Protein Identification Services
Creative Proteomics provides comprehensive protein identification services powered by high-resolution LC-MS/MS and MALDI-TOF technologies. Our end-to-end solutions identify, characterise, and annotate proteins across complex biological samples—helping researchers, CROs, and biotech teams reveal unknown proteins and validate key targets with accuracy and reproducibility.
What We Solve
- Identify unknown or low-abundance proteins that hinder pathway or biomarker studies.
- Confirm protein sequence, structure, and post-translational modifications for R&D reliability.
- Eliminate uncertainty in mass-spectrometry-based protein identification through validated workflows and expert analysis.
Our Advantages
- State-of-the-art mass spectrometry for protein identification with ultra-high sensitivity.
- Flexible LC MS MS protein identification workflows for diverse sample types.
- Publication-ready data interpretation and technical support tailored to CRO and academic needs.
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- Introduction
- Service Packages
- Tech
- Workflow
- Applications
- Why Choose Us
- Qualitative/Quantitative
- FAQ
- Client Case
Introduction: Unlocking the Power of Protein Identification
Understanding which proteins exist in a system—and how their levels change—is essential for translating molecular data into functional insight. Creative Proteomics' protein identification services integrate advanced LC-MS/MS, MALDI-TOF, and quantitative proteomics workflows to precisely identify, characterise, and compare proteins across complex biological systems.
Our end-to-end process converts raw mass-spectrometry signals into reliable biological meaning. By coupling qualitative identification with quantitative proteomic analysis, we reveal low-abundance proteins, structural variants, and differential expression patterns that drive disease, metabolism, and therapeutic response. Whether for biomarker discovery, target validation, or functional proteome profiling, we provide data you can act on with confidence.
Why Protein Identification Matters in Modern Research
In today's life-science landscape, protein identification services form the foundation for meaningful discovery and reliable translational research. Whether for quantitative proteomics, drug-target validation or disease biomarker discovery, knowing which proteins are present is indispensable.
Unlocking Biological Mechanisms
Precise identification of proteins enables researchers to map expression patterns, interactions and structural features across complex systems. According to a key review: "Protein identification is a fundamental aspect of proteomics research … essential for understanding the composition, structure, function and interactions of proteins in biological systems."
For example, knowing that a low-abundance signalling protein is present and active can pivot a study from hypothesis to actionable insight.
Addressing Complex Sample Challenges
Many modern research problems involve highly complex samples—such as tissue biopsies, post-translationally modified proteins or membrane-associated proteomes. One authoritative source states that identifying all proteins in a biological sample "represents a central task in a majority of proteomics projects."
Our advanced platforms help differentiate isoforms, resolve unknown proteins and support downstream quantitative workflows.
Supporting Drug Development and Biomarker Discovery
In drug development, accurate protein identification informs target selection, mechanism-of-action studies and therapeutic monitoring. Recent articles highlight proteomics as a key tool for early diagnosis and personalised medicine.
By combining identification with quantitative proteomics, we empower clients to measure changes in protein levels under treatment or disease conditions—bridging discovery and translation.
Beyond Identification: Enabling Insights
While many services stop at which proteins exist, we extend into how they behave. Our workflows integrate domain-mapping, motif recognition and structure annotations so you can interpret function, not just identity. According to a review, advanced proteomics "offers new opportunities for biomedical applications and therapeutic interventions."
That means our clients move from data to decision: identifying novel biomarkers, opening new drug-target niches, or validating high-confidence CRO study endpoints.
Service Packages: Choosing the Right Pathway
At Creative Proteomics, our protein identification services support a wide variety of sample types—including gel spots, gel bands, solution samples, cells, tissues and body fluids—using the latest LC–MS and MALDI–TOF technologies.
