J. Proteome Res. [JOURNAL]
Sun
200 papers
Reduction-Free Thermolysin Digestion Enables Absolute Protein Quantitation in Plasma in 35 min from Sample to Result.
Jiang X, Lao Y, Johnston JB … +2 more , Banerji V, Zahedi RP
J Proteome Res · 2026 Jul · PMID 42113895 · Publisher ↗
We previously reported that the broad-specificity protease thermolysin yields reproducible, near-complete proteome digests within 1-2 min. Here, we demonstrate rapid absolute protein quantitation in human plasma by combi...
We previously reported that the broad-specificity protease thermolysin yields reproducible, near-complete proteome digests within 1-2 min. Here, we demonstrate rapid absolute protein quantitation in human plasma by combining reduction/alkylation-free thermolysin digestion on S-Trap cartridges with full-length stable isotope-labeled (SIL) protein standards and parallel reaction monitoring (PRM). Post-digest dilution of S-Trap eluates enabled immediate EvoTip loading, yielding LC-MS-ready samples in under 20 min. Using the anti-CD20 monoclonal antibody rituximab as a showcase, a lower limit of quantitation of 5 amol on-column per ∼250 ng plasma protein injection could be achieved on an Orbitrap Exploris 480 in 60/100 samples-per-day mode. We applied the assay to 23 total pretreatment and on-treatment plasma samples from 12 chronic lymphocytic leukemia patients, demonstrating fit-for-purpose absolute quantitation in a clinical matrix. In 100 samples-per-day mode, the full workflow enables on-demand absolute protein quantitation in 35 min from sample to fully acquired LC-MS data. The achieved sensitivity indicates the feasibility of transfer to other targets or matrices with lower concentrations. Because the required SIL proteins are used at femtomole levels (here, 40 fmol of SIL rituximab spiked into 10 μg of plasma protein), a single 10-μg SIL IgG vial is sufficient as internal standard for ∼1700 injections.
Metabolomics Integrated with Mass Spectrometry Imaging Reveals Novel Action of Rb1 in Ischemic Stroke.
Li M, Qian S, Qian L … +7 more , Cui G, Tan S, Guo W, Chen S, Zheng G, Liao J, Fan X
J Proteome Res · 2026 Jun · PMID 42102236 · Publisher ↗
Ischemic stroke is a leading cause of death and disability, yet effective pharmacological interventions remain limited. Ginsenoside Rb1, a principal bioactive compound of , has demonstrated neuroprotective activity, but...
Ischemic stroke is a leading cause of death and disability, yet effective pharmacological interventions remain limited. Ginsenoside Rb1, a principal bioactive compound of , has demonstrated neuroprotective activity, but its metabolic mechanisms remain incompletely defined. Here, we combined lipid metabolomics with matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) to investigate the spatially resolved metabolic effects of Rb1 in a rat model of cerebral ischemia/reperfusion injury. Rb1 treatment significantly reduced infarct volume and improved neurological outcomes. Metabolomic profiling revealed that Rb1 reversed ischemia-induced disturbances in the glycerophospholipid and amino acid metabolism, while MSI demonstrated recovery of phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine distributions in the ischemic cortex. These metabolic improvements were strongly correlated with reduced levels of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) and oxidative stress marker malondialdehyde, along with increased superoxide dismutase activity. Rb1 also preserved blood-brain barrier integrity by enhancing the expression of tight-junction proteins ZO-1 and Occludin. Together, these findings indicate that Rb1 confers neuroprotection through metabolic reprogramming linked to anti-inflammatory and antioxidant actions, and they highlight the value of integrating metabolomics with MSI to elucidate spatially defined drug mechanisms in the brain.
Proteomic Profiling Reveals the Synergistic Effects of Astaxanthin and Melatonin on the Inhibition of Cryoinjuries in Ram Sperm.
Li C, Zhang Y, Ni X … +4 more , Zhao X, Liang J, Wu G, Quan G
J Proteome Res · 2026 Jun · PMID 42101457 · Publisher ↗
The present study aimed to investigate the protective effects of astaxanthin (AST) and melatonin (MLT) on ram sperm quality-associated indicators during cryopreservation, and to explore the molecular effects of the two c...
