#massSpec

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Metabolic disparities of potentially toxic components derived from Psoraleae Fructus and Euodiae Fructus within the Sishen wan influenced by varying compatibilities and physiological conditions in an ... Sishen wan (SSW) is utilized in the treatment of irritable bowel syndrome (IBS). This study aimed to compare gut microbiota-mediated metabolic profile…

Metabolic disparities of potentially toxic components derived from Psoraleae Fructus and Euodiae Fructus within the Sishen wan influenced by varying compatibilities and physiological conditions in an in vitro gut microbiota model #JPBA #MassSpec www.sciencedirect.com/science/arti...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides Heparan sulfates (HS) are a group of heterogenous linear, sulfated polysaccharides that play a role in in health and many diseases including cancer, cardiovascular, and kidney diseases. The structural...

Glycoinformatic profiling of label-free intact heparan sulfate oligosaccharides #MCP #MassSpec www.mcponline.org/article/S153...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Supramolecular Solvent Extraction for Doping Control Analysis of Prohibited Substances in Horse Urine This paper describes the first application of supramolecular solvent extraction for doping control analysis of prohibited substances in horse urine.

Supramolecular Solvent Extraction for Doping Control Analysis of Prohibited Substances in Horse Urine #DTA #MassSpec analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Spatial localization and pharmacodynamic assessment of intracrine androgen metabolism in CRPC xenograft tumor tissues upon active vitamin D treatment - Analytical and Bioanalytical Chemistry Castrate-resistant prostate cancer (CRPC) progression is driven by intracrine androgen synthesis despite low circulating androgens. This study investigates the effects of active vitamin D (1,25-(OH)₂-...

Spatial localization and pharmacodynamic assessment of intracrine androgen metabolism in CRPC xenograft tumor tissues upon active vitamin D treatment #ABC #MassSpec link.springer.com/article/10.1...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

A new multi-residue method for PFAS analysis in wastewater for environmental and public health risk assessment - Analytical and Bioanalytical Chemistry This work focuses on the detection and quantification of per-/polyfluorinated alkyl substances (PFAS) in influent wastewater, using wastewater-based epidemiology via a new multi-residue ultra performa...

A new multi-residue method for PFAS analysis in wastewater for environmental and public health risk assessment #ABC #MassSpec link.springer.com/article/10.1...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Proteomics and Lipidomics Analysis Reveal That Membrane Remodeling and Extracellular Matrix Alterations Are Crucial for Cisplatin Resistance in Triple-Negative Breast Cancer 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.

Proteomics and Lipidomics Analysis Reveal That Membrane Remodeling and Extracellular Matrix Alterations Are Crucial for Cisplatin Resistance in Triple-Negative Breast Cancer #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

7 hours ago

Combined Quantitative and Qualitative Statistical Analyses Improve Benzodiazepine Target Discovery in Label-free Affinity-Based Protein Profiling Data 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 GABAA 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 GABAA 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.

Combined Quantitative and Qualitative Statistical Analyses Improve Benzodiazepine Target Discovery in Label-free Affinity-Based Protein Profiling Data #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

Proteomes MDPI

@proteomesmdpi.bsky.social

2 days ago

This article is now available in Proteomes: Proteome-Wide Analysis of Functional Phosphosites in the FGFR Family of Proteins: Insights from Large-Scale Phosphoproteomic Analysis 🧬🖥️🧪🧫🥼

www.mdpi.com/2227-7382/14...

#proteomes #proteomics #proteoform #phosphoproteomics #MassSpec

BioMassSpec

@realbiomassspec.bsky.social

3 days ago

Site-Specific and Quantitative O-GlcNAc Proteomics for Hepatocellular Carcinoma O-linked β-N-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.

