Herein, the ubiquitome of five life-stages (unsporulated oocyst, early stage of sporulation (i.e., 7 h into sporulation of the oocyst), sporulated oocyst, sporozoite, and second-generation merozoite) of was investigated and compared. Correlation analysis of label-free quantitative proteomic and ubiquitomic data was performed. Ubiquitin proteomes were detected and dynamically expressed during the oocyst sporulation process and other developmental stages. This implies that protein ubiquitination is perhaps a key regulator of parasite developmental transitions, biology, and pathogenicity. In brief, this study lays the foundation for future in-depth analysis and functional validation of the ubiquitin proteome and modified proteins in the life cycle of the avian parasite. The raw ubiquitome and parallel reaction monitoring (PRM) data sets are accessible via the iProX repository, assigned with accession numbers PXD043159 and PXD067512, respectively.
Exploring the Impact of Two DNA Minor Groove Binder Compounds on HCT-116 Cells: A Comprehensive Multiomics Analysis Using Mass Spectrometry.
Al-Daffaie FM, Zenati RA, Alniss HY … +9 more , Al-Hroub HM, El-Awady R, Abuhelwa AY, Ramadan WS, El-Huneidi W, Abu-Gharbieh E, Alzoubi KH, Bustanji Y, Semreen MH
J Proteome Res · 2026 Apr · PMID 41789925 · Publisher ↗
Colorectal cancer (CRC) remains a major global health burden, necessitating innovative therapeutic approaches with improved selectivity and reduced toxicity. DNA minor groove binders (MGBs) represent a promising class of...
Colorectal cancer (CRC) remains a major global health burden, necessitating innovative therapeutic approaches with improved selectivity and reduced toxicity. DNA minor groove binders (MGBs) represent a promising class of agents that modulate DNA-associated processes without inducing permanent DNA damage. In this study, two previously reported distamycin-like DNA minor groove binders, MGB30 and MGB32, were investigated to elucidate their molecular mechanisms of action in HCT-116 human colorectal cancer cells. An integrated multiomics approach combining metabolomics and proteomics was employed using TIMS-QTOF-UHPLC-MS. Four biological replicates were used for each treatment condition. Following MGB30 treatment, 12 metabolites and 187 proteins were significantly dysregulated, whereas MGB32 treatment resulted in alterations of 41 metabolites and 409 proteins using a Student's -test with -value <0.05. Pathway enrichment analysis revealed that both compounds significantly disrupted purine metabolism, while MGB32 additionally affected beta-alanine metabolism, glutathione metabolism, and spermidine and spermine biosynthesis. Proteomic analysis further demonstrated deactivation of RNA processing, translation, and ribosome biogenesis, leading to impaired protein synthesis and reduced cancer cell proliferation. This study provides mechanistic insights into the downstream molecular effects of MGB30 and MGB32 that disrupt key mechanisms underlying tumor growth, offering new avenues for CRC treatment.
EasyFigAssembler: Enhance Omics Data Storytelling through Effective Figure Assembly.
Long NP, Thu NQ
J Proteome Res · 2026 Apr · PMID 41781195 · Publisher ↗
An effective figure helps communicate the data and findings clearly. The assembly of multi-panel omics-based figures for scientific publications is a time-consuming and error-prone process that often requires specialized...
An effective figure helps communicate the data and findings clearly. The assembly of multi-panel omics-based figures for scientific publications is a time-consuming and error-prone process that often requires specialized software and skills. There is a lack of a quick and effective tool for assembling complex omics-based figures. We present EasyFigAssembler, a user-friendly web application that significantly simplifies and accelerates the making of multi-panel omics-based figures. The app supports nondestructive panel editing, multi-figure project management, and high-resolution export to TIFF, PDF, PNG, and JPEG formats, providing a complete solution for figure assembly without requiring programming expertise. Its Smart Layout feature automates the initial arrangement of panels into optimal, publication-ready grids. The advanced controls for column and row spanning enable the rapid assembly of complex, non-uniform layouts that are typically time-consuming to create. The workflow is ensured by an integrated Quality Advisor module that provides real-time feedback on effective resolution and color-blind-friendly palettes to warrant journal compliance. Finally, users can manage multiple figures and save their projects effortlessly. The source code of EasyFigAssembler is available at https://github.com/Pharmaco-OmicsLab/EasyFigAssembler. The web interface for users can be accessed at https://easyverse.app/easyfig/.