The present study aimed to investigate the protective effects of astaxanthin (AST) and melatonin (MLT) on ram sperm quality-associated indicators during cryopreservation, and to explore the molecular effects of the two cryoprotectants on the protein profile of cryopreserved sperm. First, ram sperm were diluted with freezing media supplemented with different concentrations of AST and MLT, and then cryopreserved. The effects of different concentrations of AST and MLT were assessed by evaluating the motility and motile parameters, functional and structural indicators, antioxidant capacity, and associated indicators of post-thawed sperm. The concentrations of 50 μM AST (AST group), 0.5 mM MLT (MLT group), and 50 μM AST and 0.5 mM MLT (AST.MLT group) were the most effective, as compared to the control (CON group). Furthermore, alterations in the sperm proteomic profile among the three comparisons (AST vs CON, MLT vs CON, AST.MLT vs CON) were determined using an Orbitrap Astral coupled with a data-independent acquisition (DIA) proteomic approach. After comprehensive bioinformatics analysis, significantly differentially abundant proteins (DAPs) among the three comparisons (32 DAPs in AST vs CON, 34 DAPs in MLT vs CON, 116 DAPs in AST.MLT vs CON) and their enriched molecular pathways were discovered, suggesting that AST and MLT may have synergistic effects on frozen sperm by regulating the abundance changes in proteins. In particular, certain positive proteins like ACAT2, PRDX6, G6PD, HSP90a, HSPA8, HSL, ACTN1, and Ezrin, and negative proteins like Cyt , CTSF, and AFU, which are tightly associated with the regulation of sperm motility, oxidative stress, and other metabolic processes, may serve as novel potential biomarkers for evaluating sperm quality after freeze-thawing. In conclusion, this study provides valuable insights into the protective effects of AST and MLT on ram semen quality and replenishes information for further clarifying the molecular mechanism based on the modification of the sperm proteome during cryopreservation.
Offline Two-Stage SEC and LC-MS/MS for Comprehensive Characterization of Yeast Ribosomal Populations.
Spiteri AJ, Hamey JJ, Wilkins MR
J Proteome Res · 2026 Jun · PMID 42101145 · Publisher ↗
We report two-dimensional size exclusion chromatography tandem mass spectrometry (2D-SEC MS/MS), a workflow that couples two MS-compatible size exclusion chromatography steps to bottom-up proteomics for rapid, high-resol...
We report two-dimensional size exclusion chromatography tandem mass spectrometry (2D-SEC MS/MS), a workflow that couples two MS-compatible size exclusion chromatography steps to bottom-up proteomics for rapid, high-resolution characterization of ribosomes. Building on the established Ribo Mega-SEC protocol, we show that a size exclusion chromatography (SEC) run on a 1000 Å column separates intact polysomes from mixed 80S/60S/40S particles, while a reinjection of the pooled 80S/60S/40S peak onto a second-dimension, 500 Å SEC column yields resolved monosome, 60S, and 40S subunit fractions. This method is thereby able to deliver four distinct ribosomal subpopulations in <90 min. Bottom-up LC-MS/MS of 2D-SEC fractions showed that our method can identify 78 of the 79-core yeast ribosomal proteins in the polysome fraction, with a 93% mean sequence coverage. It could also resolve and differentially quantify 36 of 38 paralogous protein pairs, revealing isoform-specific incorporation biases. Furthermore, our method could map all 12 known yeast ribosomal methylation sites and two canonical phosphorylation sites, enabling site-specific post-translational modification measurements. Applied to the study of ribosomes in nutrient deprivation and upon knockout, we show that 2D-SEC MS/MS detects rapid polysome collapse and changes to the polysome profiling ratios, illustrating its capacity to link ribosome composition to functional perturbations.
2-Mercaptoethanol/DMSO Workflow Enables Highly Reproducible Quantitative Proteomics.
Suto A, Ishikawa Y, Matsumoto T … +3 more , Itakura M, Kodera Y, Matsui T
J Proteome Res · 2026 May · PMID 42099107 · Publisher ↗
Proteomics provides a systematic and high-throughput approach to comprehensively characterize protein networks, enabling insights into cellular functions and disease mechanisms. Carbamidomethylation using iodoacetamide (...
