Your end-to-end proteomics partner,
from samples to insights
Trusted proteomics services, handling everything around your study. We source samples for you and we handle the lab processes and generate high-resolution MS data. We also perform the data analysis and deliver interpretations that turn into decisions. The whole journey, end to end, with one trusted partner.
Step-by-Step
At ions.bio, we provide tailored proteomics services to fit your needs. Whether you require end-to-end support, from clinical samples to data analysis, or tailored assays, we deliver high-quality results you can trust. Beyond data, we offer access to our interactive analysis software VeriDyne Navigator to explore results, generate new hypotheses, and seamlessly obtain publication-ready figures or complete project brochures.
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Not sure which approach fits? Not sure about the required samples? Unsure about your study design? We'll scope your project with you, free of charge.
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Reproducible SOPs for high peptide recovery and deep coverage, optimized for each individual workflow, e.g. global proteomics or PTM analysis.
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Discovery or validation: precise and consistent protein and peptide data using the Orbitrap Astral.
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Dedicated quality-marker panels flag pre-analytical variation and sample-related biases, identified, quantified, and where possible corrected before they reach your results.
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Advanced processing and statistics, tailored to your project’s goals.
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Publication/brochure-ready report plus access to our interactive results platform, VeriDyne Navigator.
We don't only ship a spreadsheet of numbers.
We bring in all our proteomics domain expertise and take care of the technical details to deliver the highest quality data. Our scientists work through the results with you to find the insights that matter most and prioritize them so you can make clear decisions.
You also get direct access to your data through VeriDyne Navigator, our interactive results platform: explore results, test new hypotheses, and pull publication-ready figures or complete project brochures whenever you need them. And we don't stop at the first analysis. We take your feedback and run the additional analyses you need, so you always get the answers your project calls for.
Sample types
From biofluids to fixed tissue, we can work with almost any sample type from any organism. We have extensive experience with human samples, preclinical models and various cell lines. Our sample-specific SOPs ensure a highly sensitive and robust sample preparation and data analysis. And our quality-marker panels flag pre-analytical variation — the handling and processing artifacts that can masquerade as biology — building on our published work on sample-related bias in plasma proteomics.
- Blood, plasma & serum 1 µL
- Blood cards whole card
- Cerebrospinal fluid 10 µL
- Urine 150 µL
- Saliva 10 µL
- Aqueous/Vitreous humor 5 µL
- Cell culture cells/supernatants 1,000–10,000 / 100 µL
- HLA peptides on request
- Fresh-frozen tissue 1 mg
- FFPE tissue (block) 5 µm section
- FFPE tissue (slide) 5 µm section
Your sample type isn't depicted here? Don't worry, our experts can advise you on almost all commonly used sample types, as we've worked with many of them before.
Additional Services
- Only FFPE blocks available? We can support FFPE sectioning and staining, with experienced pathology expertise available to distinguish tumor from normal tissue areas.
- In addition, we can prepare an H&E section and directly annotate the tumor region for easier review and downstream analysis.
Services across the proteomics workflow
Discovery proteomics
Unbiased, deep profiling across thousands of proteins in a single run, so you see what is changing without deciding in advance where to look. We run data-independent acquisition on state-of-the-art instrumentation like the Orbitrap Astral and Orbitrap Astral Zoom for reproducible quantification and deep proteome coverage, reaching well into low-abundance proteins. It is the natural starting point for exploratory studies and biomarker discovery, surfacing the candidates worth pursuing before you commit to a targeted follow-up.
Targeted assays
Precise, absolutely quantified readouts of the specific proteins you care about. We develop and validate targeted mass spectrometry assays that stay consistent from sample to sample and reach low-abundance proteins, ready for high-throughput monitoring across large cohorts. The right fit for translational research and validation, when you already know your markers and need robust numbers you can compare with confidence.
We partner with the Stockholm-based company ProteomEdge, who offer multiple panels of heavy-labelled protein standards, targeting a large set of clinically relevant plasma biomarkers such as apolipoproteins, complement factors, and liver biomarkers. If you are interested in a targeted panel, reach out to our team.
Book a consultation
PTM analysis
Post-translational modifications drive much of protein function, and we map them at depth and scale. Combining dedicated enrichment with high-resolution mass spectrometry, we identify, quantify, and localize modification sites, from phosphorylation and acetylation or methylation to other key modifications. The result is a functional view of signaling and regulation, not just protein abundance.
Immunopeptidomics
Identify the peptides naturally presented on MHC and HLA molecules, the actual signals the immune system reads. With sensitive enrichment and high-resolution mass spectrometry, we characterize the immunopeptidome directly instead of inferring it. Applications span neoantigen discovery, vaccine design, and the immunogenicity assessment of therapeutics.
Surface proteomics
The cell surface is where most therapeutics act, yet it is easy to miss with standard workflows. We profile the cell-surface proteome to reveal accessible, druggable targets and to track how they shift with disease or treatment. A focused view for target discovery, antibody development, and mechanism-of-action studies.
Interactomics
Proteins rarely act alone. We map protein-protein interactions and complexes, who binds whom and under which conditions, using affinity purification and proximity-labeling approaches coupled to high-resolution mass spectrometry. The result is a network view of function: interaction partners, complex composition, and how this wiring shifts with disease, treatment, or perturbation. A strong fit for mechanism-of-action studies and target validation.
Secreted protein analysis
Much of how cells communicate happens through the proteins they release. We profile the secretome, the proteins secreted into conditioned media or biofluids, to surface signaling factors, candidate biomarkers, and therapeutic targets that intracellular profiling would miss. Sensitive, low-input workflows capture secreted proteins even when they are scarce, giving you a direct window into cell-to-cell signaling and disease processes.
Data analysis
Raw spectra are only valuable once they become clear answers. Our bioinformaticians run the full pipeline, from processing and quality control through statistics tailored to your study design, and deliver decision-ready results. You also get access to VeriDyne Navigator, our interactive results platform, to explore the data yourself, test new hypotheses, and pull publication-ready figures.
ML/AI model training
Your data becomes far more powerful when a model learns from it. We develop and train custom machine-learning and AI models on your proteomics data, from predictive signatures and classifiers to more advanced architectures, tailored to your biological question and validated on held-out data, so the results are ones you can trust and act on. A bespoke, client-commissioned service, distinct from the foundation models in the VeriDyne data layer.
Sample sourcing
Not every study starts with samples in hand. We help you source high-quality biosamples from our in-house collection or our trusted partner network, matched to your indication, cohort, and study design. Each sample arrives with the documentation and quality you need for defensible results, so you can move straight into measurement.
AI-designed minibinders
We design, screen, express, and optimize an AI-designed minibinder against any target of interest, and can customize it for your preferred application. If desired, we also determine the affinity.
Complementary services through our partner network
- RNA-seq
Transcriptomics to complement the proteome layer.
- Lipidomics
Lipid profiling for a fuller view of the biology.
- Metabolomics
Small-molecule metabolite profiling alongside proteins.
- Olink / NULISA / SomaScan
Affinity-based proteomics panels, run alongside MS for breadth.
Let's plan your study
Every study that is executed incorrectly consumes valuable sample material, and, more importantly, wastes time and manpower. In our fast-paced scientific environment, these resources cannot be recovered.