Spatial Proteomics by Parallel Accumulation‐Serial Fragmentation Supported MALDI MS/MS Imaging: A First Glance Into Multiplexed and Spatial Peptide Identification

Rapid Communications in Mass Spectrometry, Год журнала: 2025, Номер 39(9)

Опубликована: Фев. 5, 2025

ABSTRACT Rationale In spatial proteomics, matrix‐assisted laser desorption/ionization (MALDI) imaging enables rapid and cost‐effective peptide measurements. Yet, in situ identification remains challenging. Therefore, this study aims to integrate the trapped ion mobility spectrometry (TIMS)–based parallel accumulation‐serial fragmentation (PASEF) into MALDI of tryptic peptides enable multiplexed MS/MS imaging. Methods An initial TIMS MS1 survey measurement was performed, followed by a manual generation precursor list containing mass over charge values windows. Inside dual system, submitted precursors were trapped, separately eluted their analyzed quadrupole time‐of‐flight device, thereby enabling Finally, identified spectrum matching. Results This presents first (iprm‐PASEF) peptides. Its applicability showcased on two histomorphologically distinct tissue specimens four‐plex five‐plex setup. Precursors successfully search engine MASCOT one single experiment for each respective tissue. Peptide identifications corroborated liquid–chromatography tandem experiments fragment colocalization analyses. Conclusions study, we present novel pipeline, based iprm‐PASEF, that allows Hence, it marks step towards integration emerging field proteomics.

Язык: Английский

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Extensive modulation of the circulating blood proteome by hormonal contraceptive use across two population studies

Communications Medicine, Год журнала: 2025, Номер 5(1)

Опубликована: Апрель 22, 2025

Abstract Background The study of circulating blood proteins in population cohorts offers new avenues to explore lifestyle-related and genetic influences describing shaping human health. Methods Utilizing high-throughput mass spectrometry, we quantified 148 highly abundant proteins, functioning the innate adaptive immune system, coagulation nutrient transport 3632 plasma, 500 serum samples from CHRIS BASE-II cross-sectional studies, respectively. Through multiple regression analyses, aimed identify main factors influencing proteome at level. Results Many demographic covariates common medications affect concentration high-abundant plasma but most significant changes are linked use hormonal contraceptives (HCU). HCU particularly alters amongst others levels Angiotensinogen Transcortin. We robustly replicated these findings cohort. Furthermore, our results indicate that combined with ethinylestradiol have a stronger effect compared bioidentical estrogens. Our analysis detects no lasting impact on proteome. Conclusions is dominant factor reshaping two studies. Given high prevalence among young women, it essential account for this treatment studies avoid misinterpreting its as sex- or age-related effects. Although did not investigate influence HCU-induced proteomic health, data suggest future topic warranted.

Язык: Английский

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Integrated Multi-Omics Mapping of Mitochondrial Dysfunction and Substrate Preference in Barth Syndrome Cardiac Tissue

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Апрель 20, 2025

Abstract Barth syndrome (BTHS) is a rare X-linked recessively inherited disorder caused by variants in the TAFAZZIN gene, leading to impaired conversion of monolysocardiolipin (MLCL) into mature cardiolipin (CL). Accumulation MLCL and CL deficiency are diagnostic markers for BTHS. Clinically, BTHS includes cardiomyopathy, skeletal myopathy, neutropenia, growth delays. Severely affected patients may require early cardiac transplants due unpredictable phenotypes. The pathophysiological mechanisms poorly understood, treatments remain symptomatic. This study analyzed heart samples from five pediatric male (5 months-15 years) compared them tissues 24 non-failing donors (19-71 using an integrated omics method combining metabolomics, lipidomics, proteomics. analysis confirmed changes (CL MLCL), severe mitochondrial alterations, metabolic shifts, elevated heart-failure markers. It also revealed significant interindividual differences among patients. With this describe powerful analytical tool in-depth disorders solid foundation understanding disease phenotypes tissues.

Язык: Английский

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Mini Review: Highlight of Recent Advances and Applications of MALDI Mass Spectrometry Imaging in 2024

Analytical Science Advances, Год журнала: 2025, Номер 6(1)

Опубликована: Май 10, 2025

Abstract Matrix‐assisted laser desorption/ionisation mass spectrometry imaging (MALDI‐MSI) is an emerging tool that allows visualisation of hundreds analytes unbiasedly in a single experiment. This paper highlights the adaptations MALDI‐MSI different context 2024, such as clinical diagnostic, pharmacology, forensics applications, plant metabolism and biology. Challenges advancements were also discussed regarding sample preparation, instrumentations, data analysis, integration machine learning trend cell resolution multi‐omics. There are still rooms for improvements sensitivity, spatial resolution, acquisition algorithm across multi‐omics to enable at subcellular level.