Proteomics provides a systematic and high-throughput approach to comprehensively characterize protein networks, enabling insights into cellular functions and disease mechanisms. Carbamidomethylation using iodoacetamide (IAA), a common method for cysteine alkylation, is known to cause nonspecific modifications that increase spectral complexity in mass spectrometry and reduce quantitative accuracy. Here, we established a reproducibility-focused 2-mercaptoethanol (2-ME)/dimethyl sulfoxide (DMSO) workflow and systematically evaluated its quantitative performance at the proteome-wide level. Mouse liver proteomes were processed using either 2-ME/DMSO or conventional IAA treatment, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. The optimized 2-ME treatment increased the number of cysteine-modified peptides by 1.6- to 1.9-fold. Although total protein identifications were comparable, 77% of proteins exhibited improved sequence coverage with the optimized 2-ME treatment. Quantitative reproducibility was also enhanced, with the peptide quantified CV ≤ 20% increasing from 61.4% with IAA treatment to 86.1% with 2-ME treatment, and protein quantified CV ≤ 20% increasing from 80.6% with IAA treatment to 93.5% with 2-ME treatment. Application of this new workflow to ovarian clear cell carcinoma reliably detected cisplatin-induced alterations. The 2-ME/DMSO workflow offers a simple and highly reproducible proteomics strategy for accurate quantitative proteomics.
Multiomics Integrated Analysis of the Inhibitory Mechanism of Tannic Acid on MRSA Biofilms.
Yang M, Li F, Wu Z … +3 more , Qu Q, Wang S, Zhou Y
J Proteome Res · 2026 Jun · PMID 42099085 · Publisher ↗
Methicillin-resistant (MRSA) represents a significant threat to global public health due to its inherent antibiotic resistance and robust biofilm-forming capability. Biofilms markedly enhance bacterial resilience by imp...
Methicillin-resistant (MRSA) represents a significant threat to global public health due to its inherent antibiotic resistance and robust biofilm-forming capability. Biofilms markedly enhance bacterial resilience by impeding antibiotic penetration and evading the host immune responses. Tannic acid (TA), a naturally occurring polyphenolic compound, exhibits broad-spectrum antimicrobial and antibiofilm properties; however, the underlying mechanisms remain poorly understood. In this study, the inhibitory effects of subinhibitory concentrations of TA on MRSA biofilm formation were systematically investigated through an integrative multiomics approach (encompassing transcriptomic, proteomic, and metabolomic analyses) complemented by comprehensive phenotypic validation. Phenotypic assays demonstrated that TA effectively disrupted the biofilm architecture and reduced biofilm biomass without exerting bacteriostatic or bactericidal effects. Integrated multiomics analysis revealed that differentially expressed genes, proteins, and metabolites following TA treatment were significantly enriched in key metabolic pathways, including glycolysis/gluconeogenesis, the pentose phosphate pathway, glycerophospholipid metabolism, and glycine, serine, and threonine metabolism. Suppression of these pathways likely diminished the availability of precursors for extracellular polysaccharide synthesis and compromised the membrane lipid integrity, thereby impairing biofilm development. These findings provide a mechanistic foundation and novel insights into the potential application of TA as a therapeutic agent targeting biofilm-associated MRSA infections.
Leveraging the Metabolic Fingerprint of Sleep Deprivation and Sleep Restriction for Forensic Applications: A Machine Learning Study in Oral Fluid Metabolomics.
Scholz M, Steuer AE, Dobay A … +2 more , Landolt HP, Kraemer T
J Proteome Res · 2026 Jun · PMID 42090244 · Full text
As sleep loss leads to accidents and impaired safety, a direct metabolic marker would be beneficial for forensic interpretation. In a sufficiently powered, randomized, controlled, crossover trial under realistic conditio...
As sleep loss leads to accidents and impaired safety, a direct metabolic marker would be beneficial for forensic interpretation. In a sufficiently powered, randomized, controlled, crossover trial under realistic conditions, we examined the salivary metabolome of 20 young men (habitual sleep duration 7-9 h) following three interventions: one night of total sleep deprivation, four consecutive nights of sleep restriction to 6 h, and control (8 h of sleep). Oral fluid specimens were repeatedly collected and analyzed using liquid chromatography coupled to mass spectrometry. Logistic regression models were trained to classify unseen samples without reference samples from the same individual. Acute sleep deprivation exhibited a unique metabolic fingerprint that could be detected precisely (F = 0.90) when using only 12 molecular features. This fingerprint was more pronounced in samples collected in the morning/midday hours. Nevertheless, at all time points, the overall correct predictions by far outweighed the incorrect ones. Four nights of sleep restriction did not lead to exploitable metabolic changes. This study presents a metabolic fingerprint of acute sleep deprivation in oral fluid under realistic conditions and explores practical implications and limitations of its machine learning-aided classification. Metabolomics-based, reference-free sleep loss detection holds potential for applications in forensic, clinical, and occupational contexts.