Site-Specific and Quantitative O-GlcNAc Proteomics for Hepatocellular Carcinoma #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

3 days ago

EIQuan: A Stacked Ensemble Learning-Based Predictor for Quantification of Nontargeted Chemicals in Gas Chromatography Coupled with Electron Ionization High-Resolution Mass Spectrometry Analysis Nontargeted analysis using gas chromatography coupled with electron ionization high-resolution mass spectrometry (GC-EI-HRMS) is a vital tool for identifying a large quantity of compounds in complex environmental samples. Herein, we employed GC-EI-HRMS to profile chemicals in wastewaters from an iron and steel corporation. To address the challenge of quantifying compounds without authentic standards, we developed a stacked ensemble learning model using bootstrap aggregation to integrate the predictions from three distinct base learners. A total of 910 compounds were tentatively identified across all wastewater samples, which were primarily categorized into 19 subgroups. Based on these major categories, 278 reference standards were used to develop a stacked ensemble learner. This model outperformed semiquantitative methods based on surrogates, with 95% of quantification errors falling within a 3.79-fold range. Total quantified concentrations ranged from 8.86 × 105 (influent) to 7.01 × 103 μg/L (effluent) in coking wastewater and from 331 μg/L (influent) to 47.1 μg/L (effluent) in mixed wastewater. Notably, 97.1% of tentatively identified chemicals fell within the model’s applicability domain. To facilitate the model application, a user-friendly predictor, EIQuan, was developed, providing an efficient tool for predicting response factors of GC-amenable environmental pollutants. This study establishes a robust framework for accurate semiquantification of unknown pollutants in complex industrial wastewater.

EIQuan: A Stacked Ensemble Learning-Based Predictor for Quantification of Nontargeted Chemicals in Gas Chromatography Coupled with Electron Ionization High-Resolution Mass Spectrometry Analysis #EST #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

3 days ago

Polychlorinated Alkane Profiles and Concentrations in Bolivian Andes Soils Point to a Long-Range Transport Influence High-altitude terrain may intersect the upper atmospheric boundary layer and exhibit distinct environmental dynamics. We investigated the anthropogenic pollutants polychlorinated alkanes (PCAs, also known as chlorinated paraffins) in surface soils along a transect from the La Paz-El Alto metropolitan area in Bolivia (3200–4100 masl) to the upper slopes of Mount Chacaltaya (>5200 masl), around 16 km away. Concentrations of PCAs in urban soils (750–5,230 ng/g organic carbon [OC]) decreased exponentially with increasing distance from the urban boundary, declining to ∼150 ng/g OC at elevations below 4,700 masl. Beyond 4,700 masl concentrations increased again, reaching levels comparable to those in the urban area, 1,670–4,300 ng/g OC, above 5,000 masl. Given that pollutant concentrations typically decline with distance from their source, this altitudinal trend, together with a pronounced shift in PCA forensic fingerprints near 4,700 masl, strongly suggests contributions from sources beyond the local metropolitan area. Carbon and nitrogen isotope signatures in organic carbon further support long-range transport as a source, consistent with previous modeling and observations that the upper slopes of Mount Chacaltaya predominantly receive air masses and organic carbon from distant regions via transport in the free troposphere. Our observation that pollutant levels in high-altitude areas are comparable to those in the metropolis of 1.8-million inhabitants underscores the efficiency of long-range atmospheric transport.

Polychlorinated Alkane Profiles and Concentrations in Bolivian Andes Soils Point to a Long-Range Transport Influence #EST #MassSpec pubs.acs.org/doi/10.1021/...

Magnetic Resonance News

@nmr900.bsky.social

3 days ago

RT Parastoo Azadi @CCRCUGA Advance your expertise in carbohydrates, glycoproteins, and glycomics through our hands-on, laboratory-focused training at the

RT Parastoo Azadi @CCRCUGA Advance your expertise in carbohydrates, glycoproteins, and glycomics through our hands-on, laboratory-focused training at the #CCRC.

ast.uga.edu/training-in-...

