Advances In Mass Spectrometry Research Articles

Comparison of Shared Class I HLA-bound Non-canonical Neoepitopes between Normal and Neoplastic Tissues of Pancreatic Adenocarcinoma.

Developing T cell or vaccine therapies for pancreatic ductal adenocarcinoma (PDAC) has been challenging due to a lack of knowledge regarding immunodominant, cancer-specific antigens, as a scarcity of genomic mutation-associated neoepitopes characterizes PDAC and there are limited availability of effective approaches to discover them. We utilized an advanced mass spectrometry approach to compare the immunopeptidome of PDAC tissues and matched normal tissues from the same patients. We identified HLA class I-binding variant peptides derived from canonical proteins, which had single amino-acid substitutions not attributed to genetic mutations or RNA editing. These amino-acid substitutions appeared to result from translational errors. The variant peptides were predominantly enriched in tumor tissues, with some peptides shared across patients. Importantly, several of these variant peptides were more immunogenic than their wild-type counterparts. The shared non-canonical neoepitopes identified in this study offer promising candidates for vaccine and T cell therapy development, potentially providing new avenues for immunotherapy in PDAC.

Advancements in mass spectrometry-based proteomics: anew era in pathology research and diagnostics.

Mass spectrometry (MS)-based proteomics is rapidly transforming pathology research and diagnostics by enabling comprehensive studies of protein expression and post-translational modifications (PTMs). This article discusses recent advancements in MS-based proteomics, focusing on emerging technologies in sample preparation, MS instrumentation, and data analysis. These developments are scrutinized for their applications in clinical cohort studies and molecular pathology diagnostics. The article reviews innovations in automated sample preparation, chromatography systems, advanced MS technologies, and proteomic data analysis in the context of pathology. Specific applications such as liquid biopsy, spike-in heavy peptide panels, immunopeptidomics, and PTM screening are highlighted alongside opportunities for data integration. Recent technological improvements have significantly increased the throughput, precision, and scope of proteomic studies, enabling the analysis of large clinical cohorts and small specimens with unprecedented sensitivity. Advanced MS techniques have broadened applications, opening new avenues for discovery and diagnosis of marker proteins and therapeutic targets. Advancements in MS-based proteomics have created new opportunities in clinical research and diagnostics. By facilitating more comprehensive and integrated analyses of proteomes, these technologies are set to play apivotal role in the future of personalized medicine and pathology research.

Unraveling the redox code to improve physiological research in human health and disease.

Redox reactions, involving electron transfer, are critical to human physiology. However, progress in understanding redox metabolism is hindered by flawed analytical methods. This review highlights emerging techniques that promise to revolutionize redox research, enhancing our comprehension of human health and disease. Oxygen, vital for aerobic metabolism, also produces reactive oxygen species (ROS), such as superoxide and hydrogen peroxide. While historically seen as harmful, ROS at low concentrations are now recognized as key regulators of cell signaling. A balance between ROS and antioxidants, known as redox balance, is crucial, and deviations can lead to oxidative stress. Recent studies have distinguished beneficial "oxidative eustress" from harmful "oxidative distress." New techniques, such as advanced mass spectrometry and high-throughput immunoassays, offer improved accuracy in measuring redox states and oxidative damage. These advancements are pivotal for understanding redox signaling, cysteine oxidation, and their implications for disease. Looking ahead, the development of precision redox medicine could lead to better treatments for oxidative stress-related diseases and foster interventions promoting health.

Mouse liver sinusoidal endothelial cell responses to the glucocorticoid receptor agonist dexamethasone.