Comparison of Common Plasma Proteomics Workflows Reveals Distinct Preanalytical Biases by Sample Preparation and Nanoparticle Enrichment.
Völlmy F, Kaushik P, Eckert S … +5 more , Paschen C, Tavalaei S, Fidelin J, Weiser S, Bantscheff M
J Proteome Res · 2026 Jun · PMID 42089287 · Publisher ↗
Human plasma proteomics is critical for biomedical research but challenged by an extraordinary dynamic range. We evaluated six mass spectrometry workflows, including bead-based enrichment (Proteograph XT, P2, Mag-Net), d...
Human plasma proteomics is critical for biomedical research but challenged by an extraordinary dynamic range. We evaluated six mass spectrometry workflows, including bead-based enrichment (Proteograph XT, P2, Mag-Net), depletion of the 14 most abundant proteins, and neat plasma analysis. Enrichment methods achieved superior proteome coverage, identifying up to 4600 proteins, but exhibited acute susceptibility to preanalytical bias from cellular contaminants and vesicles in plasma. Increased centrifugation stringency before proteomics analysis drastically decreased protein identifications. Crucially, the abundance of the vast majority of secreted proteins was not significantly affected by centrifugation for all tested workflows, suggesting that their quantification is little influenced by contaminating cells or vesicles, whereas depleted proteins are enriched for cellular components like cytoskeleton organization and platelet activation. Our results underscore that nanoparticle-based methods allow robust and deep measurement of the secreted plasma proteome, providing additional insights by reporting the contributions of proteins of cellular origin when applying the common practice of 2000 × centrifugation prior to analysis.
Phosphorylation of YBX1 in the Kidneys is Altered in Legumain Knockout-Mice.
Sever T, Sinožić T, Kolarič M … +2 more , Turk B, Fonović M
J Proteome Res · 2026 Jun · PMID 42087759 · Full text
Protein phosphorylation is a common post-translational modification that plays a crucial role in cellular signal transduction. Disruptions in this process can lead to phenotypic deviations in healthy organisms. Legumain...
Protein phosphorylation is a common post-translational modification that plays a crucial role in cellular signal transduction. Disruptions in this process can lead to phenotypic deviations in healthy organisms. Legumain is a cysteine proteinase present in plants and animals. Legumain is involved in the regulation of kidney and hematopoietic homeostasis, as well as immune response. Its dysregulation is associated with various types of cancers and neurodegenerative diseases. Legumain knockout mice generally exhibit a normal phenotype, except for altered kidney function, hemophagocytic syndrome, and extramedullary hematopoiesis. In this study, we analyzed the changes in protein phosphorylation in legumain knockout mice compared to their wild-type counterparts to elucidate how legumain deficiency affects protein phosphorylation and related cell signaling. Phosphopeptides from the kidney and liver samples were enriched and analyzed using mass spectrometry and validated with Western blot and immunohistochemistry. Several phosphorylation sites on the RNA- and DNA-binding protein Y-box binding protein 1 were identified. A site on the serine 100 residue was found to activate the NF-κB pathway in legumain knockout mice, resulting in an enhanced inflammatory response. This was supported by the increased expression of several NF-κB genes. Overall, this study provides valuable insights into the role of legumain and its impact on various cellular processes.
Proteomic and Metabolomic Analysis of PCK2-Dependent Alterations in Group 3 Medulloblastoma Cells.
Pai MGJ, Patra S, Bharambe H … +2 more , Shirsat N, Srivastava S
J Proteome Res · 2026 Jun · PMID 42087405 · Publisher ↗
Group 3 medulloblastoma (G3MB) is an aggressive pediatric brain tumor subtype accounting for 20-25% of cases and characterized by poor prognosis and frequent metastasis. This subgroup frequently exhibits MYC amplificatio...
