Why Neuropeptidome Profiling?
Neuropeptides are a unique class of signaling molecules processed from precursor proteins and secreted by neurons to regulate pain, behavior, appetite, circadian rhythms, and stress responses. Unlike classical proteomics, neuropeptidomics specifically targets these short, bioactive peptides that often carry post-translational modifications critical for receptor binding and activity.
By profiling the endogenous neuropeptidome, researchers gain a direct molecular readout of neural communication and peptidergic regulation, especially under neurodegenerative, metabolic, or behavioral perturbations.
What Makes Immunopeptidomics Powerful?
Traditional methods like transcriptomics and conventional proteomics often fall short when it comes to detecting biologically active neuropeptides. That's because they typically measure gene expression or precursor proteins — not the actual, functional molecules at work in the nervous system.
Neuropeptidomics goes further. It directly detects mature peptides that are secreted or stored in neuronal tissues, providing insights into real-time biological activity.
At Creative Proteomics, we've built an advanced neuropeptidomics platform designed to overcome the biggest challenges in peptide detection:
- Short peptide lengths (as small as 5 amino acids)
- Hydrophobic or highly basic sequences
- Complex post-translational modifications (e.g., amidation, pyroglutamylation, acetylation)
- Low abundance in complex biological samples
Our technology captures these elusive molecules with exceptional sensitivity and specificity, delivering actionable, biologically relevant data that other platforms may miss.
Key Application Areas
When paired with transcriptomic, proteomic, or metabolomic studies, neuropeptidomics provides a missing link—how encoded peptides are processed and functionally deployed in vivo.
Neurodegeneration & CNS Diseases
Profile neuropeptides altered in Alzheimer's, Parkinson's, Huntington's, or ALS models.
Pain, Addiction & Behavior Research
Identify peptides involved in nociceptive signaling, dopaminergic reward, or stress response.
Endocrine & Metabolic Regulation
Explore hypothalamic peptides controlling hunger, satiety, and glucose homeostasis.
Psychiatric Disorders & Biomarker Discovery
Quantify peptide differences in depression, anxiety, or schizophrenia models.
What We Offer: Comprehensive Neuropeptidome Profiling and Beyond
Creative Proteomics delivers a turnkey neuropeptidomics solution, combining low-MW peptide enrichment, advanced LC-MS/MS, and deep PTM-aware bioinformatics. Whether from brain regions, CSF, or neuroendocrine tissue, our platform uncovers functional neuropeptides with high precision.
Brain Region–Specific Neuropeptidome Profiling
Reveal region-specific peptide signatures across cortex, hippocampus, hypothalamus, brainstem, and other discrete brain areas. Supports paired-condition or groupwise comparisons for neurological disease models, behavioral studies, or neuroanatomical mapping.
Stress, Drug, or Genetic Perturbation–Induced Peptidome Changes
Characterize how acute stress, chronic exposure, gene knockout/knock-in, or pharmacological interventions reshape the endogenous neuropeptide landscape.Profiling of extracellular, endocytic, and autophagy-derived peptides (13–25mers) relevant to CD4⁺ T cell immunity.
CSF and Biofluid-Based Neuropeptidomics
Non-invasive analysis of cerebrospinal fluid (CSF) or plasma/serum-derived exosomal neuropeptides. Useful for biomarker discovery in neurodegenerative diseases, psychiatric conditions, or CNS injury.
Quantitative Comparison Across Experimental Groups
Label-free or TMT/iTRAQ-based multiplexed quantification of neuropeptides across different conditions, time points, or sample cohorts. Includes statistical analysis and clustering for biological interpretation.
Post-Translational Modification–Focused Peptidomics
Detect and quantify amidated, phosphorylated, pyroglutamylated, acetylated, and sulfated peptides using optimized PTM-sensitive MS workflows and open-modification searches.
Novel and Cryptic Peptide Discovery (De Novo Sequencing)
Identify previously unannotated peptides arising from non-canonical cleavage, alternative splicing, or untranslated regions using de novo sequencing and open database search pipelines.
Neuropeptide Precursor Mapping & Processing Pathway Reconstruction
Link mature peptides back to their precursor proteins (e.g., POMC, NPY, CRH, CART) and visualize cleavage patterns to understand biosynthetic pathways and enzyme activity shifts.
Bioinformatics and Functional Enrichment Analysis
Annotation of peptide source proteins, GO term classification, pathway enrichment (e.g., neuroactive ligand–receptor interaction, synaptic signaling), and peptidergic network mapping.
