Accurate Mass Sample Submission

Sample Preparation and Submission Protocols


Sensitive Samples:

For time and air sensitive samples see an IMSERC Staff member 2 days prior to submission.  We will make sure instrumentation is configured to analyze your sample immediately.

Intellectual Property Concerns:

In cases where intellectual property is a concern, users may either submit samples in an envelope or may email the sample submission form to a staff member and tape the samples to a submission form with only the submitter’s name on the form.

General Submission tips

If you have not submitted a sample before, consult an IMSERC staff member first. In general, IMSERC is equipped to handle either neat purified compounds or purified compounds in solution. Neat samples may require additional processing, at increased cost, but are the safest method to submit samples for very infrequent users. IMSERC staff must know the identity of likely contaminants to successfully analyze samples. IMSERC staff will frequently request neat samples if the first attempt fails. After discussing your sample with a staff member, follow the instructions for the appropriate ionization technique. A neat sample can always be submitted as a backup sample.

NUCORE Submission Form / Sample Labeling

In the cases where accurate mass is required for publication or staff assistance is needed for analysis, samples should be submitted to IMSERC staff through NUCORE.  IMSERC staff can help the first time you complete a form, or you can view a short demo here.

Samples must be loaded  in a 2 mL vial compatible with an Agilent 1100/1200 autosampler.  Vials  should be filled between 0.5mL and 1mL. Example part numbers are Agilent 5182-0714(vial) and 5182-0718(cap).    If sample volume is an issue, 100 uL inserts (Agilent part #5183-2089) can be purchased. Amber vials are also available for light sensitive samples (Agilent part #5188-6536)

Correct Concentration and Solvents

Submit two samples. The first sample should be preferably neat or relatively concentrated (~1mg/mL). The second sample should be  diluted to ~1-10 uM. Both samples must be loaded in a 2 mL vial compatible with  an Agilent 1100/1200 autosampler.  Vials should be filled between 0.5mL  and 1mL. Example part numbers are Agilent 5182-0714 (vial) and 5182-0717 (cap). Amber vials are available for light sensitive samples (Agilent part #5188-6536). The  approximate fill level is shown in the picture below:

Users  who do submit samples in this manner receive the regular discounted rate for  sample analysis and will receive much faster turn-around times. The  samples not submitted in this manner which require dilution by staff get a  surcharge.  Improperly labeled samples will not be analyzed.


Mixtures, Proteins, other types of samples:   IMSERC can provide  assistance with purifying samples for analysis, analysis of complex mixtures  and determination of protein molecular weight. IMSERC is not in general equipped  to handle biological hazardous or radioactive materials, even though some  extracts maybe OK.  Please consult a MS staff member or the director when these types of analyses are required.

AppropriateSolvents, Additives &  Contaminants
Most mass spectrometry techniques detect materials in the uM to nM  levels.  In addition, as little as 0.1% addition of some salts, triflouroacetic acid  (TFA) or detergents can suppress the signal in the mass  spectrometers.


Organic solvents leach plasticizers and  glues from plastic bottles and lids.  Organic solvents should be  stored in glass containers.  Water can leach ions (sodium, calcium and  potassium) from glass containers.  Amber containers preserve UV sensitive  samples and prevent growth in solvents.  Always store aqueous solutions in  polyethylene containers.

“Do’s and Don’ts:”

In order to prevent  contamination and consistently obtain high quality data, adhere to the  following Do’s and Don’ts ; Do:

  • Use only HPLC grade solvents
  • Transfer solvents from large containers to smaller containers (<100 mL) to limit impacts of contamination events
  • Use only new, clean pipette tips when transferring solvents.  Use separate pipettes to transfer concentrated samples.
  • Immediately cap solvents when not in use
  • Store organics in glass containers and water in plastic containers
  • Rinse / Rinse / Rinse
    • syringes before storing
    • Glassware before transferring solvents


  • Ever put anything but a clean pipette in HPLC grade solvent container
  • Return solvents to an HPLC grade solvent container
  • Use a sample container with a lid liner which is glued in place.  Solvents leach glues and cause  contamination of the instruments
  • Take samples from deuterated solvents, especially if samples contain exchangeable protons.
  • Submit samples in DMF or DMSO.  These solvents dissolve the HPLC tubing which then must be replaced.

Polar LC MS samples  should typically be submitted in MeOH or Water/ Acetonitrile mixtures. Non-polar samples can frequently be dissolved in a small amount of chloroform  or dichloromethane and then diluted in solvents such as MeOH.  Samples  that react with water or MeOH can be submitted in pure acetonitrile or  dichloromethane. Most LCMS samples are  analyzed using a MeOH/water mixture with a small amount of formic acid to protonate samples.  If your sample is water or acid sensitive, it is important to notify the staff on the sample submission form or spurious results  will be returned.

Submit samples—Where?

Unless other arrangements have been made, all samples must be  submitted in the “Sample Submission” box  on the table in BG70. 

Where to get your data?

Data can be returned by  paper copy or emailed as a pdf. Users may elect to have remainder  of the sample returned-please let the staff know ahead of time if you have  limited amount of sample, or samples that you need returned.  Paper  reports and samples will discarded after two weeks if not picked up. All Data is also backed up on the server as per the data  from user-run instruments.