Group 3 medulloblastoma (G3MB) is an aggressive pediatric brain tumor subtype accounting for 20-25% of cases and characterized by poor prognosis and frequent metastasis. This subgroup frequently exhibits MYC amplification, driving oncogenic transcription, biosynthesis, and metabolic reprogramming, which is crucial for the rapid growth of tumor cells. Prior proteomic analysis of G3MB samples showed disrupted glucose and pyruvate metabolism, with notable overexpression of mitochondrial phosphoenolpyruvate carboxykinase (PCK2). This links the TCA cycle and pyruvate metabolism, aiding metabolic flexibility under nutrient stress. Consistent with this observation, we observed PCK2 overexpression in two independent patient data sets. To investigate its functional role, we performed shRNA-mediated knockdown of PCK2 in HD-MB03 and G3MB cells. Quantitative proteomics using Evosep-Tims TOF revealed dysregulation of metabolic interactors along with enrichment of ribosomal and RNA processing pathways. Complementary metabolomic profiling showed alterations in phosphocholine, carnitine, and metabolites related to redox imbalance upon PCK2 loss. Together, these findings provide insights into PCK2's role in Group 3 MB cells and expose vulnerabilities for therapeutic targeting.
Ultrahigh-Throughput Liquid Chromatography with Tandem Mass Spectrometry Method for Targeted Protein Degradation Compound Screening Using the Orbitrap Astral Mass Spectrometer.
Lin H, Yang YY, Maity S … +2 more , Sun Q, Wang J
J Proteome Res · 2026 Jun · PMID 42087393 · Publisher ↗
Targeted protein degradation (TPD) is a therapeutic strategy that utilizes small molecules to induce the proximity-driven degradation of disease-causing proteins. Because the efficacy and selectivity of TPD compounds mus...
Targeted protein degradation (TPD) is a therapeutic strategy that utilizes small molecules to induce the proximity-driven degradation of disease-causing proteins. Because the efficacy and selectivity of TPD compounds must be validated across thousands of proteins, high-throughput proteomics is essential for the rapid screening and characterization of these novel degraders. Here, we developed a 300 samples per day (SPD) LC-MS/MS method using the Orbitrap Astral mass spectrometer for ultrahigh-throughput TPD compound screening. We identified close to 8000 protein groups from a single cell line with a coefficient of variation (CV) of less than 10%, highlighting the deep proteome coverage and method reproducibility even at 300 SPD. This high degree of precision provides the statistical confidence to detect subtle, yet significant, changes in protein abundance that were previously challenging to quantify in high-throughput workflows. To evaluate the quantitation accuracy of this method, we further mixed the digests from two or three species at different ratios. Our three-proteome mixture results demonstrated highly accurate quantitation for proteins with both small and large fold changes. Moreover, our two-proteome mixture experiment, where 20 to 160 ng of yeast digest was spiked into 200 ng of HeLa digest, showed an R of 0.999 for the yeast proteome, underscoring the quantitation accuracy of the method. Utilizing this workflow, we studied dose-dependent protein degradation patterns induced by pomalidomide, iberdomide, and mezigdomide. Our results indicate that mezigdomide may possess enhanced efficacy in T cells by degrading additional proteins such as IKZF2, thereby boosting anticancer immunity. Together, we developed an ultrahigh-throughput LC-MS/MS method with excellent proteome coverage and quantitation accuracy that is highly suitable for chemoproteomics screening of drug libraries.
Taxonomic Source Identification of Hair.
Keane RE, Gummer JPA, Tidy RJ … +1 more , Parker GJ
J Proteome Res · 2026 Jun · PMID 42085601 · Publisher ↗
Hair fibers are a common form of biological trace evidence. Taxonomic classification can provide valuable forensic intelligence and aid in evidence prioritization. Traditional methods of classification, based on hair mor...
Hair fibers are a common form of biological trace evidence. Taxonomic classification can provide valuable forensic intelligence and aid in evidence prioritization. Traditional methods of classification, based on hair morphology, require expert interpretation, offer limited taxonomic resolution, and are not easily scalable. Mass-spectrometry-based proteomics provides a biomolecular alternative through taxon-specific amino acid polymorphisms to resolve species identification. In this study, a proteomics workflow was developed for the discovery and characterization of taxonomically diagnostic hair peptides in humans and 14 additional species, selected based on relevance to crime scene investigation. A panel of 226 taxonomically informative peptides were identified, with 207 novel to this study. This included 59 peptides with single-species resolution, while the remainder were diagnostic due to restricted taxonomic distribution or convergent evolution. The panel of taxa-discriminating markers was subsequently integrated into a forensic workflow. The developed workflow was used to analyze single fur-hair (20 mm), from four individuals from each species of interest. The data were processed using a curated hair protein database, providing an efficient bioinformatics workflow that did not require prior source information for identification. The method was able to classify all hairs analyzed with genus- or species-level resolution.