Detectable Neuropeptide Types
| Neuropeptide Family | Representative Peptides | Functions |
|---|---|---|
| Opioid Peptides | β-Endorphin, Dynorphin A, Enkephalins | Pain modulation, reward, stress |
| Tachykinins | Substance P, Neurokinin A/B | Nociception, inflammation, mood |
| Neuropeptide Y Family | NPY, PYY, PP | Appetite regulation, circadian rhythm |
| Hypothalamic Releasing Hormones | CRH, TRH, GnRH, GHRH | Stress, growth, reproduction control |
| Vasopressin/Oxytocin Family | AVP, Oxytocin | Social behavior, water balance |
| Somatostatin Family | Somatostatin-14, -28 | Hormone secretion inhibition |
| CART Peptides | CART(55–102) | Feeding, drug response, energy homeostasis |
| Melanocortins | α-MSH, ACTH | Pigmentation, adrenal activation |
| RFamide Peptides | NPFF, Kisspeptin, PrRP | Pain, reproductive signaling |
| Orexin/Hypocretin | Orexin A, Orexin B | Wakefulness, energy metabolism |
| Cholecystokinin Family | CCK-8, Gastrin | Digestion, satiety |
| Secretin Family | VIP, PACAP, Secretin | Vasodilation, neuroprotection |
| Novel/Unannotated Peptides | From non-canonical cleavage or UTRs | De novo discovery via open search |
Notes:
- Detection supports modified forms: amidated, pyroglutamylated, phosphorylated, etc.
- Peptides can be mapped to precursor proteins (e.g., POMC, NPY, CRH, CART, SST).
- Coverage includes both canonical neuropeptides and cryptic peptides from alternative splicing or stress-induced processing.
Platform Advantages
Ultra-Sensitive Peptide Detection
Captures low-abundance, short neuropeptides (5–40 aa) with high confidence using Orbitrap Astral™ or timsTOF Pro.
Deep PTM-Resolved Profiling
Identifies multiple post-translational modifications (amidation, pyroglutamylation, phosphorylation, acetylation, etc.) simultaneously—no separate enrichment needed.
Low Input Sample Compatibility
Suitable for limited sample amounts (≥10 mg tissue or 200 µL CSF); ideal for rare brain regions or clinical specimens.
Flexible Acquisition Modes
Supports DDA, DIA, PRM, and PASEF workflows tailored to different experimental goals.
Multiplexed Quantification Ready
Compatible with TMT/iTRAQ labeling for up to 16-condition comparative analysis with statistical outputs.
De Novo + Precursor Mapping
Integrates de novo sequencing with precursor protein mapping (e.g., POMC, CRH, NPY) to uncover peptide biosynthesis pathways.
Step-by-Step Neuropeptidome Profiling Workflow
Sample Recept & QC
Visual inspection, tissue integrity assessment, and peptide/protein content estimation.
Peptide Extraction & Cleanup
Solid-phase extraction and cation exchange chromatography under acidic conditions to enrich endogenous peptides and remove contaminants.
LC-MS/MS Analysis
High-resolution nanoLC-MS/MS using Orbitrap ExplorisTM or timsTOF Pro
Bioinformatics & ldentification
De novo sequencing, database search, PTM annotation, precursor mapping, and peptide quantification
Report Generation
Includes peptide lDs, quant data, PTMs, source proteins, and pathway annotations
1
Sample Receipt & QC
All submitted samples undergo visual inspection, tissue integrity verification, and initial protein/peptide content estimation. This ensures input material is suitable for low-abundance neuropeptide extraction and downstream MS analysis.
2
Peptide Extraction & Cleanup
Neuropeptides are enriched using solid-phase extraction (SPE) and cation exchange chromatography under acidic conditions, optimized to preserve labile PTMs and remove interfering high-MW proteins. This step is critical for maximizing short peptide recovery.
3
LC-MS/MS Analysis
Enriched peptides are separated via NanoLC and analyzed using high-resolution tandem mass spectrometry (Orbitrap Exploris™ or timsTOF Pro). Acquisition modes include DDA, DIA, or PRM depending on project design. Short and modified peptides are prioritized in the scan strategy.
4
Bioinformatics & Identification
We apply de novo sequencing, database search, and open modification analysis to identify known and novel neuropeptides. PTMs such as amidation and pyroglutamylation are specifically annotated, and precursor mapping links each peptide to its prohormone origin.
5
Report Generation
Final deliverables include peptide identification tables, quantitative profiles, PTM annotations, and precursor mapping. Functional enrichment and pathway annotation can be added to highlight biological relevance. Data files are formatted for publication or reanalysis.
Deep and Accurate Peptidome Discovery
At Creative Proteomics, our neuropeptidomics platform is optimized for the sensitive detection of short, modified, and low-abundance neuropeptides using high-resolution mass spectrometry and customized enrichment workflows. From complex brain tissue to cerebrospinal fluid, we enable deep neuropeptidome coverage with reproducibility and confidence.
