Fios Genomics offers established, cost-efficient and rapid turnaround analysis services for proteomics data from a range of platforms including labelled or label-free LC-MS/MS, and protein immunoassays. We are able to receive data in various formats for the analysis such as peptide- or protein-specific intensities and spectral count matrices.
Proteomics analyses are relevant for a range of applications such as:
- Profiling of proteomes between normal and diseased tissues
- Identification and quantification of protein biomarkers and PTMs associated with drug response or survival
- Identification of direct targets and indirect effects of drugs and other active molecules
- Exosome research (exosome profiling, identifying exosome signatures and biomarkers etc.)
Proteomics is the investigation of the protein composition of cells, tissues, organisms or other biological systems in a high throughput manner. In addition to steady-state abundances, proteomics can also help to determine the location and rate of protein production and degradation at a specific time. Other proteomics techniques enable the identification of post-translational modifications (PTMs), interactions, and movement between subcellular compartments.
Most analyses of proteomics data are designed to quantify the changes in protein abundance, modification, location or binding specificity between groups of samples that differ with respect to tissue of origin, treatment, experimental condition or outcome.
Our routine proteomics data analysis pipeline includes:
- Assessment of sample metadata to identify associations between biological and technical study variables
- Quality control evaluation of raw protein or peptide abundance data
- Normalisation across samples using appropriate data normalisation techniques.
- Identification and correction of batch-related effects
- Assessment, and where appropriate, imputation of missing values
- Exploratory analysis and evaluation of all types of data using unsupervised clustering and dimension reduction techniques to assess overall sample quality and identify possible outliers
- Differential abundance analysis with a range of tools (e.g. voom/limma, DESeq2, EdgeR)
- Functional enrichment analysis using resources such as the Reactomepathway knowledgebase and the Gene Ontology (GO) database
Where required we can include a range of further bolt-on analyses, for example, gene set enrichment analysis (GSEA) to assess functional enrichment, or an integrated congruence analysis with other ‘omics’ data sets such as gene expression data to obtain a more holistic view of a biological system.
We were very pleased with the service provided by Fios Genomics. In particular, the Fios team were flexible and willing to spend time understanding our specific project needs and the key scientific questions we were asking of the experiments. They tailored the data output in a way that specifically addressed these questions, which was really helpful. The data package was Web-based and interactive and we were delighted with the way it was presented and explained to us. We will certainly work again with the Fios team for any future projects.
Every time our clients work with us, they benefit from:
- A dedicated analyst backed by an experienced team to curate all data, identify the most appropriate statistical approach to take and provide a biological interpretation of results.
- An interactive data analysis report, internally peer-reviewed, including all analysis methods and results.
- Post-report follow ups: upon receipt of our data analysis report, we arrange a teleconference so that our lead analyst can talk through the results.
Access to large capacity computing and secure data storage facilities.
What we have helped with:
We have helped our clients with the following projects:
- Investigation of drug or gene knockout-induced changes to the proteome of cancer cells or tissues from various model organisms
- Identification of the protein response to drug treatment in blood samples taken from cancer patients in a clinical trial
- Integration of RNAseq and proteomics data to assess congruence
- Correlation of protein levels with patient response to treatment to identify predictive biomarkers
WHAT YOU WILL GET
Transparency
All methods and analysis tools utilised are detailed in the final report. This means no blackbox of analysis.
Fast Turnaround
We help you to achieve your research goals in a quick and timely manner.
Rigorous QC
We always perform Quality Control as part of an analysis project.
Getting Your Data Ready For Analysis
We can analyse:
- Recent data, generated within your own laboratory or that of a 3rd party provider
- In-house historic data
- Data sourced from the public domain and database (data mining).
While we prefer to receive data in the raw format (eg .CEL files) we can also receive pre-normalised files.
If you have yet to generate the data, we can help by arranging for the generation of your data. We have a list of providers located worldwide to which can take care of data generation. This service is usually only available as part of an analysis contract.
Alternatively, we are able to source and mine data from available databases. We are happy to work with you at every stage of your study to ensure the best outcome for your research.
Our Reports
Our analysis reports at Fios are provided as an HTML link hosted on our secure server. The secure link leads the user to a password-protected HTML document which is clickable, searchable and dynamic. This format allows you to easily interrogate and explore your data. Additionally, all methods, tools and thresholds are fully documented within the report.
We offer a wide range of services:
Discovery
Selecting the correct targets and/or the correct indication is essential for development success. We help support the process with robust analysis of historic or new data.
Preclinical Research
We help in experimental design and statistical analysis and guide our clients in making informed decisions during the preclinical stage.
Clinical
Research
We offer a comprehensive analysis approach for augmenting clinical trial outcomes, ensuring you get the most information out of your research.
Drug Repurposing
We have strong experience with identifying in silico new potential indications for existing drugs, reducing the cost and time of downstream wet lab validation.