Liver sinusoidal endothelial cells (LSECs) which make up the fenestrated wall of the hepatic sinusoids, are active scavenger cells involved in blood waste clearance and liver immune functions. Dexamethasone is a synthetic glucocorticoid commonly used in the clinic and as cell culture supplement. However, the response is dependent on tissue, cell type, and cell state. The aim of this study was to investigate the effect of dexamethasone on primary mouse LSECs (C57BL/6J); their viability (live-dead, LDH release, caspase 3/7 assays), morphology (scanning electron microscopy), release of inflammatory markers (ELISA), and scavenging functions (endocytosis assays), and associated biological processes and pathways. We have characterized and catalogued the proteome of LSECs cultured for 1, 10, or 48h to elucidate time-dependent and dexamethasone-specific cell responses. More than 6,000 protein IDs were quantified using tandem mass tag technology and advanced mass spectrometry (synchronous precursor selection multi-notch MS3). Enrichment analysis showed a culture-induced upregulation of stress and inflammatory markers, and a significant shift in cell metabolism already at 10h, with enhancement of glycolysis and concomitant repression of oxidative phosphorylation. At 48h, changes in metabolic pathways were more pronounced with dexamethasone compared to time-matched controls. Dexamethasone repressed the activation of inflammatory pathways (IFN-gamma response, TNF-alpha signaling via NF-kB, Cell adhesion molecules), and culture-induced release of interleukin-6, VCAM-1, and ICAM-1, and improved cell viability partly through inhibition of apoptosis. The mouse LSECs did not proliferate in culture. Dexamethasone treated cells showed upregulation of xanthine dehydrogenase/oxidase (Xdh), and the transcription regulator Foxo1. The drug further delayed but did not block the culture-induced loss of LSEC fenestration. The LSEC capacity for endocytosis was significantly reduced at 48h, independent of dexamethasone, which correlated with diminished expression of several scavenger receptors and C-type lectins and altered expression of proteins in the endocytic machinery. The glucocorticoid receptor (NR3C1) was suppressed by dexamethasone at 48h, suggesting limited effect of the drug in prolonged LSEC culture. Conclusion: The study presents a detailed overview of biological processes and pathways affected by dexamethasone in mouse LSECs in vitro.

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

BackgroundMicrobial communities are essential in human health and environmental regulation, but present a challenge for the analytical science due to their diversity and dynamic range. Tandem mass spectrometry provides functional insights on microbial life cycle, but is time-consuming. MALDI TOF excels in rapid species identification, but not functional assessment. To address critical challenges in human health and environmental sustainability, microbiology needs advanced mass spectrometry methods and bioinformatic tools enabling both rapid identification and accurate assessment of functional activity of microbial communities. ResultsWe show for the first time that both identity and functional activity of microorganisms and their communities can be accurately determined in experiments as short as 7 min per sample, using the basic Orbitrap MS configuration without peptide fragmentation. The approach was validated using strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. Our new bioinformatic algorithm identifies the bacterial species with an accuracy of 95 %, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified components of 12 %. For mock microbiomes, Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed the accurate assessment of functional activity of strain isolates, compared with the standard label-free and label-based approaches. SignificanceOur approach makes microbial proteomics fast, functional and insightful using the Orbitrap instruments even without employing peptide fragmentation technology. The approach can be applied to any microorganisms and can take a niche in routine functional assessment of microbial pathogens and consortiums in clinical diagnostics together with MALDI TOF MS and 16S rRNA gene sequencing.

Cannabidiol and fluorinated derivative anti-cancer properties against glioblastoma multiforme cell lines, and synergy with imidazotetrazine agents

BackgroundGlioblastoma multiforme (GBM) is an aggressive cancer with poor prognosis, partly due to resistance to the standard chemotherapy treatment, temozolomide (TMZ). Phytocannabinoid cannabidiol (CBD) has exhibited anti-cancer effects against GBM, however, CBD’s ability to overcome common resistance mechanisms to TMZ have not yet been investigated. 4’-Fluoro-cannabidiol (4’-F-CBD, or HUF-101/PECS-101) is a derivative of CBD, that exhibits increased activity compared to CBD during in vivo behavioural studies.MethodsThis anti-cancer activity of cannabinoids against GBM cells sensitive to and representing major resistance mechanisms to TMZ was investigated. Cannabinoids were also studied in combination with imidazotetrazine agents, and advanced mass spectrometry with the 3D OrbiSIMS was used to investigate the mechanism of action of CBD.ResultsCBD and 4’-F-CBD were found to overcome two major resistance mechanisms (methylguanine DNA-methyltransferase (MGMT) overexpression and DNA mismatch repair (MMR)-deficiency). Synergistic responses were observed when cells were exposed to cannabinoids and imidazotetrazine agents. Synergy increased with T25 and 4’-F-CBD. 3D OrbiSIMS analysis highlighted the presence of methylated-DNA, a previously unknown anti-cancer mechanism of action of CBD.ConclusionsThis work demonstrates the anti-cancer activity of 4’-F-CBD and the synergy of cannabinoids with imidazotetrazine agents for the first time and expands understanding of CBD mechanism of action.