#glycotime #glycoscience #glycomics #MassSpec #NMR #glycobiology #ResearchTraining #UGA

IET

@ietltd.bsky.social

4 days ago

Chemistry Cat welcomed some special guests today! We love when customers visit our lab equipment showroom. www.ietltd.com

#masssspectrometry #teammassspec #massspec #hplc #lab #phd #nmrchat

Consortium for Top-Down Proteomics

@proteoforms.bsky.social

4 days ago

Welcome! You are invited to join a meeting: Proteoform Thursday: Jeffrey Huang presents - A Catenin Phospho-Code for Adherens Junction Organization. After registering, you will receive a confirmation... Proteoforms, defined by the precise primary structure of proteins, are becoming a central currency in modern proteomics because they more directly link to cellular functions and disease phenotypes. Re...

Join us March 26 for Proteoform Thursday: Jeffrey Huang presents - "A Catenin Phospho-Code for Adherens Junction Organization"
us06web.zoom.us/meeting/regi... #proteomics #massspec

BioMassSpec

@realbiomassspec.bsky.social

4 days ago

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 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.

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 #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

4 days ago

Simple and sensitive cellulose paper-based microextraction of 25 steroid esters from human serum/plasma for doping control purposes - Analytical and Bioanalytical Chemistry Blood is increasingly used as a biological matrix in the doping control field; however, the limited volume typically available for analysis poses a significant challenge, particularly when multiple te...

Simple and sensitive cellulose paper-based microextraction of 25 steroid esters from human serum/plasma for doping control purposes #ABC #MassSpec link.springer.com/article/10.1...

Shimadzu UK

@shimadzuuk.bsky.social

5 days ago

Revealing the hidden structural diversity of lipids

Conventional MS/MS techniques often miss carbon–carbon double bond positions in lipids, making isomer distinction tricky. A researcher is working on improving LC-MS methods for ESI & MALDI. Read more👉 cutt.ly/HtTvbmbt
#Research #MassSpec #Biochemistry🌟
#SciSky #AcademicSky #ChemSky #EduSky #Edchat 🧪

Proteomes MDPI

@proteomesmdpi.bsky.social

5 days ago

This article is now available in Proteomes: PTMs_Closed_Search: Multiple Post-Translational Modification Closed Search Using Reduced Search Space and Transferred FDR 🧬🖥️🧪🧫🥼

www.mdpi.com/2227-7382/14...

#proteomes #proteomics #proteoforms #MassSpec

BioMassSpec

@realbiomassspec.bsky.social

5 days ago

Glucocorticoid-Induced Proteome and Phosphoproteome Changes in Breast Cancer Cell Lines 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.

Glucocorticoid-Induced Proteome and Phosphoproteome Changes in Breast Cancer Cell Lines #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

5 days ago

Salivary Proteomics Reveals Oxidative Markers in E-Cigarette Users 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 altera...

Salivary Proteomics Reveals Oxidative Markers in E-Cigarette Users #JProteomeRes #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Metabolite Profiling and Identification of Semaglutide in Liver S9 Across Species and Rat Plasma Semaglutide, a glucagon-like peptide-1 receptor agonist, stands as a paradigm of successful peptide drug development. Although absorption, distribution, metabolism and excretion characteristics of se...

Metabolite Profiling and Identification of Semaglutide in Liver S9 Across Species and Rat Plasma #BiomedChrom #MassSpec analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Species- and Tissue-Specific Accumulation of Polycyclic Aromatic Compounds in Three Arctic Seabirds Polycyclic aromatic compounds (PACs) are a complex class of toxic organic contaminants whose environmental fate and risk in the Arctic are poorly understood. The accumulation potential and risk to mar...