Discovery of Novel Protein Biomarkers in Urine for Diagnosis of Prediabetes Using Label-Free Proteomics.
Liao WL, Liao HY, Chang CT … +3 more , Chang YW, Chen CJ, Tsai FJ
J Proteome Res · 2026 Jun · PMID 42084901 · Publisher ↗
Type 2 diabetes (T2D) often develops insidiously, and many individuals with prediabetes (preDM) remain undiagnosed. While current diagnostic methods rely on blood sampling, urine-based proteomic biomarkers offer a promis...
Type 2 diabetes (T2D) often develops insidiously, and many individuals with prediabetes (preDM) remain undiagnosed. While current diagnostic methods rely on blood sampling, urine-based proteomic biomarkers offer a promising noninvasive alternative for early risk stratification. Here, we applied label-free nanoLC-MS/MS-based proteomics to identify urinary protein biomarkers associated with prediabetes and to evaluate their potential in predicting progression to T2D. The discovery phase included urine samples from 43 control and 58 preDM participants, with protein quantification performed using two independent software platforms to ensure analytical robustness. Candidate proteins showing consistent differential expression were further validated by enzyme-linked immunosorbent assay (ELISA) in an expanded sample set comprising 91 control and 68 preDM subjects. Two proteins─alpha-1-acid glycoprotein 1 (AGP1) and zinc-α2-glycoprotein (ZAG)─were identified as candidate biomarkers. When combined with age and sex, AGP1 and ZAG showed good discriminative performance (AUCs of 0.936 and 0.926, respectively), comparable to fasting blood glucose (AUC = 0.944). Overall, these findings suggest that AGP1 and ZAG may serve as potential urinary biomarkers reflecting early metabolic alterations associated with prediabetes and progression to T2D, although further validation in independent cohorts is warranted.
Serum Exosomal ADGRF5: A Potential Diagnostic Biomarker for Metastasis in Triple-Negative Breast Cancer.
Zhao M, Jiang Y, Kong X … +7 more , Liu Y, Gao P, Li M, Zhu H, Cao Y, Li X, Ma L
J Proteome Res · 2026 Jun · PMID 42081321 · Publisher ↗
Triple-negative breast cancer (TNBC) is associated with frequent recurrence, early metastasis, and poor prognosis, making timely detection of metastatic spread clinically important. Because exosomes are involved in tumor...
Triple-negative breast cancer (TNBC) is associated with frequent recurrence, early metastasis, and poor prognosis, making timely detection of metastatic spread clinically important. Because exosomes are involved in tumor metastasis and immune evasion, they may provide useful early biomarkers. This study aimed to identify and preliminarily validate serum exosomal markers for TNBC metastasis using high-throughput proteomics. Two sequential, independent 4D-label free proteomic analyses of serum exosomes were performed. The exploratory phase used pooled serum samples from 6 metastatic TNBC patients, 6 nonmetastatic TNBC patients, and 6 healthy controls, generating 9 exosome samples. A second analysis was conducted in an expanded cohort of 10 metastatic and 10 nonmetastatic TNBC patients. Differentially expressed proteins identified in both analyses were compared and further evaluated by Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and receiver operating characteristic analyses, with selected candidates validated by ELISA. Distinct exosomal protein expression profiles were observed among metastatic TNBC, nonmetastatic TNBC, and healthy controls. ADGRF5 showed strong diagnostic performance in distinguishing metastatic from nonmetastatic TNBC, with an area under the curve of 0.94. These findings suggest that ADGRF5 is a promising serum biomarker for TNBC metastasis and may aid future breast cancer biomarker discovery.
Correction to "Pancreatic Digestive Enzyme Dispersion into Human Organs Outside the Gastrointestinal Tract".
Chavan R, Schmid-Schönbein GW
J Proteome Res · 2026 Jun · PMID 42081283 · Publisher ↗
Abstract loading — click title to view on PubMed.
Advanced Proteomic Profiling Demonstrates Clinical Utility of Patient-Centric, at-Home Dried Blood Sample Collection.