MALDI-TOF mass spectrometry from nucleic acid: development and evaluation of a novel platform for identification of mycobacteria and detection of genetic markers of resistance.

Complete identification methods are critical for evaluating nontuberculous mycobacteria (NTM). Here, we describe a novel diagnostic method for identification of eight NTM, Mycobacterium tuberculosis complex, and three drug resistance markers using PCR/matrix-assisted, laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) from cultured organisms. With this technology, a multiplex end-point PCR is performed for targets of interest. Detection probes that are extended in the presence of a target are added. The extended probes have greater molecular weight and can be detected by MALDI-TOF MS. An AFB Primary Panel was designed to differentiate Mycobacterium avium; Mycobacterium intracellulare subsp. chimaera; Mycobacterium avium complex (other); Mycobacterium abscessus subsp. abscessus, bolletii, and massiliense; Mycobacterium kansasii, and M. tuberculosis complex. This design should cover 90% (3,483/3,691) of mycobacteria seen onsite. A development set of unblinded isolates (n = 217) was used to develop PCR primers, detection probes, and probe barcodes. It demonstrated 99.1% (215/217) agreement with reference methods. An evaluation set using blinded isolates (n = 320) showed an overall sensitivity of 94.3% (range by target: 90.0-100%). Overall specificity from negative media, non-target mycobacteria, and bacteria was 99.1% (108/109; range by target: 94.4-100%). Three drug resistance markers erm (41), rrl, and rrs demonstrated 100%, 91%, and 100% sensitivity, respectively, and >99% specificity. Limit of detection per target ranged from 2.2 × 103 to 9.9 × 106 CFU/mL. The AFB Primary Panel allows for mycobacterial speciation, subspeciation, and resistance mutation detection, which is essential for diagnosis, appropriate therapy, identifying outbreaks, and managing treatment-refractory disease. It can perform with high-throughput and high specificity and sensitivity from isolates.IMPORTANCEEven closely related mycobacteria can have unique treatment patterns, but differentiating these organisms is a challenge. Here, we tested an innovative platform that combines two commonly used technologies and creates something new: matrix-assisted, laser-desorption ionization time-of flight mass spectrometry was performed on PCR amplicons instead of on proteins. This created a robust system with the advantages of PCR (high discriminatory power, high throughput, detection of resistance) with the advantages of mass spectrometry (more targets, lower operational cost) in order to identify closely related mycobacterial organisms.

Evaluation of atmospheric-plasma-source absorption mode Fourier transform Orbitrap mass spectrometry for chlorinated paraffin mixtures

Chlorinated paraffins (CP) are complex molecular mixtures occurring in a wide range of isomers and homologs of environmental hazards, whose analytical complexity demand advanced mass spectrometry (MS) methods for their characterization. The reported formation of chlorinated olefins (COs) and other transformation products during CP biotransformation and degradation can alter the MS analysis, increasing the high resolution required to distinguish CPs from their degradation products. An advanced setup hyphenating a plasma ionization source and an external high-performance data acquisition and processing system to the legacy hybrid LTQ Orbitrap XL mass spectrometer is reported. First, the study demonstrated the versatility of a liquid sampling atmospheric pressure glow discharge, as a soft ionization technique, for CP analysis. Second, enhanced resolution and sensitivity provided by the absorption mode Fourier transform spectral representation on this legacy mass spectrometer are shown. The developed Orbitrap-based platform allowed the detection of new isotopic clusters and CPs and COs to be distinguished at medium resolution (setting 30,000 at m/z 400, ~ 400 ms transients), and even chlorinated di-olefins (CdiOs) at higher resolution (setting 100,000 at m/z 400, ~ 1500 ms transients). Overall, such proof-of-principle instrumental improvements are promising for environmental and analytical research in the field of CP analysis.Graphical

