Mass spectrometry based proteomics

The UWPR offers analytical and instructional expertise in state-of-the-art mass spectrometric techniques and data analysis, with the primary aim of providing UW investigators with hands-on training and access to the resources needed to pursue their proteomics research.

Access to UWPR resources is through collaborations with Resource members or affiliated research labs. We strongly recommend discussing your proteomics project and sample preparation with Resource members before preparing samples; see the sample preparation guidelines on our Resources page.

Using the resources requires the appropriate training and adherence to the usage guidelines (pdf). After the initial training (usually 4 to 6 hours) and several periods of supervised use, a researcher may operate an instrument independently with instructor approval. Training is instrument specific, takes place during your signed-up instrument time, and must be coordinated with UWPR staff.

The UWPR operates as a cost center: institutional users contribute to the upkeep of the resource through a recharge system, with rates based on operating costs and individual instrument usage. To keep operating costs low, collaborators supply all the consumables needed for sample preparation and mass spec analysis (LC columns, vials, etc., per the usage guidelines).

All rates are reviewed and approved by the University of Washington administration and are subject to change without notice. To view the current fee schedule, register and log in to the internal Proteomics Resource website.

Access to UWPR resources and services

To initiate a new collaboration, register and log in. On the Welcome page, click “Start new collaboration” and submit a detailed project description.

UW employees billing to a UW worktag (budget number) can choose between self service (you run the LC-MS analyses yourself) and full LC-MS service (analyses run by UWPR personnel; additional labor rates apply). In the project description, set “Mass spec analysis by UWPR personnel” to NO for self service or YES for full LC-MS service.

Self Service

Download the Self service guidelines (pdf).

  • After submitting the project details and billing information, request sign-up privileges by email. Once access is granted, you can schedule up to 20 days (480 hours) of instrument time.
  • Do NOT block instrument time unnecessarily. Your self sign-up rights can and will be revoked.
  • There is a non-refundable sign-up fee, a percentage of the total cost, billed even if you cancel your instrument time. One setup fee is charged per consecutive time span.
  • Cancellation closes 48 hours before the start time; after that the system no longer allows changes, and you will be charged the sign-up fees and any instrument time you cannot cancel.
  • Coordinate with UWPR personnel for facility access, and schedule instruction time if training is needed.
  • Start and end times are strictly enforced. If you start early, or do not finish, clean up, and return the key card on time, you will be charged the extra time at the hourly rate (rounded up to the next full hour).
  • Instrument start times are 10 am and 2 pm (UWPR personnel may need time at the beginning of your block to prep the instrument). End times are 10 am, 2 pm, and 6 pm.
  • If you finish early and clean up and return the key card before the next time block starts, unused instrument time is backed out to the end of your last acquisition (rounded up to the next full hour), but no further back than the end of the previous time block. The sign-up fee is not backed out. For example, if you sign up through Monday 10 am so you do not have to clean up during the weekend, and your last run finishes Saturday morning, you will be charged through Sunday 6 pm.
  • If you cannot make it in and ask UWPR personnel to clean up for you, the full time block is charged and no time is backed out.
  • If you sign up into the weekend, be prepared to come in and clean up during the weekend in case someone signs up to use the instrument.
  • Provide your own consumables (columns and autosampler vials); download the list of commonly used LC-MS consumables (xls).
  • UWPR personnel can also help with your data analysis needs; contact us to discuss details.

Full LC-MS Service

For small projects with a limited number of samples, we offer full LC-MS service (guidelines (pdf)): you prepare the samples, and UWPR personnel run the LC-MS analyses and can help with data analysis. Contact us if you need help with project design or sample preparation procedures. All samples must be submitted “mass spec ready”, i.e. you do all the sample preparation.

To start the collaboration, submit the project details and billing information online. When your samples are ready, submit the Sample Submission Form (xlsx), which we also use to track experimental details for future reference, and coordinate with UWPR personnel to drop off the samples. Once we receive both the samples and the form, UWPR personnel will schedule the instrument time to analyze your samples.

The same sign-up terms apply: a non-refundable sign-up fee (a percentage of the total cost, billed even if you cancel) and a 48-hour cancellation cutoff before the start time.

Billing

The cost consists of the setup fee, the sign-up fee, and the instrument time you signed up for, invoiced on the first business day of the month following the signed-up time. The sign-up fee cannot be canceled. Instrument time can be canceled up to 48 hours before the start of the time block; any time not canceled is charged.

For full LC-MS service, the cost is based on the time it takes to analyze your samples plus a minimum of 2 hours to prepare the column and run quality control samples. The Sample Submission Form (xlsx) can help estimate the time needed.

The current rates can be downloaded from the Welcome page after logging in. The billing cycle is monthly.

Publication/Citation

It is our policy that key collaborators within the UWPR share co-authorship of any manuscripts resulting from work performed at the Resource. At a minimum, the Proteomics Resource should be acknowledged in publications as follows:

This work is supported in part by the University of Washington’s Proteomics Resource (UWPR95794).

See also the ABRF guidelines for authorship for personnel working in facilities such as the UWPR.

Data retention

Short and long term storage of the acquired files is the sole responsibility of the users of the Resource. The UWPR strives to maintain, but does not guarantee, copies of acquired raw data files for up to one year from the acquisition date. After that, the files may be purged from our storage systems.

Other local core facilities

A list of other local and commercial core facilities that may help with your mass spec or proteomics needs.