Fine-Tuning of Label-Free Single-Cell Proteomics Workflows.
Perdu-Alloy P, Keller C, Seth A … +1 more , Carapito C
J Proteome Res · 2026 Apr · PMID 41779902 · Publisher ↗
Mass spectrometry-based single-cell proteomics emerges as the most promising method for studying cellular heterogeneity at the global proteome level with unprecedented depth and coverage. Its widespread application remai...
Mass spectrometry-based single-cell proteomics emerges as the most promising method for studying cellular heterogeneity at the global proteome level with unprecedented depth and coverage. Its widespread application remains limited due to robustness, reproducibility, and throughput requirements, still difficult to meet as analyzing large cohorts of single cells is necessary to ensure statistical confidence. In this context, we conducted method optimizations at three levels. First, we benchmarked three distinct workflows compatible with the nanoElute2 platform using different sample collection/preparation plate supports (EVO96 oil-free, LF48 oil-based, and LF48 oil-free, a streamlined automated sample resuspension, and direct injection protocol). Then, we compared the optimized EVO96 workflow on nanoElute2 with Evosep-based separations operating at two analytical throughputs (80 and 120 samples per day). Subsequently, we evaluated digestion efficiency using a range of enzyme/protein ratios (1:1; 10:1; 20:1; 50:1) to maximize peptide recovery. Finally, the chromatographic setup was refined to determine the best compromise between throughput and robustness. Altogether, these optimizations allowed to establish a robust workflow quantifying up to 5000 proteins in 10 min gradient time per single HeLa cell at a 55 samples-per-day throughput.
Optimization of the Identification Rate and Reproducibility of an Untargeted diaPASEF Method Applicable for Quantitative Peptide Profiling of Hydrolyzed Infant Formula.
Kupfer A, Gensberger-Reigl S, Stützer J … +1 more , Pischetsrieder M
J Proteome Res · 2026 Apr · PMID 41779542 · Publisher ↗
Quality control of hydrolyzed infant formula (HIF) requires comprehensive and precise quantification of its peptide components. Quantitative peptidome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
Quality control of hydrolyzed infant formula (HIF) requires comprehensive and precise quantification of its peptide components. Quantitative peptidome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) with data-independent acquisition (DIA) and parallel accumulation-serial fragmentation (PASEF) is used for this application. Here, an optimization strategy was developed to increase the peptide identification rate and the qualitative and quantitative reproducibility of this approach. To expand the peptide identification rate, the originally assigned equidistant ion mobility (IM) windows were transferred to variable ion mobility windows with manually adjusted window placement. To improve the reproducibility, major acquisition parameters, such as the number of diaPASEF scans and ion mobility windows as well as the resulting cycle time, were systematically optimized. Thus, the approach was modified from 17 equidistant windows with a cycle time of 1.8 s to 30 variable windows with a cycle time of 1.7 s. The optimization process led to the identification of 628 peptides versus 522 peptides, increasing the identification rate by 20.3%. Concurrently, the coefficient of variation (CV) for peptide identification was reduced from 10.9 to 0.8%, and for quantitative reproducibility, it was reduced from 24.3 to 17.2%. Based on these results, an optimization workflow is presented to systematically improve the identification rate and reproducibility for other sample types and instruments.
Identification of Novel Drug Targets for Pulmonary Arterial Hypertension through Integrated Plasma Proteomics.
Chen H, Chen J, Hou C … +2 more , Rui H, Xie L
J Proteome Res · 2026 Apr · PMID 41777075 · Publisher ↗
This study aimed to identify plasma proteins causally associated with pulmonary arterial hypertension (PAH) by using a proteome-wide Mendelian randomization (PWMR) approach. We integrated two large proteomic genome-wide...