Our technology stack combines the speed of next-generation Orbitraps, the precision of ion mobility-enhanced PASEF acquisition, and the flexibility of triple TOF systems, giving researchers the power to resolve complex peptidomic dynamics in a wide range of neurological models.
Technical Highlights
- >90% MS/MS Peptide Coverage
Advanced tandem MS with HCD, CID, and ETD fragmentation enables high-confidence identification of endogenous neuropeptides ranging from 5 to 40 amino acids. - 1% FDR Stringent Filtering
Peptide and protein-level false discovery rate is controlled below 1%, ensuring data reliability and reproducibility across biological replicates. - PRM & SureQuant™ Quantification
Enables absolute quantification of low-abundance neuropeptides using high-sensitivity targeted acquisition strategies. - Comprehensive PTM Detection
Supports detection of key neuropeptide post-translational modifications, including amidation, pyroglutamylation, phosphorylation, acetylation, and sulfation. - Low Input Compatibility
Delivers deep neuropeptidome coverage from as little as 10 mg tissue or 200 µL cerebrospinal fluid, making it ideal for small, precious samples. - Flexible Acquisition Modes
Supports multiple acquisition strategies—DDA, DIA, PRM, and PASEF—tailored to project-specific depth and quantification needs. - Curated Neuropeptide Databases
Spectral search and annotation are powered by integrated neuropeptide-specific resources such as NeuroPedia, PeptideAtlas, UniProt neuropeptide entries, and proprietary in-house libraries.
Orbitrap Astral™
(Fig from Thermo Scientific)
Orbitrap Exploris™ 480
(Fig from Thermo Scientific)
Q Exactive HF-X
(Fig from Thermo Fisher)
timsTOF Pro
(Fig from Bruker)
Instrument Capability Overview
| Feature | Orbitrap Astral™ | Exploris™ 480 | timsTOF Pro | TripleTOF 6600 | Q Exactive HF-X |
|---|---|---|---|---|---|
| Scan Speed | Up to 200 Hz | ~40 Hz | ~100 Hz (PASEF) | ~30–40 Hz | ~20–25 Hz |
| MS/MS Coverage | >90% | >90% | >90% | ~85–90% | ~85% |
| PTM Sensitivity | Ultra-sensitive (amidation, pyro-Glu, phosphorylation) | High | High | Moderate | Moderate |
| Quantification Modes | Label-free, PRM, SureQuant™ | Label-free, TMT, PRM | Label-free, DIA, PRM | Label-free, iTRAQ | Label-free, TMT |
| Sample Input | 100K–100M cells / 10–200 mg tissue | 1M–100M cells / 20–200 mg tissue | 100K–50M cells / low-volume CSF | 1M+ cells / >50 µg peptide | 2M+ cells / >100 µg peptide |
| Applications | Single-peptide resolution, PTM mapping | Multiplexed neuropeptide profiling | Low-abundance peptide capture | High-throughput screens | Discovery-based workflows |
Sample Requirements for Neuropeptidomes
| Sample Type | Minimum Amount | Preservation Method | Shipping Condition | Notes |
|---|---|---|---|---|
| Brain Tissue (Fresh/Frozen) | ≥10 mg | Snap-frozen preferred | Dry ice | Avoid fixatives or embedding; store at –80°C immediately after dissection |
| Cerebrospinal Fluid (CSF) | ≥200 µL | Aliquoted, low-protein bind tubes | Dry ice | Use protease inhibitors; avoid multiple freeze-thaw cycles |
| Cultured Neurons or Glia | ≥1×10⁶ cells or equivalent | Pellet snap-frozen | Dry ice | Wash with PBS before freezing; record confluence and cell count |
| Plasma or Serum | ≥100 µL | Frozen in aliquots | Dry ice | Not ideal for neuropeptides; consult before submission |
| FFPE Tissue Sections (optional) | ≥2 unstained 10 µm slides | FFPE blocks or sections | Ambient (slides) / Dry ice (blocks) | Yield and coverage may vary; prior consultation required |
Demo Results
Deliverables | What You Will Receive
- Identified Peptides (CSV)
Sequences, charge states, retention times, PTMs, and confidence scores. - Quantitative Profiles
Relative abundance per sample or condition, ready for statistical analysis. - PTM Annotation Table
Amidation, pyroGlu, phosphorylation, and other relevant modifications. - Precursor Protein Mapping
Links mature peptides back to their prohormone or precursor protein. - Functional Enrichment (Optional)
GO terms, KEGG pathways, and neuropeptide-related signaling processes. - Executive Summary (PDF)
Visual highlights including length distribution, PTM prevalence, and condition-specific differences.
Can I identify novel neuropeptides or PTM variants? +
Yes, we support de novo sequencing and open-modification search modes for unknown or modified peptides.