Species- and Tissue-Specific Accumulation of Polycyclic Aromatic Compounds in Three Arctic Seabirds #EST #MassSpec pubs.acs.org/doi/10.1021/...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Presence of Emerging Contaminants in UK Honey─Human Pharmaceuticals a Concern for Honeybees? Emerging contaminants can accumulate in water, soils, and crops; however, little is known about the potential exposure to honeybees. Using samples collected surrounding arable farming in Great Britain and nontarget techniques, we identified 119 suspect chemicals in hives. On average, each hive contained 6.8 (±3.01) active ingredients, these included human pharmaceuticals (64%), industrial chemicals (10%), surfactants (8%), and plasticizers (5%). Elevated concentrations of the anti-inflammatory flurandrenolide (582.3 ± 348.4 ng/g), the nonsteroidal anti-inflammatorydrug aspirin (358.2 ± 390.1 ng/g), the fungicide azoxystrobin (298.5 ± 159.9 ng/g), the antihypertensive methyldopa (123.4 ± 60 ng/g), and the anticonvulsant carbamazepine (79.97 ± 54.2 ng/g) were identified. Elevated concentrations of human-origin contaminants of emerging concern (CECs), and their increased frequency in arable areas, indicate that the reuse of contaminated fertilizers contributes to accumulation in hives across English landscapes. Critically, most of these contaminants lack toxicity data for honeybees, making it impossible to assess their acute or chronic risks.

Presence of Emerging Contaminants in UK Honey─Human Pharmaceuticals a Concern for Honeybees? #JAFC #MassSpec pubs.acs.org/doi/10.1021/...

Proteomes MDPI

@proteomesmdpi.bsky.social

1 week ago

This article is now available in Proteomes: Evaluating the Impact of Two Different Diets on the Protein Profile of the Brain, Liver, and Intestine of the Barramundi 🧬🖥️🧪🧫🥼

www.mdpi.com/2227-7382/14...

#proteomics #proteomes #proteoforms #MassSpec

Matrix Science

@matrixscience.bsky.social

1 week ago

Pie chart illustration of the top species detected: Mycobacteroides abscessus (61%); Sus scrofa (22%); Homo sapiens (11%); Mycolicibacterium goodii (5.6%).

Using the blib2msp converter, Mascot Server can now search DDA spectral libraries in BLIB format. Here's an example for identifying mycobacteria.

www.matrixscience.com/blog/identif...

#proteomics #massspec

@jjotto.bsky.social

1 week ago

Recently started to test some of our DIA data from the Astral Zoom coupled with EvoSep Uno. We've processed some files with a local version of Chimerys through PD and DIA-NN. Wow 𝐃𝐈𝐀-𝐍𝐍 is fast. #massspec #proteomics

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Diagnosing melioidosis and tracking treatment outcomes using breath Diagnosing melioidosis and tracking treatment outcomes using breath, Gao, Antao, Mayo, Mark, Woerle, Celeste, Currie, Bart, Hill, Jane E

Diagnosing melioidosis and tracking treatment outcomes using breath #JBreathRes #MassSpec iopscience.iop.org/article/10.1...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Comparison of metabolite differences and pharmacologically active constituents between Piper longum and Piper sarmentosum based on non-targeted metabolomics #PeerJ #MassSpec peerj.com/articles/207...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Unraveling the Heterogeneity of Hyperuricemia Using Untargeted Metabolomics and Statistical Modeling Hyperuricemia is the second most prevalent metabolic disorder globally and exhibits pronounced heterogeneity in clinical practice. Only about 10% of i…

Unraveling the Heterogeneity of Hyperuricemia Using Untargeted Metabolomics and Statistical Modeling #JPBA #MassSpec www.sciencedirect.com/science/arti...

BioMassSpec

@realbiomassspec.bsky.social

1 week ago

Leveraging Dissolved Organic Matter Collections as a Natural Chemical Library to Link Molecular Traits with Cellular Morphological Responses Dissolved organic matter (DOM) exhibits a highly complex molecular composition and maintains ecosystem stability, acting as a crucial interface between biotic and abiotic processes. Although DOM’s mol...

Leveraging Dissolved Organic Matter Collections as a Natural Chemical Library to Link Molecular Traits with Cellular Morphological Responses #EST #MassSpec pubs.acs.org/doi/10.1021/...