This study aimed to identify plasma proteins causally associated with pulmonary arterial hypertension (PAH) by using a proteome-wide Mendelian randomization (PWMR) approach. We integrated two large proteomic genome-wide association study (GWAS) data sets with two PAH GWAS data sets and applied PWMR, Bayesian colocalization, and SMR to prioritize candidate proteins. Drug prediction, molecular docking, single-cell RNA sequencing (scRNA-seq) profiling, and a phenome-wide association study (PheWAS) were further used to assess druggability and potential phenotypic associations. PWMR identified 271 PAH-associated proteins, which were refined to the following three targets: CASP10, NOTCH3, and NCAM2. Molecular docking showed strong predicted binding between CASP10 and usnic acid and masoprocol and between NOTCH3 and 2-mercaptobenzothiazole. scRNA-seq data revealed CASP10 expression in endothelial and inflammatory cells and NOTCH3 expression in smooth muscle cells and fibroblasts. The PheWAS did not detect any adverse associations that survived the false discovery rate (FDR) correction. Overall, this integrated analysis highlights CASP10 and NOTCH3 as potential therapeutic targets for PAH. CASP10, as supported by stronger predicted druggability and multiomics evidence, warrants priority for further experimental evaluation.
The Peptonizer2000: Bringing Confidence to Metaproteomics.
Holstein T, Verschaffelt P, Van Den Bossche T … +4 more , Van de Vyver S, Martens L, Mesuere B, Muth T
J Proteome Res · 2026 Apr · PMID 41776819 · Full text
Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on sim...
Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available data sets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities.
Reliable Identification of Cardiac Maturation Markers Using Robust and Flexible Label-Free Proteomic Quantitation by Spectral Counting on Relatively Abundant Proteins.
Chang G, Torkamannejad S, Muraoka N … +2 more , Murry CE, Sun B
J Proteome Res · 2026 Apr · PMID 41770908 · Publisher ↗
The identification of biomarkers has been one of the major applications in proteomics research. The high specificity and sensitivity of a good biomarker can be evaluated only in population studies, which is costly and a...
The identification of biomarkers has been one of the major applications in proteomics research. The high specificity and sensitivity of a good biomarker can be evaluated only in population studies, which is costly and a limited number of candidate proteins can be evaluated. However, high throughput proteomics usually identifies thousands of proteins from a biological sample and yields tens to hundreds of candidate biomarkers. We demonstrate the use of robust and flexible spectral counting, a label-free semiquantitative method, on relatively abundant proteins to integrate proteomic results from different samples obtained from different laboratories for reliable biological insights and high-quality biomarkers. Furthermore, this strategy can be easily tuned for one or a few biomarkers on demand. We illustrate the use of this strategy to reveal the biological differences between terminally differentiated myocardium and rapidly proliferating HEK293T cells, as well as the successful selection of both positive and negative maturation markers for cardiomyocytes differentiated from human induced pluripotent stem cells (hiPSCs). The advantage of this strategy is the capacity to utilize the exponentially growing number of proteomic results deposited in the public repository for candidate biomarker selection and to derive biological insights.
Proteomics-Driven Molecular Mechanism of Cinnamaldehyde against Methicillin-Resistant Infection: Covalent Modifications of Sortase A and Aconitase.
Peng H, Wu F, Ma X … +5 more , Wang J, Jin L, Ling Y, Zhao G, Yang D
J Proteome Res · 2026 Apr · PMID 41769793 · Publisher ↗
Cinnamaldehyde (CA) from shows strong antimicrobial activity against MRSA. This study used proteomics and high-resolution mass spectrometry with an MRSA-infected cell model to explore CA's antimicrobial mechanisms. CA c...
Cinnamaldehyde (CA) from shows strong antimicrobial activity against MRSA. This study used proteomics and high-resolution mass spectrometry with an MRSA-infected cell model to explore CA's antimicrobial mechanisms. CA covalently modifies Sortase A's active site cysteine (Cys184), a key enzyme for anchoring virulence factors to the MRSA cell wall. This modification inhibits Sortase A's activity, blocking virulence factor anchoring and impairing MRSA's adhesion, infection, and immune evasion. CA also covalently modifies Aconitase's [4Fe-4S] cluster active sites (Cys509, Cys512), disrupting citrate isomerization in the TCA cycle and causing ATP depletion. These modifications lead to NADH and glutathione depletion, increased ROS levels, oxidative stress, and bacterial death in MRSA. CA forms thiohemiketal and thioester structures with the active site cysteines of Sortase A and Aconitase. These findings provide potential targets for new anti-MRSA drugs and support CA's antibacterial application.