How many peptides can I expect to detect? +
Depending on the sample type and input amount, 500–2000 neuropeptides are commonly detected per run.
Is quantification supported? +
Both label-free and TMT/iTRAQ multiplexed quantification are supported for comparative studies.
How does neuropeptidomics differ from general proteomics in terms of analyte complexity and identification strategy? +
Unlike conventional proteomics that focuses on tryptic peptides from large proteins, neuropeptidomics targets naturally occurring, mature peptides, often non-tryptic, with extensive PTMs. Identification requires open search, unspecific enzyme settings, and PTM-aware algorithms to accommodate the biological diversity of neuropeptides.
Are your workflows optimized for capturing labile or low-stoichiometry modifications such as amidation or pyroglutamylation? +
Yes. Our extraction and LC-MS/MS workflows are designed under acidic, protease-inhibiting conditions that preserve sensitive PTMs. We employ fragmentation strategies (e.g., HCD, ETD) and tailored search parameters to improve detection confidence of low-abundance modified species.
What database or spectral library resources do you use for neuropeptide identification? +
We use a combination of curated neuropeptide databases (e.g., UniProt neuropeptide entries, NeuroPedia, PeptideAtlas) and custom user-provided FASTA files when needed. We also apply de novo sequencing and open modification search to detect unannotated or novel peptides.
How is false discovery rate (FDR) controlled in neuropeptidomic datasets? +
Due to the short length and PTM variability of neuropeptides, we implement stringent FDR control (<1%) at both peptide-spectrum match (PSM) and protein/precursor levels. Decoy-based validation is adapted for unspecific cleavage and open modification contexts.
Can your platform distinguish between peptide isoforms or proteoforms derived from the same precursor? +
Yes. High-resolution MS/MS combined with PTM annotation allows us to resolve isoforms differing by cleavage site, modification, or alternative processing events. Precursor mapping enables reconstruction of processing pathways for precursors like POMC or NPY.
How do you address peptide redundancy or ambiguous precursor assignment? +
We use sequence-context matching and precursor annotation tools to minimize ambiguity. Redundant sequences are consolidated with confidence scoring, and ambiguous assignments are flagged for manual review when needed.
What is the minimum peptide length or mass range reliably detected in your workflow? +
Our platform routinely detects peptides as short as 5 amino acids and up to ~50 residues, with an optimal range between 8–30 aa. MS1 scan settings and ion trap dwell times are tuned to enhance detection of low-mass, high-charge state peptides typical of neuropeptidomes.
Can post-translationally modified peptides be quantified with the same accuracy as unmodified ones? +
Generally yes, although modified peptides often ionize differently and may exhibit varied fragmentation efficiency. Our quantification workflows account for PTM-specific behavior, and targeted methods (e.g., PRM) further enhance quantitative reliability for modified species.
What strategies are available for distinguishing closely related peptides across sample groups? +
We apply label-free or multiplexed quantification (TMT/iTRAQ) coupled with retention time alignment, MS/MS spectral clustering, and normalization to resolve subtle differences. Statistical modules detect condition-specific peptide enrichment or suppression.
Do you support multi-region brain comparisons or tissue-compartment-specific profiling? +
Yes. Our workflows are compatible with dissected brain regions, CSF, exosomes, or microdissected compartments. We support differential peptidome analysis across spatial locations or sample subtypes with proper statistical and bioinformatics support.
Combined Omics Approaches Reveal Resistance Mechanisms to Beet Curly Top Virus in Sugar Beet Genotypes
Journal: International Journal of Molecular Sciences
Published: 2023
https://doi.org/10.3390/ijms241915013BRCA1 Antibodies Matter: Benchmarking Reagent Specificity in Cancer Research
Journal: International Journal of Biological Sciences
Published: 2021
https://doi.org/10.7150/ijbs.63115In Vitro Identification of Phosphorylation Sites on TcPolβ by Protein Kinases TcCK1, TcCK2, TcAUK1, and TcPKC1 and Effect of Phorbol Ester on Activation by TcPKC of TcPolβ in Trypanosoma cruzi Epimastigotes
Trypanosoma cruzi DNA Polymerase β Is Phosphorylated In Vivo and In Vitro by Protein Kinase C (PKC) and Casein Kinase 2 (CK2)
The Interplay Between GSK3β and Tau Ser262 Phosphorylation During the Progression of Tau Pathology
Journal: International Journal of Molecular Sciences
Published: 2022
https://doi.org/10.3390/ijms231911610Inactivation of Myeloperoxidase by Benzoic Acid Hydrazide
Journal: Archives of Biochemistry and Biophysics
Published: 2015
https://doi.org/10.1016/j.abb.2015.01.028