✅ Our Approach
We tailor service packages to meet both qualitative and quantitative proteomics needs:
- Determine protein purity, quantity and identity
- Analyse protein expression and sub-cellular localisation
- Investigate post-translational modifications (PTMs)
- Study protein induction, turnover and dynamic behaviour
- Map protein-protein interactions via IP/pull-down workflows
Sample-to-Insight Package Breakdown
Essential Protein Identification Package
- Ideal for simple samples such as a single gel band or purified protein
- Utilises MALDI-TOF or basic LC–MS/MS workflows to identify major proteins or confirm identity quickly
- Perfect for labs needing a turnaround for target validation
Advanced Discovery Package
- Suitable for complex mixtures (cell lysates, tissues, exosomes)
- Employs high-resolution LC–MS/MS plus data-independent acquisition (DIA) for deeper coverage and low-abundance detection.
- Provides qualitative and quantitative proteomics output—ideal for biomarker discovery or large-scale profiling
CRO/High-Throughput Package
- Designed for large projects in contract research organisations, pharma R&D or academic core facilities
- Offers multi-sample formats, automated sample prep, multidimensional separations and extensive data analysis
- Integrates add-on services like sample preparation, molecular-weight determination and full sequence/structure annotation
Related Protein Analysis & Identification Services
To support each package, we offer complementary services:
Why This Matters for You
Whether your focus is identifying unknown proteins, mapping protein domains or motifs, or measuring changes in protein expression, our tiered packages let you select the right depth and budget. By aligning the service to your sample complexity and research question, you accelerate the path from sample to meaningful data.
Technical Platforms: High-Resolution Tools for Accurate Identification
Our protein identification services employ state-of-the-art instrumentation and workflows to deliver high confidence results across qualitative and quantitative proteomics. Below is a comparative table summarising the key platforms, their strengths, sample suitability and best-use cases.
| Platform | Technology & Description | Strengths for Protein Identification | Best-Use Scenarios | Keywords Emphasised |
|---|---|---|---|---|
| MALDI-TOF / TOF | Matrix-Assisted Laser Desorption/Ionisation-Time of Flight; rapid peptide mass fingerprinting | High throughput, simple sample prep, fast turnaround | Gel spots, purified proteins, screening unknown proteins | maldi tof protein identification, protein identification by peptide mass fingerprinting |
| LC–MS/MS (High-Resolution) (see Protein Identification by Tandem Mass Spectrometry) provide deep proteome coverage and confident peptide sequencing. | Nano-LC separation + tandem mass spectrometry (e.g., Orbitrap, Q-Exactive) | Deep proteome coverage, high sensitivity & resolution, supports PTM mapping | Complex mixtures (cell lysate, tissues, sub-cellular fractions) | lc ms ms protein identification, mass spectrometry for protein identification, protein identification services |
| Multidimensional/ MudPIT | Multidimensional LC fractionation + MS/MS for ultra-deep proteome profiling | Handles very complex samples, resolves low-abundance proteins & unknowns | Whole-cell proteomics, discovery-scale CRO projects | multidimensional protein identification technology, unknown protein identification |
| Targeted/Quantitative MS | High-resolution MS with label-free, SILAC, TMT or MRM workflows | Quantifies changes in protein expression, supports biomarker/target studies | Follow-up quantification after identification; comparative studies | quantitative proteomics, quantitative proteomics mass spectrometry, protein quantitative analysis |
Why These Platforms Matter
- Choosing the right platform ensures accurate protein identification and supports downstream quantitative proteomic analysis of your samples.
- Our lab infrastructure is optimised for both high-throughput screening (MALDI-TOF) and high-depth discovery (LC–MS/MS, MudPIT).
- Robust instrumentation combined with rigorous workflows enables reliable detection of low-abundance proteins, isoforms and post-translational modifications — delivering data you can trust for CRO, academic or biotech applications.
- Integrating both identification and quantification platforms strengthens translational value: once a protein is identified, you can monitor its expression dynamics or response to treatment.
Trusted Workflow
Instrument choice is guided by the sample type, complexity and research goal. For example:
- Simple gel band → MALDI-TOF for rapid screening.
- Tissue lysate requiring deep coverage → High-resolution LC–MS/MS.
- Comparative expression study → Quantitative MS workflow with TMT or label-free.
- Whole‐cell proteome profiling in a CRO context → Multidimensional LC + MS/MS (MudPIT).
These platform options mean your project receives a tailored technical approach rather than a one-size-fits-all service.