Enrichment and Preservation of Urine Metabolites Using Styrene Divinylbenzene Reversed Phase Sulfonate (SDB-RPS) Disks for Enhanced Biomarker Discovery and Disease Monitoring.
Wang A, Xu J, Sun J … +7 more , Ma J, Wang L, Liu X, Sun H, Guo Z, Wang Y, Sun W
J Proteome Res · 2026 Apr · PMID 41744491 · Publisher ↗
Urine metabolomics plays a crucial role in biomarker discovery and disease monitoring, but challenges in metabolite preservation remain. This study evaluates the use of styrene divinylbenzene reversed phase sulfonate (SD...
Urine metabolomics plays a crucial role in biomarker discovery and disease monitoring, but challenges in metabolite preservation remain. This study evaluates the use of styrene divinylbenzene reversed phase sulfonate (SDB-RPS) disks for enriching and preserving urine metabolites utilizing ultraperformance liquid chromatography-mass spectrometry (UPLC-MS) for analysis. We compared SDB-RPS-enriched urine samples with untreated urine across three experimental parts: (1) metabolic profiling using C18 and HILIC chromatography under both positive and negative ion modes; (2) degradation kinetics, where SDB-RPS and untreated urine samples were incubated at 55, 65, and 75 °C with constant humidity (75%); and (3) disease classification using hepatitis ( = 72) and cirrhosis ( = 72) samples. The results revealed that metabolite identification was highly consistent between SDB-RPS and urine samples, with an overlapping rate of 88.26%. Additionally, in the disease classification task, the SDB-RPS panel demonstrated consistent performance, with AUC values of 0.867 and 0.828 in training and validation data sets, respectively, outperforming the urine panel (AUC: 0.765 and 0.691, respectively). These findings suggest that SDB-RPS disks significantly enhance the enrichment and long-term preservation of urine metabolites, offering a promising tool for clinical sample analysis and biomarker discovery.
Comparative Proteomic Analysis of the Secretome of Control and BRAF/MEK Inhibitor-Resistant Melanoma Cells.
Simiczyjew A, Surman M, Kot M … +2 more , Przybyło ME, Nowak D
J Proteome Res · 2026 Apr · PMID 41742019 · Full text
Treatment based on BRAF/MEK kinase inhibitors is one of the most commonly used methods in advanced melanoma therapy, but patients often develop resistance to treatment. Treatment-resistant cells can affect other cancer c...
Treatment based on BRAF/MEK kinase inhibitors is one of the most commonly used methods in advanced melanoma therapy, but patients often develop resistance to treatment. Treatment-resistant cells can affect other cancer cells and the tumor microenvironment through the factors that they secrete. Therefore, this study aimed to examine the protein composition of the secretome of cells resistant to vemurafenib (a BRAF inhibitor) and cobimetinib (a MEK inhibitor) and to compare it with that of nonresistant cells. Proteomic analysis, followed by gene ontology (GO) analysis, identified many differences in resistant melanoma cells' secretomes compared to controls (nonresistant). Many proteins upregulated in resistant melanoma cells compared to their nonresistant variants were directly related to cancer progression and associated with cell adhesion, actin cytoskeleton, matrix organization, proteolysis, and drug resistance. Proteins secreted by resistant melanoma cells can undoubtedly influence the surrounding microenvironment in a way that promotes the formation of a pro-tumor niche. Among the proteins secreted in significantly higher amounts by resistant cells (compared to the control group), which may be potential biomarkers or therapeutic targets in melanoma, plasminogen activator inhibitor 1, thymosin beta-4, clusterin, interleukin-6, superoxide dismutase, and selected matrix metalloproteinases can be distinguished.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe