PROTEOMIC SERVICES
The most cost effective way to do proteomics is to collaborate with proteomics experts.
Our research focuses on marine proteomics, ocean proteomics, metaproteomics, non-model proteomics, and extreme environment proteomics. We have completed studies on a range of aquatic environments including sediments, bacteria, phytoplankton, and marine invertebrates.
We offer a variety of services (see below). Please email us with:
- A description of your project
- Questions you are trying to answer
- Types of samples you have
- Information on accompanying genome or metagenome
|
|
We can help guide your graduate students or postdoctoral fellows through their analyses.
We have been working in the field of environmental proteomics for over 15 years. We exclusively use Thermo Fisher mass spectrometers with inline Waters NanoAcquity HPLCs, providing us with state-of-the art chromatographic separation and high mass accuracy on all peptides analyzed.
Our lab has access to over 10 Thermo Fisher mass spectrometers dedicated to proteomics experiments and maintained full time by senior scientists.
Our lab has access to over 10 Thermo Fisher mass spectrometers dedicated to proteomics experiments and maintained full time by senior scientists.
|
|
COST CENTER
We decided to establish a cost center because so many PIs were discovering the power of proteomics and our lab's abilities after grants were funded. This provides us with an avenue to work together, even if the funding is already in place. We are also seeking new, long-term collaborations in the fields of ocean and environmental proteomics.
Cost Overview
The cost of proteomics analysis depends on the sample matrix, experimental design, and the level of analytical development required. Environmental samples often vary widely in biomass, chemical composition, and genome annotation, which can influence both preparation strategies and data analysis requirements.
As a general estimate, analyzing a standard sample on a high resolution Orbitrap mass spectrometer (Lumos, Q Exactive, Astral, or similar platforms) is approximately $450 per sample injection. This estimate is most appropriate for relatively straightforward samples such as cell pellets or cultured organisms that require minimal method development.
More complex environmental matrices such as seawater filters, sediments, soils, tissues, or microbiome samples may require additional development and will be discussed collaboratively prior to project initiation.
What the Standard Analysis Includes
The approximate $450 per sample estimate reflects a comprehensive workflow designed to generate publication quality proteomics data and includes:
Expertise in Environmental Proteomics
Unlike other proteomics resources, the UW Environmental Proteomics Center specializes in proteomics from complex environmental matrices, including seawater, sediments, soils, microbial filters, corals, tissues, and environmental microbiomes and biofilms. These systems often contain low biomass, highly diverse communities, and poorly annotated genomes that require specialized analytical strategies.
Our workflows are specifically designed to support these challenging sample types. This includes custom chromatographic separations, strict carryover control, robust quality monitoring, and bioinformatic strategies that combine de novo peptide discovery with database based identification.
This focus allows our center to support projects involving novel organisms, environmental microbiomes, and extreme environments that often fall outside the capabilities of conventional proteomics facilities.
Replication and Experimental Design
To meet typical publication standards for mass spectrometry based proteomics, we generally recommend 5 to 10 biological replicates for culture based experiments or tissue studies. Environmental microbiome studies, ocean time series datasets, and other complex ecological systems often require customized sampling strategies and requirements for publication can be as low as 1 to 3 biological replicates .
- Both Emma Timmins Schiffman and Brook Nunn have >15 years of experience with a range of ecosystems and sample types and can inform you on the complexity we have seen with in situ sample differences and how many replicates are likely needed in order to answer your question.
We can work closely with collaborators to design experiments that meet publication standards while maximizing the biological insight gained from each dataset.
Bioinformatics and Data Analysis
Downstream bioinformatics is often the most time intensive portion of environmental proteomics projects. Basic analysis of well annotated model organisms is included in the standard analysis estimate.
Projects involving environmental microbiomes, custom protein databases, or poorly annotated genomes often require expanded computational analysis. These efforts are scoped collaboratively to ensure that datasets can be fully interpreted and used for publication. Some of the tools we use include: Comet, Percolator, Carafe, DIA-NNE, Magnum, CasaNOVO, CascaDIA, Skyline and Panorama.
Collaboration and Training
The UWEPC operates as a collaborative research environment. Proteomics experiments represent a substantial investment and the resulting datasets are complex. Our goal is to ensure that data generated through the center leads to meaningful interpretation and successful publication.
We work directly with investigators and trainees throughout the project to assist with experimental design, data interpretation, and analytical training. This collaborative model helps ensure that valuable datasets are fully used and that students gain the skills necessary to analyze and publish their results.