Smith WJ, Patel MT, Said R … +5 more , Trinder KM, Drolet DW, Westacott MJ, Loureiro J, Mikhailov D
J Proteome Res · 2026 Jun · PMID 42080795 · Full text
Patient-centric, at-home, dried blood collection can increase compliance, reduce cohort size, decrease shipping costs, and open the door for broader applications of affinity proteomics. Dried blood samples from 16 indivi...
Patient-centric, at-home, dried blood collection can increase compliance, reduce cohort size, decrease shipping costs, and open the door for broader applications of affinity proteomics. Dried blood samples from 16 individuals, collected by Tasso M20 "smart" devices, were analyzed by the SomaScan Assay using conditions modified for this new matrix. These assay results were compared to plasma and serum from the same donors. The cross-section of proteins that can be measured in both plasma and dried blood was determined. Complete blood counts (CBCs) were also taken from these donors. We generated models to predict these counts based on SomaScan Assay measurements. Over 800 proteins can be measured in both plasma and DBS. These proteins are actively secreted by cells or found on cellular surfaces. The remainder of the SomaScan Assay menu contains information on the cellular component of whole blood. Models generated from DBS data can more accurately predict complete blood counts than those generated from plasma.
An AI-Ready Phosphorylation Meta-Analysis for .
Boswell EL, Ramsbottom KA, Fan J … +9 more , Perez-Riverol Y, Bowler-Barnett EH, Sun Z, Mesdaghi S, Rigden DJ, Martin MJ, Deutsch EW, Vizcaíno JA, Jones AR
J Proteome Res · 2026 Jun · PMID 42080562 · Full text
We, the PTMeXchange Consortium, present a meta-analysis of eight high-quality data sets to map 56,694 phosphosites in brewer's yeast () using strict control for false identifications. Each site has been classified into t...
We, the PTMeXchange Consortium, present a meta-analysis of eight high-quality data sets to map 56,694 phosphosites in brewer's yeast () using strict control for false identifications. Each site has been classified into the Gold-Silver-Bronze confidence categories. First, we identified 55 significant motifs and grouped these into kinase classes to perform pathway enrichment analysis. Next, we leveraged disorder region predictions and AlphaFold 3's ability to consider post-translational modifications (PTMs) when modeling proteins to understand the structural context of phosphosites. Here, we determined that phosphorylation tends to occur on disordered serine and threonine residues. AlphaFold predictions suggest that phosphosites induce alpha helices to form in proteins, although many "induced helices" appear to be unusually short and require further validation. As artificial intelligence (AI) is being applied in proteomics, we must ensure that publicly available data are accurate and of high-quality to be used for downstream analyses and training models. With this motivation, our results are available in PRIDE (PXD071918), PeptideAtlas and UniProtKB, ensuring that this PTM data is FAIR and "AI-ready".
Benchmarking Plasma Proteomics Workflows and Their Correlation to Clinical Routine Protein Assays.
Kverneland AH, Østergaard O, Schmidt L … +5 more , Østergaard Johansen M, Ullitz Thorsen S, Frikke Schmidt R, Christoffersen C, Olsen JV
J Proteome Res · 2026 Jun · PMID 42068309 · Full text
Plasma proteomics based on mass spectrometry has great potential for biomarker discovery. Plasma is challenging for mass spectrometry due to the high dynamic range in protein abundance. Several workflows have been develo...
Plasma proteomics based on mass spectrometry has great potential for biomarker discovery. Plasma is challenging for mass spectrometry due to the high dynamic range in protein abundance. Several workflows have been developed to overcome this, and in this study, we compare prominent enrichment and depletion workflows using platelet-poor plasma (PPP), platelet-rich plasma (PRP), and serum (SER). Our results show that depletion workflows including Top14 depletion and acid precipitation allow quantification of very different proteomes than methods based on enrichments of extracellular vesicles such as bead-based enrichment or ultracentrifugation. Enrichment methods are superior in terms of proteome depth and quantitative performance but may be less robust in large cohorts. There is a very high correlation between PPP and PRP samples for all methods and less to SER samples, especially with enrichment workflows. The correlation of 10 protein measurements, performed by clinical routine processes on a Cobas system, showed heterogeneous results. Low-abundant proteins with biological dynamics within a healthy cohort, including C-reactive protein and lipoprotein(a), correlated very well to proteomics-based workflows, while others, including albumin and transferrin, correlated poorly. In conclusion, the workflow for plasma proteomics should be aligned with the aim of the analysis and setup of the sample collection.
