Sample Submission

Sample Submission

Welcome to the Sample Submissions site for the Duke University Proteomics and Metabolomics Shared Resource (DPMSR). The School of Medicine and GCB have collaboratively created this facility to provide protein/metabolite characterization resources for the Duke Research Community. These services include identification and quantitation from a wide variety of sample types, including cell lines, tissues and biofluids. DPMSR is located on the third floor of the Chesterfield Building, 701 West Main Street, Durham. It is a short trip from West Campus.

Aerial view of the Chesterfield building and surrounding area

Directions to the Chesterfield Building

Duke Downtown Shuttle to the Chesterfield

  • DukeCardID required for all passengers
  • Operates from 7 A.M. - 6 P.M. Monday - Friday
  • Track in real-time with Duke Transloc ("Shuttle: Downtown Pilot")
  • Free WiFi is available via Carolina Livery
  • Serviced by two 36-passenger shuttles operated by Carolina Livery
  • Shuttles are ADA compatible

Also, the Bull City Connector provides free transportation from Research Drive to the Chesterfield

Parking at the ChesterfieldDuke visitors have a two-hour parking option, which is first come/first served access, to the visitor parking lot at the back of the building near the railroad tracks. We share this 2hr parking with other tenant's visitors, and are not designated a certain proportion of parking for our guests at this site. Do not park beyond the fencing or cones; this is a construction area.

We have designated guest parking under the building and that can be reserved for up to six spaces for School of Medicine, and seven spots for School of Engineering per day. There are two calendars (below) that you can use to reserve parking spaces under the building. Please note if the current total of 13 spaces has already been met, then other accommodations will need to be made.

For larger events that might exceed the total number of parking or events lasting longer than two hours, we typically work with the building management to open up the 704 W Pettigrew St parking deck for more visitors on the day of the event. This can be accomplished through validation stickers or having the gates up during certain periods of the day.

1.) Sample Submission Consultations

You can submit samples and check the status of samples submitted to the DPMSR.

If you have questions about the use of this web-based submission application, please contact gcb-help@duke.edu.

Prior to submitting any samples for new projects, please contact Dr. Arthur Moseley.

If the samples are extentions of previous projects, please contact the DPMSR scientist with whom you have worked before for a discussion of these samples:

Regretfully, we cannot accept samples without consultation and the electronic submission of the sample (see below).

We make every effort to respond to emails in a timely fashion; however, if you have not received a reply within 48 hours, please resend the email with a high importance flag and copy our Senior Laboratory Administrator, Ms. Laura Dubois.

Priority will be given to DCI members and time-sensitive projects, including preliminary data needed for timely grant submissions and additional experiments needed for manuscript resubmissions.

2.) Electronic Sample Submission Process

Sample submission and data return from Duke Proteomics and Metabolomics Shared Resource takes advantage of the GCB data respository to return customer data in digital format. This submission and data return protocol uses a single sign-on system, which can be accessed by both Duke and non-Duke collaborators. Three steps are required to submit a sample to our facility:

1. Create a single sign-on account (or log in).

2. Go to Express Data Repository Account and create an Express project where you would like your proteomics data to be delivered. Please create a new project number for each new project. Do not use your old project numbers. If you are not the PI, please Grant Access to this Project to your PI and any other scientists in your lab or project group who will need access to this project’s data.

3. When you are ready to submit your samples, go to Proteomics Sample Submission to complete your submission. Then follow the drop-off instructions detailed below.

**Note: The first time you wish to submit a sample, we will have to grant you access to the submissions page. Email a facility member with your NetID, and we will enable your account.

We have generated a few helpful slides to walk you through Steps 2 and 3:

Creating an Account, Project, Submission

Questions about creating a single sign-on, an Express account, or an Express project can be addressed to GCB IT help at gcb-help@duke.edu. Please contact the Proteomics and Metabolomics Shared Resource with any other questions about sample submission. An email notification will be sent to the submitting scientist when the data has been delivered to your Express project.

3.) Instructions for Sample Delivery

Our expansion and relocation to the Chesterfield will allow us to provide you with superior service. To better serve you, we have created new procedures for sample delivery. Please follow the instructions on our website for project consultations and subsequent sample delivery, and review the new sample delivery procedures below. If you have any questions, please email or call the DPMSR staff member who is your point of contact.

To continue providing face-to-face project consultations, we will have pre-determined office hours on campus in the CIEMAS building and will utilize video conferencing solutions for times outside of those hours. DPMSR staff may be able to visit your lab upon request.

On behalf of DPMSR, thank you for allowing us to serve your research needs

Procedures for Sample Delivery

  1. Submit your order into our system and prepare samples for delivery.
  2. Bring samples and a hard copy of the electronic submission(s) to Heather Hemric, ZhengZheng Wei, or Holly Dressman in CIEMAS 2208B.
    Use wet ice if samples need to be stored at 4oC.
    Use dry ice, if samples need to be stored at -80oC.
  3. Ensure that the sample name on each tube matches the sample name on the order, and the number of samples delivered matches the number of samples in your order.
  4. The staff at CIEMAS will review your order in the system with you, help make any necessary changes and ensure your samples are properly packaged for transport.
  5. Scientists from DPMSR will be available by phone to discuss any issues that may arise.

Sample Drop-Off Hours at CIEMAS 2208B:

  • Monday – Friday: 2 – 3 P.M. (sample will arrive in Chesterfield next business day)

A courier will pick samples up from CIEMAS between the drop-off periods and will bring samples to Chesterfield once a day, arriving at Chesterfield at ~ 2:30 P.M.

We are committed to ensuring that your samples are properly transported for analysis. Please do not hesitate to contact any DPMSR scientist with questions or concerns.

*NOTE: If you have samples that need to be processed in a time-sensitive manner (e.g. co-IP samples that have not been eluted off a resin or beads), please let us know prior to drop-off so we can coordinate same-day delivery and sample prep.

*NOTE: Due to transport issues, we can no longer accept your full SDS-PAGE gel.

  1. Cut out the bands to be analyzed using the normal precautions to minimize keratin contamination.
  2. Place the bands in a small volume of water, PBS or 50mM ammonium bicarbonate buffer in a micro-centrifuge tube.

We offer SDS-Page protein separation as a service. If we perform this step, we will share the image of the gel with you prior to cutting bands to ensure that the appropriate band(s) are excised and analyzed. See pricing details.

SDS-PAGE Gel-band Handling Recommendations

Although nearly any SDS-PAGE system can be utilized upstream of an LC-MS analysis, DPMSR recommends Invitrogen’s NuPAGE Bis-Tris mini-gel system. A good general purpose gel covering a large MW range (6-200 kDa) is the 4-12% gradient gel (Cat. No NP0321) using MES running buffer. These pre-cast gels provide excellent resolution, fantastic staining sensitivity (10 ng BSA using colloidal blue staining kit, Cat. No. LC6025), and are highly compatible with downstream LC-MS analysis. Additional product information.

Important reminders to avoid keratin contamination:

  1. Any gel manipulation prior to trypsin digestion should be done in a BSC or laminar flow hood.
  2. Wear nitrile (not latex) gloves.
  3. Wear a lab coat and make sure there is no gap between your coat sleeve and the gloves (lab tape works well).
  4. Ensure that gels are cut against a clean glass plate (methanol rinse) using a new, methanol-cleaned scalpel or razor blade. Please cut as close to the margins of the band as possible, to avoid background contamination from the non-stained region of the gel.

Print friendly instructions for Sample Delivery

If you have questions about the use of this web-based submission application, please contact gcb-help@duke.edu.