The cost of proteomics analysis depends on the sample matrix, experimental design, and the level of analytical development required. Environmental samples often vary widely in biomass, chemical composition, and genome annotation, which can influence both preparation strategies and data analysis requirements.
As a general estimate, analyzing a standard sample on a high resolution Orbitrap mass spectrometer (Lumos, Q Exactive, Astral, or similar platforms) is approximately $450 per sample injection. This estimate is most appropriate for relatively straightforward samples such as cell pellets or cultured organisms that require minimal method development.
More complex environmental matrices such as seawater filters, sediments, soils, tissues, or microbiome samples may require additional development and will be discussed collaboratively prior to project initiation.
What the Standard Analysis Includes
The approximate $450 per sample estimate reflects a comprehensive workflow designed to generate publication quality proteomics data and includes:
- Consultation on experimental design and project planning
- Sample intake and preparation for bottom up proteomics workflows
- Data dependent (DDA) or data independent (DIA) acquisition on a high resolution Orbitrap mass spectrometer
- Instrument calibration performed immediately prior to sample analysis
- Individually pressure packed in house silica C18 nanoLC columns used for each project. These columns are packed and quality tested within our laboratory to minimize peptide carryover between studies. This level of separation control is particularly important for low biomass samples, new genomes, and novel environmental systems
- Rigorous quality control monitoring, including QC standards analyzed every fifth sample to track instrument stability, chromatography performance, and analytical reproducibility
- Delivery of raw data, processed datasets, and QC metrics for transparency and reproducibility
- In house bioinformatics using current best practice approaches including database searching, de novo peptide identification, peptide spectral matching, and quantitative analysis using spectral counting or DIA AUC methods
- Guidance and training for students and collaborators on label free quantification workflows and downstream interpretation
- Methods section language suitable for direct inclusion in manuscripts
Expertise in Environmental Proteomics
Unlike other proteomics resources, the UW Environmental Proteomics Center specializes in proteomics from complex environmental matrices, including seawater, sediments, soils, microbial filters, corals, tissues, and environmental microbiomes and biofilms. These systems often contain low biomass, highly diverse communities, and poorly annotated genomes that require specialized analytical strategies.
Our workflows are specifically designed to support these challenging sample types. This includes custom chromatographic separations, strict carryover control, robust quality monitoring, and bioinformatic strategies that combine de novo peptide discovery with database based identification.
This focus allows our center to support projects involving novel organisms, environmental microbiomes, and extreme environments that often fall outside the capabilities of conventional proteomics facilities.
Replication and Experimental Design
To meet typical publication standards for mass spectrometry based proteomics, we generally recommend 5 to 10 biological replicates for culture based experiments or tissue studies. Environmental microbiome studies, ocean time series datasets, and other complex ecological systems often require customized sampling strategies and requirements for publication can be as low as 1 to 3 biological replicates .
- Both Emma Timmins Schiffman and Brook Nunn have >15 years of experience with a range of ecosystems and sample types and can inform you on the complexity we have seen with in situ sample differences and how many replicates are likely needed in order to answer your question.
We can work closely with collaborators to design experiments that meet publication standards while maximizing the biological insight gained from each dataset.
Bioinformatics and Data Analysis
Downstream bioinformatics is often the most time intensive portion of environmental proteomics projects. Basic analysis of well annotated model organisms is included in the standard analysis estimate.
Projects involving environmental microbiomes, custom protein databases, or poorly annotated genomes often require expanded computational analysis. These efforts are scoped collaboratively to ensure that datasets can be fully interpreted and used for publication. Some of the tools we use include: Comet, Percolator, Carafe, DIA-NNE, Magnum, CasaNOVO, CascaDIA, Skyline and Panorama.
Collaboration and Training
The UWEPC operates as a collaborative research environment. Proteomics experiments represent a substantial investment and the resulting datasets are complex. Our goal is to ensure that data generated through the center leads to meaningful interpretation and successful publication.
We work directly with investigators and trainees throughout the project to assist with experimental design, data interpretation, and analytical training. This collaborative model helps ensure that valuable datasets are fully used and that students gain the skills necessary to analyze and publish their results.
EXAMPLES OF WORK WE HAVE DONE:
|
|
Additionally, there is the the University of Washington Mass Spectrometry Center in the UW Health Sciences Center is open-access self-sustaining instrument laboratory providing a wide variety of mass spectral services to the University and the research community-at-large (including commercial) on a recharge basis. Examples of routine analysis are: Low and High Resolution mass analysis, metabolomics, analyte quantitation, and structural elucidation.
Please note that we are looking for collaborations- we are not a typical cost center "drop off" service. Further, we reserve the right to turn down projects based on our schedule.