Proteomics
Our advanced proteomics capability offers protein identification, quantification and characterisation services through liquid chromatography and mass-spectrometry.
Equipped with modern instruments and specialised staff with over 15 years of experience, our team provides end-to-end support from experimental design and sample preparation to data acquisition and analysis, including bioinformatics service.
We work with samples from diverse origins, including viruses, bacteria, fungi, plants and animals, and with researchers across all disciplines, including agricultural, pharmaceutical, biomedical and environmental. We are flexible and can develop research methodologies tailored for research projects and outcomes, for academic, industry, and commercial partners.
- Deep proteomic profiling
Through refined methodologies, using direct or fractionation strategies to identify proteins present in complex biological samples
- Quantitative proteomics
Precise measurement of protein abundance in samples using both label-free and label-based quantification approaches. Multiplexed analysis of protein and/or peptide mixtures is possible.
- Protein biomarker discovery
Identify statistically significant biomarkers and pathways/networks associated with disease or biological condition
- Post-translational modifications analysis
Proteins and their associated post-translational modifications (PTMs) can be identified including phosphoproteomics and glycoproteomics. Our approaches include sample enrichment, acquisition and analysis strategies, and informatic analyses.
- Proteomics diversity
With projects covering cell signaling, low sample input amounts (low nanogram quantity), subcellular organelles (extracellular vesicles, microsomes, mitochondria), and biofluids and cell-specific proteome analyses, our team and collaboration network has a broad diversity in proteomic experience.
- Intact protein mass determination
Determine the accurate mass of purified proteins (e.g., over-expressed recombinant products)
- Bioinformatics and data analysis
Statistical workflows in R for data visualisation, significance and power analysis.
- Customised workflow and experimental design
We collaborate with researchers to design experiments and workflows tailored to specific needs. - Training and development
Training for users in sample preparation, data acquisition and analysis
We have a dedicated range of LC-MS instrumentation:
Thermo Scientific Orbitrap Eclipse Mass Spectrometer (with ETD and FAIMS-PRO)
The Eclipse delivers high speed and sensitivity with coupled orbitrap and ion-trap analysers. Multiple fragmentation modes and FAIMS offer unprecedented depth of analysis, especially for highly complex, low abundance, or difficult-to-analyse biological samples. It is especially suited to deep proteomes, low-input samples, and tailored PTM profiling. We run DDA, DIA and targeted acquisition methods on this instrument.
Thermo Scientific Q-Exactive HF
Used for a range of routine protein, and peptide applications. The resolution and mass accuracy of the QE-HF orbitrap mass analyser is ideal for proteomics applications, including DDA, DIA, and targeted quantitation methods.
Thermo Scientific LTQ Orbitrap Elite ETD
Provides excellent mass accuracy and resolution of proteins in high complexity samples (such as cell lysates, plasma and tissue homogenates) and the characterization of post-translational modifications (such as phosphorylation and glycosylation) using the ETD fragmentation. The LTQ elite is highly customisable for flexible analyses of recombinant proteins through to proteomes where sample is plentiful.
Thermo UltiMate 3000 RSLCnano System UHPLC, three systems
All our proteomics mass-spectrometers are coupled with identical Dionex UltiMate 3000 UHPLC systems. This enables fast method transfer between instruments to run nanoflow or capillary flow separation of complex mixtures of proteins
Agilent 6530 Q-TOF Mass Spectrometer and 1260 HPLC system
Easy to use instrument for intact protein mass-analysis. With great sensitivity and transmission it can detect and resolve large biomolecules up to 20,000 m/z. It is suitable for both native and denaturing intact mass analysis of proteins.
Quality is an integral part of our research platform's purpose and value. We are committed to providing our customers, industry partners and academic collaborators with services and products that are of high quality, consistent and compliant.
Our platforms strive to be recognised and trusted by researchers as an excellent research service provider that constantly meet or exceed customer expectations. To achieve this, we have implemented a Quality Management System (QMS) across Research Platforms that operates on all our campuses.