Workflow: From Protein Extraction to Bioinformatics
Our streamlined workflow for protein identification services combines best-in-class instrumentation with validated procedures and expert data analysis. Each step is designed to support both qualitative and quantitative proteomics and deliver actionable results for research, CRO and academic clients.
1. Sample Preparation
- Begin with your sample type: gel spots, gel bands, solution samples, cells, tissues or body fluids.
- Execute lysis, purification and concentration to optimise signal. ([Mol Omics 2022] found that optimised lysis and high-pH fractionation improved protein identifications by +15% and matched peptides by +42.4 %.)
- Clean up the sample (desalting, detergent removal) to preserve instrument performance and maximise identification rates.
2. Protein Digestion (for bottom-up workflows)
- Perform in-gel or in-solution digestion using trypsin or appropriate protease.
- Use reduction/alkylation to open disulfide bonds and enhance peptide recovery.
- Resulting peptides are ready for separation and MS analysis.
3. Mass Spectrometric Analysis
- Separate peptides via nano-LC or high-flow UPLC; then ionise and fragment in MS/MS.
- Acquire data using DDA (data-dependent acquisition) or DIA (data-independent acquisition) depending on sample complexity and project goals.
- Aim for high mass-accuracy and deep sequence coverage for confident protein identification by mass spectrometry.
4. Database Search & Bioinformatics
- Match MS/MS spectra to peptide sequences via established software (e.g., SEQUESTTM, MascotTM, Proteome DiscovererTM) controlling false discovery rates.
- Infer protein identities from peptide lists, annotate domains/motifs, identify PTMs, and prepare quantitation metrics for quantitative proteomic analysis.
- Link results to biological context: expression, localisation, interaction networks.
5. Report Generation & Decision-Ready Deliverables
- Provide detailed deliverables: list of identified proteins with accession numbers and confidence scores, peptide coverage maps, domain or motif annotations, and quantitation results if relevant.
- Offer interpretation notes: how the data speak to your research question (e.g., biomarker discovery, target validation).
- Support CRO/academic workflows with publication-ready figures, supplementary tables, and structured data outputs.
Instrument Platforms
Creative Proteomics provides mass spectrometry-based protein sequence analysis using the high-resolution Obitrap Fusion Lumos mass spectrometer,Thermo Q Exactive series, Thermo Exploris 480, and timsTOF Pro for proteomics analysis. Our platform ensures 100% sequence coverage, high sensitivity for low-abundance peptides, and combines HCD and ETD fragmentation for accurate N-terminal, C-terminal, and full-length protein sequencing, including de novo sequencing for unknown samples.
Advanced Applications and Specialized Protein Identification
Our advanced protein identification services extend beyond standard workflows to support complex research use-cases—such as membrane proteomics, sub-cellular proteomics, exosome proteomics, cell-surface exploration and protein-protein interaction identification. These niche applications empower researchers to identify proteins in context and uncover functional insights.
Membrane & Sub-cellular Proteomics
Investigating proteins embedded in membranes or localized to organelles poses unique challenges: hydrophobicity, low abundance and compartment-specific localisation. Global sub-cellular proteome profiling now reveals dynamic protein relocalisation and complex architecture in disease states.
Our service employs targeted workflows to extract and enrich membrane or organelle fractions, followed by high-resolution LC–MS/MS and quantitative analytics. We enable accurate protein identification services for components that standard workflows miss.
Exosome & Cell-Surface Proteomics
Extracellular vesicles (exosomes) and cell-surface proteomes carry vital biomarker information and therapeutic targets. Recent reviews highlight exosomal membrane-protein composition as a foundation for diagnostics and therapeutic strategies.
Our pipeline applies ultra-sensitive MS workflows to small‐volume vesicle samples, delivering confident identifications of surface markers, internal loading proteins, motifs and domains.
Protein–Protein Interaction (PPI) Identification
Understanding protein networks is critical for drug discovery, signalling pathway mapping and target validation. Our PPI identification service combines Co-immunoprecipitation (Co-IP) or pull-down methods with downstream LC–MS/MS to map interacting partners and annotate identified motifs or functional domains.