Dependency of fentanyl analogue protomer ratios on solvent conditions as measured by ion mobility-mass spectrometry.

Recently, our group has shown that fentanyl and many of its analogues form prototropic isomers ("protomers") during electrospray ionization. These different protomers can be resolved using ion mobility spectrometry and annotated using mobility-aligned tandem mass spectrometry fragmentation. However, their formation and the extent to which experimental variables contribute to their relative ratio remain poorly understood. In the present study, we systematically investigated the effects of mixtures of common chromatographic solvents (water, methanol, and acetonitrile) and pH on the ratio of previously observed protomers for 23 fentanyl analogues. Interestingly, these ratios (N-piperidine protonation vs. secondary amine/O = protonation) decreased significantly for many analogues (e.g., despropionyl ortho-, meta-, and para-methyl fentanyl), increased significantly for others (e.g., cis-isofentanyl), and remained relatively constant for the others as solvent conditions changed from 100% organic solvent (methanol or acetonitrile) to 100% water. Interestingly, pH also had significant effects on this ratio, causing the change in ratio to switch in many cases. Lastly, increasing conditions to pH ≥ 4.0 also prompted the appearance of new mobility peaks for ortho- and para-methyl acetyl fentanyl, where all previous studies had only showed one single distribution. Because these ratios have promise to be used qualitatively for identification of these (and emerging) fentanyl analogues, understanding how various conditions (i.e., mobile phase selection and/or chromatographic gradient) affect their ratios is critically important to the development of advanced ion mobility and mass spectrometry methodologies to identify fentanyl analogues.

Enhancing drug analysis through advanced mass spectrometry techniques and quantitative modeling

The integration of advanced mass spectrometry (MS) techniques with quantitative modeling has revolutionized the field of drug analysis, offering unprecedented accuracy, sensitivity, and specificity in the detection and quantification of pharmaceutical compounds and their metabolites. High-Resolution Mass Spectrometry (HRMS) and Tandem Mass Spectrometry (MS/MS) have emerged as pivotal tools, capable of distinguishing isobaric species and providing detailed structural information, respectively. Ambient ionization techniques such as Desorption Electrospray Ionization (DESI) and Direct Analysis in Real Time (DART) have further simplified sample preparation, enabling rapid, direct analyses under ambient conditions. This review discusses the significant strides made in enhancing drug analysis through these innovations, alongside the application of calibration curves and mathematical models for quantitation and pharmacokinetic modeling. Additionally, it addresses the challenges inherent in quantitative MS, including matrix effects, analyte stability, and the need for improved sensitivity and specificity. Through a comprehensive overview, this article underscores the transformative impact of these advancements on drug analysis, paving the way for more accurate and efficient pharmaceutical research and diagnostics.

MIND4OLIGOS: Determining the Monoisotopic Mass of Oligonucleotides Observed in High-Resolution Mass Spectrometry.

