Sample Submission Policies

Please reach out to eipc@emory.edu to set up your initial consultation. See below for service-specific guidelines.

  • Sample submission form (provided during the initial consultation) - Fill out the form at least a day before sample submission.
  • PPMS account - Open an account in PPMS if you don't have one. Submit a project; once the project is approved, your order will be submitted by the core personnel.
  • Use 1.5 mL low protein binding tubes whenever possible. 
  • Label tubes with number (1, 2, 3....) and your initial. Write the corresponding sample names on the submission form.
  • For projects with replicates, it is best practice not to batch samples by conditions (e.g., condition 1, 1, 1,..........condition n, n, n, etc.). Randomize the samples and label the tubes in the mass spectrometry run order.
  • Do not use stickers on the tubes (especially on the side).

  • How much protein is needed?
    • For in-gel digestion, the band should be visible after Coomassie blue staining.
  • Sample storage:
    • After destaining, gel slices should be stored at 4 C.
  • Shipping instruction:
    • Gel slices should be sent with 10 µL ultrapure water with cold pack in an Eppendorf tube. Please make sure to close the tubes tightly and secure them with parafilm (to prevent from drying).
  • Special instruction:
    • For in-gel digestion, pretreat samples with DTT/IAA if that step does not interfere with the chemistry of your protein (see below). Stain gel with Coomassie G-250.
    • Take an image of the gel and mark the band that will be submitted for mass spectrometry. For running complex mixture of proteins, such as cell lysate, please see this example.
    • Gradient gels are not recommended, 10% gel should work for most samples.

Reduction & Alkylation Protocol

  1. Add loading dye/sample buffer (w/o BME) to your protein solution along with dithiothreitol (DTT; 5 mM final conc in the protein mix). Boil the sample for 5 min and let it cool down to room temp.
  2. Add iodoacetamide (IAA) (25 mM final conc) and incubate for 30 min at room temp in the dark (preferably in a rotor).
  3. Centrifuge samples for 1 min at the highest speed of your centrifuge and load the supernatant on the gel.
  4. Stain the gel with Coomassie G-250 staining solution.
  5. If required, save the gel bands with 10 µL ultrapure water at 4 C in an Eppendorf tube.

  • How much protein is needed?
    • To identify a purified protein, we require at least 10 pmol of the protein.
  • Sample storage:
    • Protein solutions should be stored at -20 C.
  • Shipping instruction:
    • Protein solutions should be sent with dry ice in an Eppendorf tube. Please make sure to close the tubes tightly and secure them with parafilm (to prevent spill).
  • Special instruction:
    • For protein samples in solution, list the composition of the buffer in the sample submission form. Avoid using detergent or high salt in the buffer.

  • How much protein is needed?
    • To determine post-translational modifications, we require up to 1 µg of purified protein depending on the abundance of the modification.
    • We can routinely determine PTMs such as phosphorylation, ubiquitination, methylation, acetylation, Met/Cys(S-oxidation), etc. Detection of other modifications may be possible.
    • EIPC currently offers phosphopeptide enrichment at an additional cost. Please consult us to learn more.
  • Shipping instruction:
    • Depends on the type of the sample, please discuss with us.

  • How much protein is needed?
    • To characterize an interactome, you should typically start with 5-10 mg lysate.
    • For streptavidin pulldown, 2 mg lysate is often sufficient.
  • Sample storage:
    • After IP/pulldown experiment, the beads should be stored at -20 C in PBS.
  • Shipping instruction:
    • Beads should be sent with dry ice in Eppendorf tubes. Please make sure to close the tubes tightly and secure them with parafilm (to prevent from drying). It is best to send the tubes in upright position in a cardboard box (to avoid beads from spreading all over the tubes).
  • Special instruction:
    • Include a negative control sample to assess the non-specific binding to the IP beads. This will be the first sample of the batch.
    • Load equal amount of protein for the negative control and the experimental samples.
    • Please follow the protocol below to prepare IP samples for mass spectrometry:

IP/Pulldown Sample Preparation Protocol

  1. When performing the pull-down assay, please wash beads with PBS 3 times after the regular IP wash. Samples with detergent are not mass spec compatible.
  2. Please stop after the wash step, do not elute your proteins of interest.
  3. Take out 10% of the beads and boil with SDS gel loading/sample buffer to elute proteins - Run western blot (use 1/3 of the supernatant) to confirm your IP and a Coomassie stained gel (use 2/3 of the supernatant) to assess the amount of protein in the pull down. Send both images before sample submission; samples will not be accepted without the Coomassie gel image (See the example).
  4. Save the remaining beads at -20 C in ~50 µL PBS while running the western blot.
  5. Send us the beads and we will prepare the samples for the mass spectrometry.

  • How much protein is needed?
    • For label free quantification, we typically require 100-150 µg of cell lysate (Lysis will be done in the core facility). 
    • Usually 3-5 million cells is sufficient (Please discuss if you have fewer cells).
  • Sample storage:
    • Cell pellets should be stored at -80 C. Please bring samples on dry ice in a cardboard freezer box with your name and the date of submission on the side of the box.
  • Shipping instruction:
    • Cell pellets should be sent with dry ice in Eppendorf tubes. Please make sure to close the tubes tightly.
  • Special instruction:
    • For cell pellets, wash cells with cold PBS to remove the serum-containing media and cell debris. Aspirate as much of residual PBS out as possible and flash freeze.
    • Always use 1.5 mL tubes; do not bring cell pellets in 15 mL or 50 mL tubes. 

  • How much protein is needed?
    • For label free quantification, we typically require 100-150 µg of tissue lysate (Lysis will be done in the core facility). 
    • Usually 50-100 mg tissue is suffiecient (Please discuss if you have less tissue).
  • Sample storage:
    • Tissue samples should be stored at -80 C. Please bring samples on dry ice in a cardboard freezer box with your name and the date of submission on the side of the box.
  • Shipping instruction:
    • Tissue samples should be sent with dry ice preferably in RINO tubes (or Eppendorf tubes). Please make sure to close the tubes tightly.
  • Special instruction:
    • For tissue samples, weigh the tissue and always work on dry ice to protect them from thawing.
    • We would supply the RINO tubes for Emory users, but encourage external users to purchase these tubes. If you are using RINO tubes, always label the cap.

  • How much protein is needed?
    • For label free quantification, we require at least 50 µg of protein (Please discuss if you have less amount). 
  • Sample storage:
    • Cell media samples should be stored at -80 C. Please bring samples on dry ice in a cardboard freezer box with your name and the date of submission on the side of the box.
  • Shipping instruction:
    • Media samples should be sent with dry ice in Eppendorf tubes. Please make sure to close the tubes tightly and secure them with parafilm (to prevent spill).
  • Special instruction:
    • For analysis with cell culture media, use serum-free (or very low serum) and phenol-red free media. Concentrate the media ~25-fold.

  • How much protein is needed?
    • Usually 50 uL volume is suffiecient for plasma or serum (Please discuss if you are bringing CSF).
  • Sample storage:
    • Biofluid samples should be stored at -80 C. Please bring samples on dry ice in a cardboard freezer box with your name and the date of submission on the side of the box.
  • Shipping instruction:
    • Biofluid samples should be sent with dry ice in Eppendorf tubes. Please make sure to close the tubes tightly and secure them with parafilm (to prevent spill).
  • Special instruction:
    • For biofluids, aliquot samples according to the volume needed by EIPC. Usually, top 14 removal columns will be added to your order at an additional cost.