Service Request and General Submission Guidelines

Submission Forms

Please review the guidelines for submitting samples (below) before submitting a sample form!

Online Sample Submission Form (PREFERRED) (either Large or Small Molecules)
Proteomics and Large Molecules Service Request Form (PDF)
Metabolomics, Lipidomics, and Small Molecules Service Request Form (PDF)

General Guidelines

  • Samples can include tissues, cells (pellets preferred), plasma/serum, other bodily fluids (e.g. urine, lavage, etc.), synthetic/synthesized compounds, environmental samples, and others
    • See Large Molecules FAQ for information on amount of each sample type that is preferred to submit for proteomics and intact analysis experiments
    • See Small Molecules FAQ for information on amount of each sample type that is preferred to submit for metabolomics and lipidomics experiments
    • The general rule of thumb is, "The more you can send, the better."
  • Samples that are radioactively labeled will NOT be accepted
  • Samples with pathogenic or harmful substances MUST be deactivated first before submitting
    • Contact a MSF staff member for acceptable methods of inactivation
  • Mass spectrometry is generally not compatible with high concentrations of salts, detergents, and other chemicals
    • If the sample is submitted with any salt or buffer, the amounts and concentrations should be indicated on the sample submission form
    • Detergents are generally not compatible with metabolomics or lipidomics analyses at all
  • Samples can NOT be processed unless submitted with an ISC#, FRS#, or credit card information

Preparing Samples

  • For protein identification experiments, it's best to purify the samples as much as possible for the sake of data quality
  • Samples should be collected or harvested all at one time, as quickly as possible, and should be kept on ice, refrigerated, and/or flash frozen by submerging in liquid nitrogen or freezing at -80°C
    • Freezing samples quickly is crucially important for the success of a metabolomics or lipidomics LCMS experiment
    • Cooling samples will slow and inactivate metabolic processes so that the metabolites and lipids reflect the state of metabolism of the samples at the time of collection
    • Failure to halt metabolism at the time of collection will alter the composition of metabolites and lipids so that the metabolic profile will no longer accurately reflect differences due to experimental sample groups but rather due to degradation and pathways responding to the effects of collection/harvesting
  • Below are suggested sample handling procedures based on the sample type:
    • Plasma/serum: after centrifuging blood to separate blood cells from plasma/serum, aliquot the plasma/serum into clearly labeled 1.5 mL or 2.0 mL microcentrifuge tubes and freeze at -80°C
    • Tissues: immediately following dissection, tissues should be flash frozen in liquid nitrogen into clearly marked tubes. They should then be transferred and stored into -80°C until ready to submit
      • Tip: we've seen great results for lipidomics and metabolomics when lyophilizing tissues after they've been frozen and then submitting the freeze-dried samples
    • Cells: cells (minimum of 1e6 cells) should be pelleted via centrifugation, then washed with PBS buffer. Cells are pelleted once more, remove the PBS supernatant, then freeze at -80°C until ready to submit

A note on batch effects

  • Batch effects occur when sets of samples are processed and analyzed separately but later the data is combined for a larger comparison
  • The data may show a separation of samples that is due to the time of processing rather than just by sample group conditions/treatments
  • These effects arise due to the accumulation of many small changes that occur from how samples were grown, acquired, processed, and to the subtle changes and differences in the LCMS system (e.g. mobile phase solvents, column age/wear, mass spectrometer status)
  • While we make every attempt to perform LCMS analyses the same each time to reduce batch effects, it is important to realize these effects can occur and affect the ability to compare samples
    • These effects are often greater the more time has elapsed between when sets of samples are processed and analyzed
  • To reduce and eliminate batch effects, it's best to submit all samples that will be compared against one another all at one time so that they are processed in the same manner and analyzed at the same time
    • For long term time course studies, it may be better to bank samples in the -80°C before processing and analyzing samples

Sample Submission

  • If shipping samples:
    • Frozen samples should be shipped on dry ice using overnight shipping (ideally shipped early in the week to avoid the weekend)
    • Samples containing IP beads in wash buffer for proteomics should be shipped on ice packs
  • If dropping off samples:
    • Bring frozen samples while still frozen on ice or on an ice block
  • Other considerations:
    • It is critical that samples remain frozen so that metabolites or lipids are not altered due to degradation or still active enzymes in the samples
    • For lipid samples, it is helpful to purge the headspace of sample tubes with nitrogen gas to prevent oxidation of lipids