Oligonucleotide therapeutics have emerged as an important class of drugs offering targeted therapeutic strategies that complement traditional modalities, such as monoclonal antibodies and small molecules. Their unique ability to precisely modulate gene expression makes them vital for addressing previously undruggable targets. A critical aspect of developing these therapies is characterizing their molecular composition accurately. This includes determining the monoisotopic mass of oligonucleotides, which is essential for identifying impurities, degradants, and modifications that can affect the drug efficacy and safety. Mass spectrometry (MS) plays a pivotal role in this process, yet the accurate interpretation of complex mass spectra remains challenging, especially for large molecules, where the monoisotopic peak is often undetectable. To address this issue, we have adapted the MIND algorithm, originally developed for top-down proteomics, for use with oligonucleotide data. This adaptation allows for the prediction of monoisotopic mass from the more readily detectable, most-abundant peak mass, enhancing the ability to annotate complex spectra of oligonucleotides. Our comprehensive validation of this modified algorithm on both in silico and real-world oligonucleotide data sets has demonstrated its effectiveness and reliability. To facilitate wider adoption of this advanced analytical technique, we have encapsulated the enhanced MIND algorithm in a user-friendly Shiny application. This online platform simplifies the process of annotating complex oligonucleotide spectra, making advanced mass spectrometry analysis accessible to researchers and drug developers. The application is available at https://valkenborg-lab.shinyapps.io/mind4oligos/.

Advanced Mass Spectrometry-Based Biomarker Identification for Metabolomics of Diabetes Mellitus and Its Complications.

Over the years, there has been notable progress in understanding the pathogenesis and treatment modalities of diabetes and its complications, including the application of metabolomics in the study of diabetes, capturing attention from researchers worldwide. Advanced mass spectrometry, including gas chromatography-tandem mass spectrometry (GC-MS/MS), liquid chromatography-tandem mass spectrometry (LC-MS/MS), and ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-ESI-Q-TOF-MS), etc., has significantly broadened the spectrum of detectable metabolites, even at lower concentrations. Advanced mass spectrometry has emerged as a powerful tool in diabetes research, particularly in the context of metabolomics. By leveraging the precision and sensitivity of advanced mass spectrometry techniques, researchers have unlocked a wealth of information within the metabolome. This technology has enabled the identification and quantification of potential biomarkers associated with diabetes and its complications, providing new ideas and methods for clinical diagnostics and metabolic studies. Moreover, it offers a less invasive, or even non-invasive, means of tracking disease progression, evaluating treatment efficacy, and understanding the underlying metabolic alterations in diabetes. This paper summarizes advanced mass spectrometry for the application of metabolomics in diabetes mellitus, gestational diabetes mellitus, diabetic peripheral neuropathy, diabetic retinopathy, diabetic nephropathy, diabetic encephalopathy, diabetic cardiomyopathy, and diabetic foot ulcers and organizes some of the potential biomarkers of the different complications with the aim of providing ideas and methods for subsequent in-depth metabolic research and searching for new ways of treating the disease.

Caffeine improves mitochondrial dysfunction in the white matter of neonatal rats with hypoxia-ischemia through deacetylation: a proteomic analysis of lysine acetylation.

White matter damage (WMD) is linked to both cerebral palsy and cognitive deficits in infants born prematurely. The focus of this study was to examine how caffeine influences the acetylation of proteins within the neonatal white matter and to evaluate its effectiveness in treating white matter damage caused by hypoxia-ischemia. We employed a method combining affinity enrichment with advanced liquid chromatography and mass spectrometry to profile acetylation in proteins from the white matter of neonatal rats grouped into control (Sham), hypoxic-ischemic (HI), and caffeine-treated (Caffeine) groups. Our findings included 1,999 sites of lysine acetylation across 1,123 proteins, with quantifiable changes noted in 1,342 sites within 689 proteins. Analysis of these patterns identified recurring sequences adjacent to the acetylation sites, notably YKacN, FkacN, and G * * * GkacS. Investigation into the biological roles of these proteins through Gene Ontology analysis indicated their involvement in a variety of cellular processes, predominantly within mitochondrial locations. Further analysis indicated that the acetylation of tau (Mapt), a protein associated with microtubules, was elevated in the HI condition; however, caffeine treatment appeared to mitigate this over-modification, thus potentially aiding in reducing oxidative stress, inflammation in the nervous system, and improving mitochondrial health. Caffeine inhibited acetylated Mapt through sirtuin 2 (SITR2), promoted Mapt nuclear translocation, and improved mitochondrial dysfunction, which was subsequently weakened by the SIRT2 inhibitor, AK-7. Caffeine-induced changes in lysine acetylation may play a key role in improving mitochondrial dysfunction and inhibiting oxidative stress and neuroinflammation.