Our QMS is aligned to the AS/NZS ISO 9001:2016 standard and the University’s Research 2030: Research and Engagement Plan 2020-2024. In alignment with the ISO standard, efforts are focused on understanding customer needs and ensuring their satisfaction, as well as continuously improving service provision in the pursuit of research excellence. The services provided by Research Platforms are also underpinned by our cultural qualities: to be connected, innovative, accountable and caring.
The Research Platforms quality policy embraces the following key principles:
- Building a mutually beneficial relationship with customers, ensuring their long-term success through the understanding of, and meeting, their needs.
- Nurturing a quality mindset with the objective of providing services that are trusted and preferred by internal and external researchers and deliver on our Research Plan Objective 1: Research Excellence.
- Complying with all relevant laws and regulations as well as internal policies and requirements.
- Continuously challenging all Research Platforms to improve the QMS to prevent quality incidents, eliminate errors, accelerate research, and ensure high quality data through efficient business processes, best-practice and well-defined goals.
- Encouraging involvement in quality responsibilities amongst all Research Platform personnel, researchers and relevant third parties through quality standards, education, training and mentoring, supervision and effective internal and external communication.
Our platforms are currently seeking to achieve ISO9001 accreditation as part of their commitment to their customers. Work to obtain verification by independent third-party certification bodies is ongoing.
The platform’s contributions to research outputs (e.g., publications, presentations, posters) should be acknowledged where possible. These contributions could include:
- paid technical help and services
- accessing research equipment
- scientific advice
- writing assistance.
Proper acknowledgement enables us to demonstrate our value to the research community and highlight our impact on research excellence, which is critical to securing continued funding for our services. Our staff are also researchers with extensive experience and citing them helps to advance their careers.
In cases where substantial intellectual and experimental contributions were made by platform staff, co-authorship must also be offered in accordance with the Australian Code for the Responsible Conduct of Research, regardless of whether payment was made for the services. Researchers should also notify the platform of any publications arising from the support provided by our staff, regardless of whether a co-authorship is offered.
Learn more about how to acknowledge us:
All publications resulting from the use of our services and facilities should include this acknowledgement:
‘The authors acknowledge the La Trobe University [Platform Name] for [support received].’
e.g., The authors acknowledge the La Trobe University Proteomics and Metabolomics Platform for the provision of instrumentation, training and technical support.
OR
e.g., The authors acknowledge the La Trobe University Statistics Consultancy Platform for providing advice on statistical analysis.
If you received significant assistance, guidance or help from our platform staff, or where staff have personally generated research data, they should be acknowledged by name:
‘The authors thank [Staff Name] from the La Trobe University [Platform Name] for [his/her/their] support and guidance in this work.’
e.g., The authors thank [Staff Name] from the La Trobe University Proteomics and Metabolomics Platform for collecting and analysing data for proteomics studies, shown in Figure X.
If a platform staff contribute more than just routine techniques or advice, they should be invited to be a co-author on the publications that describe the data. This applies to the development or adaptation of protocols to suit specific experiments, samples or materials, (re)design of experiments, and extensive data analysis and interpretation.
Co-authorship is independent of whether payment was made for the work/ service.
Access
We work with both academic researchers and industry partners, including pharmaceutical and biotechnology companies. We provide a range of access models to suit different needs, including:
- Prepaid annual subscriptions for internal academic users who have ongoing projects or large numbers of samples.
- Bronze (up to 50 samples per annum)
- Silver (up to 110 samples per annum)
- Gold (up to 240 samples per annum)
- Fee-for-service for ad hoc samples or small numbers of samples.
- Research Contracts for industry partners or external academics wishing to undertake bespoke projects.
Contact us
For more information and to discuss your requirements, please contact a team member:
- Dr Rohan Lowe, Bioinformatician in Proteomics
- Dr Bushra Amin, Mass Spectrometry (Proteomics) Specialist.
T: (+61 3) 9479 5006
E: Proteomics Metabolomics Platform