By integrating PPI workflows with our core quantitative proteomics pipeline, you can move from individual protein identification to network-level insights.
Learn more about our detailed workflows in [Protein–Protein Interaction Identification Method — Co-immunoprecipitation (Co-IP) and Pull-Down], which outlines enrichment strategies and LC–MS/MS analysis of protein complexes.
Why Choose These Specialized Applications?
- Illuminate masked proteomes: Membrane, exosome and surface sub-proteomes often hide low-abundance or novel proteins crucial for biomarker discovery.
- Functional context matters: Knowing a protein's identity is just the first step; knowing its location, interaction partners or domain structure adds actionable value.
- Support translational research: These advanced workflows feed directly into biomarker development, therapeutic-target validation and CRO deliverables.
Why Choose Us
Selecting a provider for protein identification services means investing in precision, reliability and actionable data. At Creative Proteomics, we embed these principles in every project—ensuring you receive results that drive real outcomes.
Proven Expertise & Global Reach
With over a decade of proteomics-service experience, we serve clients across more than 50 countries and territories. Our team combines PhD-level scientists, expert bioinformaticians and technical staff committed to one goal: turning your sample into confidence.
We are proficient in projects from academia, pharma R&D and CRO environments—covering everything from discovery proteomics to biomarker validation.
Advanced Platforms & Technological Excellence
Our service platform features industry-leading instrumentation such as high-resolution LC–MS/MS, MALDI–TOF/TOF, multidimensional separation systems and integrated bioinformatics workflows.
The result: high sensitivity detection, accurate protein identification by mass spectrometry, and seamless transition to qualitative and quantitative proteomics for dynamic studies.
Seamless End-to-End Support
We don't simply identify proteins; we support you from sample submission through to final reporting. Our services include sample preparation, digestion, molecular-weight determination, sequence analysis, unknown protein workflows and integrative data results.
With transparent communication, flexible add-on services and CRO-friendly deliverables, you'll experience a streamlined workflow that respects timelines and budgets.
Quality You Can Trust
Quality is our number-one focus. From validated workflows and instrument QC to rigorous data-review procedures, we ensure high confidence in each identified protein and quantified result.
Whether identifying a novel protein target, mapping domain structure or assessing induced expression changes, we deliver data you can act on with confidence.
Global Research Partnerships
Creativity in proteomic science is central to our value. We partner with biotechnology firms, pharmaceutical companies and academic labs to enable biomarker research, target discovery and proteome-wide profiling. Our cross-domain experience means your project benefits from broad technical insight and proven service delivery.
Deliverables: Turning Spectra into Actionable Results
When you select our protein identification services, you receive more than just raw spectra—you receive insights ready to move your research or project forward.
What You Will Receive
- A comprehensive report detailing each identified protein with name, accession number, sequence coverage, number of unique peptides and functional annotation.
- Annotated MS/MS spectra, peptide-coverage maps and domain/motif annotations.
- Optionally, raw data files and search engine files can be provided on request.
- For projects that include a quantitative component: protein lists with relative abundances, fold-changes, volcano plots, and heat maps.
- A glossary of methods, key instrument parameters and interpretation notes to support publication or internal decision-making.
Qualitative vs. Quantitative Proteomics: Understanding the Difference
When choosing a service for protein identification services, it's essential to distinguish between qualitative and quantitative proteomics—both offer value, but address different research questions.
Qualitative Proteomics (What proteins are present?)
Qualitative workflows focus on determining which proteins exist in a given sample. They are ideal for:
- Identifying unknown or novel proteins, isoforms and motifs
- Characterising protein composition in gel bands, purified samples or crude lysates
- Generating a comprehensive protein list as a prerequisite for downstream studies
Platforms such as MALDI-TOF or standard LC–MS/MS support qualitative analysis by delivering high confidence in protein identity. For researchers working in discovery, this approach lays the groundwork for deeper exploration.
Quantitative Proteomics (How much and how does it change?)
Quantitative proteomics goes a step further by measuring how many of each protein are present and how they change under different conditions. According to industry sources, quantitative workflows are pivotal for understanding global proteomic dynamics.