Neuropeptidomics of the American Lobster Homarus americanus.

The American lobster, Homarus americanus, is not only of considerable economic importance but has also emerged as a premier model organism in neuroscience research. Neuropeptides, an important class of cell-to-cell signaling molecules, play crucial roles in a wide array of physiological and psychological processes. Leveraging the recently sequenced high-quality draft genome of the American lobster, our study sought to profile the neuropeptidome of this model organism. Employing advanced mass spectrometry techniques, we identified 24 neuropeptide precursors and 101 unique mature neuropeptides in Homarus americanus. Intriguingly, 67 of these neuropeptides were discovered for the first time. Our findings provide a comprehensive overview of the peptidomic attributes of the lobster's nervous system and highlight the tissue-specific distribution of these neuropeptides. Collectively, this research not only enriches our understanding of the neuronal complexities of the American lobster but also lays a foundation for future investigations into the functional roles that these peptides play in crustacean species. The mass spectrometry data have been deposited in the PRIDE repository with the identifier PXD047230.

Decoding Voltammograms at the Molecular Frontier: Integration of Voltammetry and Mass Spectrometry

AbstractElectrochemical reactions are better understood by gaining insight into the molecular transformations at the electrodes. This paper introduces a straightforward experimental arrangement in which the voltammetry experiment in a standard electrochemical cell integrates with online electrospray‐ionization mass‐spectrometry. The procedure allows for monitoring of the ions produced at the working electrode. The ionic species sampling is facilitated by a silica capillary embedded in the working electrode and connected directly to the electrospray ionization source. This integration configures real‐time monitoring of the ions produced at the working electrode, enhancing our knowledge of the electrochemical process. The methodology is thoroughly described and exemplified by monitoring the reactive intermediates and products that arise during the electrochemical oxidation of carbazole. This design provides an opportunity to study intermediates in electrochemical reactions with advanced mass spectrometry methods such as ion mobility separation or ion spectroscopy.

Proteomic analysis of blood serum in bipolar disorder

IntroductionBipolar disorder (BD) often has symptoms similar to other mental disorders (BD), and there are no paraclinical criteria for differential diagnosis. (Geoffroy et al. Bip Dis 2017; 5 7). Published work on MD proteomics is scarce and focused on schizophrenia. (Dmitrieva et al. PeerJ. 2022; 10 e13907). Therefore, it is important to study potential biomarkers of BD using easily accessible material—blood serum (Rhee et al. Transl Psy 2023; 13 44). Identification of proteins involved in the pathogenesis of BD will help in the study of the pathogenetic mechanisms of BD, the development of differential diagnostic methods and pathogenetically based drugs.ObjectivesCarrying out a comparative proteomic analysis of blood serum from patients with BD and healthy individuals to identify potential biomarkersMethodsWe analyzed the protein spectrum of the blood serum of 14 patients with BD who were admitted during a depressive episode at the age of 32 [21;52] years with a disease duration of 8[5;11] years. The control group consisted of 10 mentally and somatically healthy individuals corresponding to the gender and age of the BD group. Blood serum was purified from 14 major proteins using affinity chromatography and separated by electrophoresis using the Laemmli method. After trypsinolysis, proteins were identified using HPLC/mass spectrometry on an Orbitrap instrument. Mass spectrometric analysis was performed on the Advanced Mass Spectrometry Core Facility of Skolkovo Institute of Science and Technology. Protein identification was carried out using the UniProtKB database using the Mascot search engine. The results were tested for significance using the nonparametric Fisher exact test with Yates correction.ResultsIn patients with BD, qualitative mass spectrometry revealed differential expression of 21 neurospecific proteins. Among them: Protein dispatched homolog 3, Ceroid-lipofuscinosis neuronal protein 6, SWI/SNF complex subunit SMARCC1, Neurogenic differentiation factor 4, Protein furry homolog-like, REST corepressor 1 – are involved in the proliferation, development and differentiation of neurons; Hemicentin-2, Dystrophin, Voltage-dependent L-type calcium channel subunit alpha-1D, Syntaxin-binding protein 5, Small conductance calcium-activated potassium channel protein 1– participate in synaptic transmission of ion transport and form receptors.ConclusionsStudying the role of these proteins in BD and their quantitative content in a larger number of patients is promising. This will help in the development of new diagnostic criteria and targets for drug therapy for BD.Support by the Russian Science Foundation grant No. 23-75-00023.Disclosure of InterestNone Declared

