MS Sample Submission

Mass Spectrometry Services Offered



Steps for Starting Projects

  1. Set up and account in NUCORE:nu-users-account       external-users-account
  2. Contact an IMSERC staff member before initial submission to validate that your sample is amenable to analysis by mass spectrometry and verify sample preparation protocol. If this is the first time your group is performing MS, start a new project with IMSERC.                                                                                                                                                                                                                      click-here-to-begin-a-project
  3. For accurate mass analysis, read instructions on sample preapartion, prepare samples and submit in through NUCORE. Verify that you receive a confirmation email when submitting samples to ensure that your sample is tracked.                                                                                                                                                                                                                                              hrms-submission
  4. Ship or drop off samples in the MS lab in IMSERC. You will typically be contacted within 2 business days with data or to set a schedule with you for analysis.


Sample Submission for Accurate Mass / Formula Determination:

Accurate mass analysis (typical accuracy within 0.003 Da vs theoretical value) is typically performed by an IMSERC staff member. IMSERC is able to perform accurate mass analysis using a wide variety of ionization techniques which include ESI, APCI, APPI, LIFTI, EI and MALDI. IMSERC’s mission is to perform onsite analysis for all molecular compounds synthesized in the department and makes this service available to outside users as well. Stable compounds are usually processed in order received and initial data returned within 2 business days. Customers with air or time sensitive samples should contact an IMSERC staff member before proceeding. External customers must receive approval before shipping samples to IMSERC or the package will be returned unopened. Depending on ionization technique, users will receive a 3 part report containing a full representative spectrum of the compound, a computer generated list of likely formulas for the monoisotopic peak (i.e. formula match) and either a zoomed in spectrum showing isotopic distribution (soft ionization technique) or fragmentation (hard ionization techniques). Customers requesting purity analysis and chromatographic separation should request purity analysis of sample using LC/UV/MS or GCMS.

Neat samples can be submitted for analysis which are prepared by IMSERC staff. An additional charge will be included for this time. Users who prepare samples using the IMSERC approved protocol receive a 50% discount vs neat samples. Customers with more than 5 samples should contact IMSERC staff before submitting as groups of 5, or more, samples that can run in a single batch will be analyzed at an additionally discounted rate. For more information on sample preparation protocols, click here.


Before Submitting Samples

Please read the instructions carefully. If you have never submitted samples for analysis by mass spectrometry, please discuss your experiment with a staff member before preparing and submitting your sample. Your sample history and the goal of the measurement will determine what preparation and analysis is required to support your research goals. Also, if you intend to submit large numbers of samples, more than 5 at a time, please discuss this with us so we can arrange a time to accommodate them in the sample queue. IMSERC offers substantial discounts if samples are prepared properly. Please use the right solvents and concentrations to make your samples. Please make sure to discuss with us if you have “problem” solvents (DMSO, DMF) or if you have samples which have salts, TFA, or other species that could affect ionization or the GC or LC column performance.

Samples are typically analyzed in first in, first out (FIFO) mode. However, each instrument performs multiple ionization techniques and must be reconfigured for each technique. Samples will be batched with like samples to avoid excessive reconfiguration times. Users must consult with staff members in advance to ensure that the instrument is in the proper configuration and calibrated when analyzing time sensitive samples. If you have Air Sensitive, Time sensitive or other special handling samples please discuss it with us before submitting.

You may also look at the ionization techniques and instruments available to see if you can analyze your samples yourself, and to familiarize yourself with the techniques.


Sensitive Samples:

For sensitive samples see an IMSERC Staff member 2 days prior to submission.


Intellectual Property issues:

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.


Steps to submit samples:

1) PLEASE read all the instructions carefully (especially solvent and concentration info)

2) Get Sample Submission Form

3) Get the right Vials

4) Use the Right concentration and Solvents

5) Label Samples properly

6) Submit with Form

7) Know where to get your data

8) Questions? Want to Contact MS Staff?


Sample 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. For accurate mass analysis fill out the sample submission form and submit the labeled vials on the table across from the X-ray office. There are two types of Sample Submission Forms, one for single samples and one for multiple samples. Please see the instructions on how to fill out and e-mail these forms to the IMSERC staff. First time users should always contact a staff person to determine the best method to submit samples to avoid multiple preparations of samples. Users with multiple samples (more than 5) should validate the preparation procedure on a single sample first and then prepare other samples. Multiple samples that are properly prepared also receive a substantial discount in price. Please see the sample prep instructions below for the proper procedures to ensure quality data.


Get the Right Vials!

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). The Vials are also available in the VWR “stock Room” in Tech building. If sample volume is an issue, 100 μL 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

LCMS Sample Prep (ESI, APCI, APPI) 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 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.


Sample Prep for GCT (GC/MS or Direct Probe EI, CI, FI) Sample prep is similar to LCMS prep For ESI, APCI, APPI. 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 and 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).


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.


Appropriate Solvents, Additives & Contaminants
Most mass spectrometry techniques detect materials in the μM to nM level. 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 ;


  • 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 samples, or if you there are 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.

Final checklist: Did You … ……   .. ?

1) Get Sample Submission Form

2) Get the Right Vials

3) Use the Right Concentration and Solvents

4) Labels Samples properly

5) Submit with Form

6) Know where to get your data