Use-cases include:
- Comparing protein abundance between healthy and diseased states
- Mapping change in response to drug treatment or perturbation
- Monitoring protein turnover or induction kinetics
Quantitative methods often involve isotopic labeling (SILAC, TMT/iTRAQ), label-free strategies or data-independent acquisition (DIA).
Side-by-Side: Qualitative vs Quantitative
| Feature | Qualitative Proteomics | Quantitative Proteomics |
|---|---|---|
| Primary aim | Identify which proteins are present | Measure how protein levels change |
| Common output | Protein list, sequence coverage, motif/domain data | Ratios or concentrations of proteins between conditions |
| Suitable for | Unknown-protein discovery, large sample screening | Comparative analyses, biomarker studies, drug R&D |
| Technical complexity | Moderate | Higher — includes labeling, normalization, calibration |
When to Use Which Approach
- Use qualitative proteomics when you need reliable protein identification first—especially for unknown proteins or to map a proteome.
- Use quantitative proteomics when your goal is dynamic: you're assessing expression changes, responses to treatment, or longitudinal protein behaviour.
At Creative Proteomics, we integrate both approaches
Our service platform allows clients to begin with qualitative identification and then move seamlessly into quantification workflows. The same high-resolution instrumentation and expertise supports both. This means you can first know which proteins are present, then follow how many and how fast they change.
For researchers comparing analytical strategies, our overview Protein Identification: Peptide Mapping vs. Tandem Mass Spectrometry explains how peptide fingerprinting complements high-resolution LC–MS/MS workflows.
Sample Requirements
| Sample type | Recommended sample size | |
|---|---|---|
| Animal tissues | Hard tissues (bones, hair) | 300-500mg |
| Soft tissues (leaves, flowers of woody plants, herbaceous plants, algae, ferns) | 200mg | |
| Plant tissues | Hard tissues (roots, bark, branches, seeds, etc.) | 3-5g |
| Microbes | Common bacteria, fungal cells (cell pellets) | 100μL |
| cells | Suspension/adherent cultured cells (cell count/pellet) | >1*107 |
| Fluids | Plasma/serum/cerebrospinal fluid (without depletion of high abundance proteins) | 20μL |
| Plasma/serum/cerebrospinal fluid (with depletion of high abundance proteins) | 100μL | |
| Follicular fluid | 200μL | |
| Lymph, synovial fluid, puncture fluid, ascites | 5mL | |
| Others | Saliva/tears/milk | 3-5mL |
| Culture supernatant (serum-free medium cannot be used) | 20mL | |
| Pure protein (best buffer is 8MUrea) | 300μg | |
| FFPE | Each slice: 10µm thickness, 1.5×2cm area | 15-20 slices |
FAQ
How should gel band samples be collected and submitted for identification?
Sampling: Submit gel dots or gel bands stained with Coomassie Brilliant Blue or silver staining, ensuring clear and non-degraded bands.
Notes: a) Coomassie Brilliant Blue staining enhances the likelihood of identifying the target protein compared to silver staining. b) For selective identification of bands of interest, cut the specific bands and place them in an Eppendorf tube. c) If using gel strips, cut the entire lane and place it in an Eppendorf tube.
Sample Submission: After cutting the desired bands, add a few drops of double-distilled water to cover the bands, pack with ice packs, and send under chilled conditions (4°C).
What are the precautions in the sampling process? Which components are not compatible with mass spectrometry?
In proteomics, proteasome inhibitors are not recommended during sample collection; also, try to avoid using solvents or extractants containing NP-40, Triton X-100, Tween 20, 80, high concentrations of SDS, etc. when preparing samples; Trypsin digestion is not recommended for adherent cell collection.
What factors may contribute to protein degradation?
a) Inadequate handling during sample collection, such as prolonged collection time, introduction of contaminants (e.g., fermentation broth), failure of plant roots and leaves to absorb excess water after washing, elevated processing temperature, etc.;
b) Extended sample preparation duration leading to degradation;
c) Repetitive freeze-thaw cycles for the samples.