Anthropogenic-induced ecological risks on marine ecosystems indicated by characterizing emerging pollutants in Pearl River Estuary, China

Anthropogenic Contaminants of Emerging Concern (CECs) in marine environments have raised significant concerns. Yet, analyses detailing their origins, fate, and environmental effects are limited. This study employs an integrated non-target screening methodology to elucidate CECs existence across 46 sampling sites in the Pearl River Estuary (PRE) of the South China Sea. Assisted by advanced liquid chromatography-high resolution mass spectrometry, we discovered 208 chemicals in six usage categories, with pesticides (33 %) and pharmaceuticals (29 %) predominating. Several CECs drew attention for their consistent detections, profound abundance, and significant ecotoxicities. The wide detection of them at offshore sites further implies that anthropogenic activities may contribute to large-scale contamination. Meanwhile, distinct distribution patterns of CECs across PRE are evident in semi-quantitative results, indicating regional anthropogenic influences. Identified transformation products may establish a novel and non-negligible negative contribution to ecology through elevated environmental toxicities, exemplified by HMMM and atrazine. Based on the ecological risks, we compiled a prioritized list of 21 CECs warranting intensified scrutiny. Our findings indicate the introduction of various CECs into the South China Sea via PRE, emphasizing the urgent necessity for ongoing surveillance of discharged CECs at estuary areas and assessment of their marine ecological consequences.

Abstract 1847: Human protein atlas: A resource for target expression across 19 tissues

Abstract Proteins are the primary targets and off-targets of therapeutics such as small molecule and biologics. Thus, a thorough understanding of their expression profiles across various human tissues in health and disease is essential through all stages of drug development. However, generating such a comprehensive proteome profile for each tissue poses a major analytical challenge due to the large dynamic range of protein abundance within a tissue and the enormous complexity introduced by distinct proteoforms. These proteoforms may arise from genetic variations (e.g. mutations), posttranscriptional events (e.g. isoforms from alternative splicing) or posttranslational modifications, resulting in more than a million protein species from 20,000 protein-coding genes. Thanks to advancements in sensitivity and speed in the recent years, mass spectrometry (MS)-based proteomics can now be routinely applied to quantify ten thousand of proteins in biological samples. Taking advantage of MS being an unbiased and matrix-agnostic method, we pivoted the generation of a high quality and uniform protein expression atlas of 19 healthy human tissues and 3 cancerous tissues. We constructed the atlas in two parts aiming to address the following two aspects respectively: 1) a deep library providing evidence for protein/proteoform presence in each of the 22 tissues; 2) quantitative profiles for cross-comparison in all tissues. For the first part, each tissue sample was subjected to an extensive fractionation process followed by MS analysis of each of the fractions. In total, we identified 20’025 protein groups mapped to 17’715 protein-coding genes, providing protein-level evidence for > 90% of all protein-coding genes annotated in the neXtProt repository. Among all identified proteins, 10’755 were detectable across all tissues. Notably, we identified 37 proteins mapping to putative genes. In part two of the atlas, quantitative expression profiles were generated for 15’772 protein groups using TrueDiscovery DIA-MS across the 22 tissues. These data allow us to investigate ubiquitous vs. tissue-restricted protein expression of various protein classes such as surface receptors or kinases. Moreover, we performed correlation analysis between protein expression and mRNA abundance across 19 tissues, demonstrating that for a significant portion of the proteome, mRNA level-information is not an adequate proxy for protein expression. Collectively, this MS-based resource alleviates dependency on antibody-based reagents. We envision that the tissue atlas can be expanded to cover various disease indications, providing valuable insights for target discovery and assessment of target/off-target tissue distribution. Citation Format: Sandra Schaer, Marco Tognetti, Roland Bruderer, Polina Shichkova, Yuehan Feng, Lukas Reiter. Human protein atlas: A resource for target expression across 19 tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1847.