Язык: Английский

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MS based foodomics: An edge tool integrated metabolomics and proteomics for food science

Food Chemistry, Год журнала: 2024, Номер 446, С. 138852 - 138852

Опубликована: Фев. 28, 2024

Язык: Английский

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Cross-platform Clinical Proteomics using the Charité Open Standard for Plasma Proteomics (OSPP)

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 10, 2024

Abstract The role of plasma and serum proteomics in characterizing human disease, identifying biomarkers, advancing diagnostic technologies is rapidly increasing. However, there an ongoing need to improve proteomic workflows terms accuracy, reproducibility, platform transferability, cost-effectiveness. Here, we present the Charité O pen Peptide S tandard for P lasma roteomics (OSPP), a panel 211 extensively pre-selected, stable-isotope-labeled peptides combined open, versatile, cost-effective internal standard targeted untargeted studies. selected are well suited chemical synthesis, distribute over captured analytical dynamic range chromatographic gradients, show consistent quantification properties across platforms, serum, as EDTA-, citrate, heparin plasma. Quantifying proteins that function wide biological processes, including several routinely used clinical tests or targets FDA-approved drugs, OSPP quantifies important disease. On acute COVID-19 in-patient cohort, demonstrate application i) achieve patient classification biomarker identification ii) generate comparable quantitative data with both approaches, iii) estimate peptide quantities successful cross-platform alignment data. adds low costs per proteome sample, thus making use accessible. In addition standards, corresponding spectral libraries optimized acquisition methods platforms made openly available.

Язык: Английский

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The Role of Metabolism in Shaping Enzyme Structures Over 400 Million Years of Evolution

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 27, 2024

Abstract The functions of cells and proteins depend on their biochemical microenvironment. To understand how constraints shaped protein structural evolution, we coupled the extensive genetic metabolic data from Saccharomycotina subphylum with capability AlphaFold2 to systematically predict structures sequence. Determining 11,269 enzyme catalysing 361 different reactions evolved over 400 million years alongside molecular functions, report that metabolism has evolution enzymes at levels: organism’s overall metabolism; topological organisation network; each enzyme’s properties. For example, depends reaction mechanism, variability rather than amount flux, biosynthetic cost. Evolutionary cost-optimization is stronger highly abundant acts differently domains, exception small-molecule binding sites, which are prioritised other domains lack cost-optimisation. Finally, while surfaces less constrained, surface residues can also be exposed positive selection for co-evolution protein-protein interaction sites. Accessing AlphaFold’s power across species barriers, facilitating integration functional genomics, were thus able map biological shape scale long timelines.

Язык: Английский

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Menopause Hormone Replacement Therapy and Lifestyle Factors affect Metabolism and Immune System in the Serum Proteome of Aging Individuals

medRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 23, 2024

Abstract Aging is a fundamental risk factor for wide array of diseases. The Berlin Study II (BASE-II) cohort study designed to investigate the physical, mental, and social determinants successful aging. We utilized high-throughput mass spectrometry measure proteomes 1890 BASE-II participants, divided into two age groups: 27-37 years 60-85 years. employed multiple linear regression analyses explore effects demographic factors such as age, sex, BMI, along with hormonal treatments lifestyle factors, on serum proteome. identify new associations confirm previously described proteins linked BMI contraceptive use (HCU). Notably, we observed that abundance nutrient transport proteins, particularly apolipoproteins, metabolic diseases in aged individuals, including syndrome type 2 diabetes. Additionally, identified specific alterations explained by smoking alcohol consumption. further report significant proteome signature female participants corresponding menopause hormone replacement therapy (MHT). successfully classified these based MHT status an AUROC 0.82 using Complement Component 9 Plasminogen, slightly outperforming estradiol (AUROC: 0.80), active ingredient most preparations. Overall, our underscores impact therapies during aging, primarily affecting components immune system metabolism.

Язык: Английский

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Quality Control in the Mass Spectrometry Proteomics Core: a Practical Primer

Опубликована: Апрель 25, 2024

The past decade has seen widespread advances in quality control (QC) materials and software tools focused specifically on mass spectrometry-based proteomics, yet the rate of adoption is inconsistent. Despite fundamental importance QC, it typically falls behind learning new techniques, instruments, or software. Considering how important QC a core setting where data generated for non-mass spectrometry experts confidence delivered results paramount, we have created this quick-start guide focusing off-the-shelf relatively easy to use We hope that by providing background different levels their uses, describing design options, highlighting some current software, implementing will be easier than ever. There continues development each these areas (such as software), generation proteomics more capable conveying well minimizing laboratory downtime guiding experimental, technical, analytical troubleshooting from sample results.

Язык: Английский

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Mitigating In-Column Artificial Modifications in High-Temperature LC–MS for Bottom–Up Proteomics and Quality Control of Protein Biopharmaceuticals

Analytical Chemistry, Год журнала: 2024, Номер 96(36), С. 14531 - 14540

Опубликована: Авг. 28, 2024

Elevating the column temperature is an effective strategy for improving chromatographic separation of peptides. However, high temperatures induce artificial modifications that compromise quality peptide analysis. Here, we present a novel high-temperature LC–MS method retains benefits while significantly reducing modification and degradation during reversed-phase liquid chromatography. Our approach leverages short inline trap maintained at near-ambient installed upstream column. The retentivity dimensions were optimized to shorten residence time peptides in heated without compromising performance. This easy-to-implement increased peak capacity by 1.4-fold within 110 min mapping trastuzumab provided 10% more identifications exploratory proteomic analyses compared with conducted 30 °C maintaining extent close background level. In biopharmaceuticals, where in-column can falsely elevate levels some critical attributes, reduced temperature-related artifacts 66% N-terminal pyroGlu 63% oxidized Met direct injection 60 °C, thus reliability control protein drugs. findings represent promising advancement methodology, providing researchers industry professionals valuable tool unwanted modifications.

Язык: Английский

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