How to remove the interference of high abundance protein?
a) High-abundance proteins are mainly removed using high-abundance protein removal kits, including species-specific human, rat and mouse kits;
b) Use low abundance protein enrichment kits without species bias to enrich low abundance proteins;
c) For cases where there is no suitable product for removing high abundance proteins, SDS-PAGE cleavage and chromatographic separation can be used to achieve the goal of eliminating the interference of high abundance proteins.
In which samples are high-abundance proteins typically present?
a) Generally, bodily fluid samples such as urine, blood, milk, etc., often contain high-abundance proteins. b) In immunoprecipitation (IP) solution samples, high-abundance proteins may be present due to potential interference from antibodies.
Which mass spectrometry platforms do you use for proteomics analysis?
We utilize the Thermo Orbitrap Fusion Lumos, Thermo Q Exactive series, Thermo Exploris 480, and timsTOF Pro for proteomics analysis.
How can you determine if the extracted proteins are suitable for subsequent mass spectrometry analysis?
a) Clear and evenly distributed protein bands on SDS-PAGE; b) Good parallelism within sample replicates; c) Estimate the total extracted protein amount based on SDS-PAGE results. Generally, for regular proteomics, the protein total should be above 200 μg, and for modified proteomics, the total amount may need to be increased depending on the specific modification type; d) The protein concentration of the extracted sample should not be too low.
Can enzymes related to apoptosis be detected using proteomics?
Proteomic analysis results include KEGG and GO annotations, allowing for the examination of protein annotations related to this function.
What types of samples can be used for your protein identification services?
You can submit a wide variety of sample types including gel spots or bands, solution-based proteins, cell lysates, tissue extracts, body fluids (e.g., serum, plasma) or immunoprecipitation/pull-down eluates; the key is that the sample is compatible with our high-resolution LC-MS/MS or MALDI-TOF workflows and free of interfering detergents or excessive salts.
Can you identify unknown proteins or novel isoforms using mass spectrometry?
Yes — our platform supports unknown protein identification and isoform discrimination by combining high-resolution LC–MS/MS, peptide mapping, database searches and where needed de novo sequencing; this enables detection and annotation of previously uncharacterised proteins, including domain/motif mapping.
Do you offer quantitative proteomics or only protein identification?
We provide both qualitative identification (which proteins are present) and quantitative proteomics (how protein levels change) workflows; following identification via LC-MS/MS or MALDI-TOF you may transition into label-free, TMT/iTRAQ, SILAC or other quantitation methods to measure abundance changes across conditions.
What are the typical sample preparation requirements before sending material?
Samples should come in a form compatible with proteomics analysis — minimum protein amounts depending on sample type, clean buffers (low salt, minimal detergent), clearly labelled, shipped on dry ice or as frozen material; gel bands/spots should be from visibly stained gels, solution samples should avoid non-volatile buffers or polymer contaminants.
How are post-translational modifications (PTMs) or protein-protein interactions handled in your services?
Our advanced workflows allow mapping of PTMs (phosphorylation, glycosylation, ubiquitination etc.) and investigation of protein-protein interaction networks (via Co-IP or pull-down followed by LC-MS/MS) enabling not only protein identification but also context (modification, interaction) and functional annotation.
What kind of deliverables will I receive from the protein identification service?
You will receive a detailed report that includes identified proteins (with accession numbers and confidence metrics), peptide-coverage maps, annotation of domains/motifs or PTMs, optional quantitation data if included, annotated spectra or raw data files on request, and interpretation to support your next steps in research or development.
Why choose your laboratory for protein identification by mass spectrometry rather than performing it in-house?
Our service offers specialist expertise, validated workflows and high-end instrumentation (LC–MS/MS, MALDI-TOF) that may exceed typical in-house capacity; we provide end-to-end support from sample prep, digestion, data acquisition, bioinformatics to reporting — helping reduce risk, accelerate timelines, and deliver actionable data for CRO, academic or biotech clients.
Is peptide mass fingerprinting enough for complex mixtures?
Peptide mapping is fast for simple samples; complex matrices need LC–MS/MS for confident IDs. Check out our comparison guide.
How do you control false discovery rates in protein identification?
We apply decoy strategies and strict FDR thresholds at peptide/protein levels within established pipelines.