Abstract 1842: Global proteomics reveals integrin signaling as a driver of infiltration in glioblastoma

Abstract Background: Glioblastoma (GBM), a notably aggressive brain cancer, presents significant treatment challenges due to its propensity for deep, diffuse infiltration into healthy brain tissue. This trait enables GBM to resist and survive following surgery and conventional adjuvant therapies. Emerging evidence suggests that signaling between GBM stem cells (GSCs) may be instrumental in this invasive behavior. Our study aimed to unravel the intricacies of these intercellular communication networks within glioblastoma by employing comprehensive proteomic profiling across a diverse array of patient-derived GSC lines. Methods: We conducted our study using a sex-stratified cohort comprising 17 patient-derived GSC lines. Proteomic profiling encompassed analyses of both GSC lysates and conditioned media under various oxygen conditions (normoxia at 20% O2, hypoxia at 1% and 0.2% O2). Additionally, we incorporated the glioma cerebral organoid (GLICO) system, facilitating co-cultures of GSCs with human cerebral organoids. For in-depth proteomic analysis, we utilized advanced TMT-based liquid chromatography-tandem mass spectrometry (LC-MS/MS; Q-Exactive, Thermo Fisher). Results: Our findings corroborate that GSCs adhere to the tripartite model of proliferation, invasion, and hypoxic response. A salient discovery was the consistent enrichment of integrin signaling pathways in GSCs under hypoxic conditions. Specifically, we observed a significant association between upregulation in integrin signaling (BIOCARTA_INTEGRIN_PATHWAY) and elevated KRAS activity (SWEET_KRAS_TARGETS_UP: r=0.43, p<0.01), as well as hypoxic responses (WINTER_HYPOXIA_UP: r=0.76, p<0.0001) in GSCs. Notably, in the GLICO model, both integrin signaling and KRAS pathways were markedly upregulated in the presence of GSCs compared to cerebral organoids alone (p<0.05). Conclusions: This research highlights the pivotal role of integrin signaling in mediating the invasive attributes of glioblastoma. The data underscore the importance of further exploring key modulators within the integrin signaling pathway, presenting a promising avenue for the discovery of novel therapeutic targets in glioblastoma treatment. Citation Format: Lennart J. van Winden, Rifat Shahriar Sajid, Okty Abbasi Borhani, Evelyn Rose Kamski-Hennekam, Nakita Gopal, Alberto Leon, Phedias Diamandis. Global proteomics reveals integrin signaling as a driver of infiltration in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1842.

Eliciting specialized metabolites from marine microalgae using abiotic stress

ABSTRACT Advanced mass spectrometry and molecular networking techniques have led to an increase in the discovery of novel metabolites from bacteria and fungi. However, a systematic approach to exploring the metabolite profiles of microalgae in response to stress has not been performed. Unlocking the chemical potential of microalgae could provide further biotechnology applications in nutraceutical, biofuel, and cosmetic industries. This study explored the changes in metabolite production of strains of the three microalgae Dunaliella primolecta, Nannochloropsis oculata, and Phaeodactylum tricornutum cultured under varying nitrate, NaCl, salinity and pH conditions. A total of 2284 metabolites were detected across all strains and conditions, with 49% of those metabolites specific to cultures grown under stress (i.e., not present in the control). From comparison with 33 libraries of mass spectral data, only five metabolites were identified, stressing the need for more open-access natural product databases specifically focused on microalgae.