Membrane Proteome Remodeling in Female APP/PS1 Mice Following M1 Muscarinic Receptor Modulation Revealed by Peptidisc-Enabled DIA-MS.
Bhattacharya A, Antony F, Aoki H … +4 more , Babu M, Ferguson SSG, Abd-Elrahman KS, Duong van Hoa F
J Proteome Res · 2026 Jun · PMID 42067398 · Publisher ↗
Alzheimer's disease (AD) is associated with dysregulation of membrane proteins controlling amyloid processing, synaptic signaling, and neuronal communication, yet most proteomic studies focus on soluble fractions, limiti...
Alzheimer's disease (AD) is associated with dysregulation of membrane proteins controlling amyloid processing, synaptic signaling, and neuronal communication, yet most proteomic studies focus on soluble fractions, limiting insight into membrane-centered pathology. Here, we apply a membrane-mimetic, data-independent acquisition workflow to define disease- and drug-induced remodeling of the cortical membrane proteome in an APP mouse model of AD. Female wildtype B6C3F1/J and APP/PS1 mice were aged to 9 months, treated ± the M1 positive allosteric modulator VU0486846, and validated by enrichment of APP in cortical membranes of APP/PS1 mice. This confirmed pathological context enabled direct interrogation of membrane remodeling, revealing pronounced, genotype-specific changes characterized by selective enrichment of AD-linked membrane proteins including RyR2, PLD3, ITM2C, and CNTNAP2, alongside broader shifts in pathways related to calcium signaling, synaptic organization, and membrane trafficking. In contrast, wildtype membranes were enriched in proteins associated with axon guidance and synaptic structure, such as EPHA5 and ROBO2. M1 activation produced minimal changes in wildtype mice but selectively enhanced proteins linked to neuronal trafficking and synaptic plasticity in APP/PS1 mice, including SORCS2, PLXND1, and CADM1, indicating preferential engagement of disease-altered pathways. These findings demonstrate that AD-associated remodeling is concentrated at the membrane level and highlight Peptidisc-enabled membrane proteomics as a powerful approach to resolve disease mechanisms and therapeutic target engagement.
Mass Spectrometric Detected Cancer Proteins as Resources for Cancer Research.
Huang Y, Chen L, Wu PI … +10 more , Juneja P, Chen L, Evrard YA, Jiao L, Hu Y, Zhang X, Doroshow JH, Thangudu RR, Pilozzi A, Zhang H
J Proteome Res · 2026 Jun · PMID 42065709 · Full text
Protein evidence derived from mass spectrometry (MS) across cancer cohorts and model systems is extensive but remains fragmented across individual studies and repositories, limiting rapid retrieval and evidence-based ben...
Protein evidence derived from mass spectrometry (MS) across cancer cohorts and model systems is extensive but remains fragmented across individual studies and repositories, limiting rapid retrieval and evidence-based benchmarking of cancer-context protein detection. Here we present the Mass Spectrometric Detected Cancer Proteins (MSCP) resource, an integrated database assembled from 27 large-scale cancer proteomics sources spanning human tumor cohorts, cancer cell lines, and patient-derived xenograft (PDX) models. Protein identifications were harmonized to UniProtKB-Swiss-Prot (release 2025_01) and integrated under FDR-controlled identification outputs to generate a unified catalog of 15,964 MS-supported human proteins. Benchmarking against neXtProt PE1 identified 525 proteins newly supported by MS evidence in the integrated cancer context, including proteins previously associated with chromosome-level evidence inconsistencies. Functional interpretation of the newly identified set using GO and Reactome enrichment highlighted immune- and barrier-associated processes and chromatin- and genome-regulatory pathways, including DNA methylation and histone deacetylation. Orthogonal verification using synthetic unique peptides confirmed representative newly identified proteins by concordant precursor / and fragment-ion patterns. MSCP provides a provenance-aware, UniProtKB-aligned resource for cancer proteomics that supports both cohort- and model-specific querying and coverage-oriented evidence aggregation, enabling standardized comparisons to reference proteomes and facilitating downstream assay planning and translational studies.
About
- Frequency
- Sun
- Papers found
- 200
- RSS feed
- Subscribe