When to choose MALDI-TOF vs LC–MS/MS?
MALDI-TOF suits rapid screening of simple bands; LC–MS/MS provides deep coverage in complex lysates.
Can domain or motif mapping be included?
Yes, we annotate domains/motifs and PTMs during bioinformatics, included in standard deliverables.
Learn about other Q&A about proteomics technology.
Client Case Study: Protein Interactor Mapping in Neurospora crassa Using Nano LC-MS/MS Protein Identification Services
Espino-Vázquez, A. N. et al. (2024) — Protein interactors of Spindle Pole Body (SPB) components and septal proteins in fungus Neurospora crassa: A mass spectrometry-based dataset, Data in Brief, DOI: 10.1016/j.dib.2023.109980
Service Used: Protein identification service nano LC-MS/MS
- Background / Objective
- Approach / Services Used
- Results / Findings
- Value to Client
The fungal model organism Neurospora crassa provides unique insight into eukaryotic cell organisation and cell division. A research team led by Espino-Vázquez et al. (2024) aimed to define protein interactors associated with Spindle Pole Body (SPB) components and septal proteins—key structural elements controlling mitosis and cellular compartmentalisation.
Because these complexes consist of low-abundance and membrane-associated proteins, the team required a highly sensitive, reproducible platform for large-scale protein identification and interaction analysis.
To achieve comprehensive coverage and accurate protein annotation, the group partnered with Creative Proteomics, which provided nano LC-MS/MS protein identification services tailored for complex fungal proteomes.
The workflow included:
- Sample preparation and protein extraction from N. crassa strains expressing tagged SPB or septal components.
- In-gel digestion of immunoprecipitated complexes, followed by peptide purification.
- Nano-LC-MS/MS analysis on a high-resolution mass spectrometer optimised for low-abundance protein detection.
- Database search and peptide mapping to identify specific interactors linked to cytoskeletal or septal machinery.
This end-to-end approach ensured high-confidence matches and reproducible identification of protein networks relevant to cell division and morphogenesis.
The dataset reported in Data in Brief (2024) represents one of the most extensive SPB-related proteomic resources available for filamentous fungi. The Creative Proteomics workflow enabled the identification of numerous SPB and septum-associated proteins, expanding known interaction maps and uncovering novel candidate regulators.
The resulting nano LC-MS/MS dataset provides:
- Confident identification of both structural and regulatory interactors;
- Quantitative spectral data supporting reproducibility and coverage;
- A validated methodological framework for future fungal proteome studies.
Fig. Electrophoresis of Co-IP experiments. A) Representative polyacrylamide gel following the Co-IP protocol B) Gel lanes with eluted proteins (bound) sent for LC-MS/MS analysis.
By leveraging Creative Proteomics' protein identification services, the research team achieved results that would have been difficult with conventional in-house instrumentation:
- High sensitivity and reproducibility for low-abundance proteins;
- Reliable protein–protein interaction mapping supporting functional annotation;
- Publication-ready data that met journal-level reproducibility standards.
This collaboration demonstrates how Creative Proteomics supports academic clients in generating high-quality proteomic datasets that advance basic biology while showcasing translational potential in cell-cycle and structural-protein research.
Demo for Protein Identification Service
Figures come from ( Shibata, H.et.al, J Clin Immunol,2024)
PCA Plot of Sample Grouping
Pearson Correlation Analysis
Volcano Plot of Differential Proteins
Bar Chart of GO Enrichment for Candidate Proteins
References
- Zhang, Wenli, and Xiaofang Zhao. "Method for rapid protein identification in a large database." BioMed research international vol. 2013 (2013).
- Shibata, Hirofumi et al. "A Non-targeted Proteomics Newborn Screening Platform for Inborn Errors of Immunity." Journal of clinical immunology vol. 45,1 33. 25 Oct. 2024.
- Hernandez, P., Binz, PA., Wilkins, M.R. (2007). Protein Identification in Proteomics. In: Wilkins, M.R., Appel, R.D., Williams, K.L., Hochstrasser, D.F. (eds) Proteome Research. Principles and Practice. Springer, Berlin, Heidelberg.
