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Sample Submission / Accurate Mass Verification

Before You Submit a Sample

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 que. IMSERC offers substantial discounts if samples are prepared properly. Please use the right solvents and concentrations to make your samples. Also 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.

Sample Submission Checklist

  1. Fill out the sample submission form through NUcore
  2. Label vials properly
  3. Use the correct right vials
  4. Prepare the correct concentrations and solvents
  5. Care for sensitive samples
  6. Handle of Mixtures, Proteins, and Other Types of Samples properly
  7. Know the Do's and Don'ts of Sample Subsmission
  8. General Submission Tips and Special Considerations
  9. Submit samples through NUcore
  10. Know where to get you data

  11. 1. Fill Out The Sample Submission Form

    The sample submission form must be completely filled in and contain information on solvent used as well as other appropriate solvents for the sample. NUcore sample submission instructions will help you navigate the submission process through NUcore. The staff uses this information to determine which analysis technique is most appropriate for your sample. There are 2 forms, one for single sample submission and one for sets of samples.

    The entire sample submission form must be completed to ensure the safety of lab personnel and timely return of data. Forms that do not clearly indicate sample location, appropriate solvents and safety information will be returned with no analysis performed, so they can be resubmitted with the appropriate data added.

    2. Proper Sample Labeling

    All samples must be clearly identified with a sample number which matches the submission sheet, the owners name and contact information. Mislabeled samples can lead to days of downtime due to clogging HPLC lines, fouling columns and contaminating instruments resulting in days of downtime to recover.

    3. Get The Right Vials

    Samples must be loaded in a 2 mL vial compatible with an Agilent 1100/1200 auto sampler. 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).

    4. 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 µM. Both samples must be loaded in a 2 mL vial compatible with an Agilent 1100/1200 auto sampler. 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). 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.

    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 µM and must be loaded in a 2 mL vial compatible with an Agilent 1100/1200 auto sampler. 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).

    5. Sensitive Samples

    Air, Time, and Temperature Sensitive:

    IMSERC staff will make every effort to return critical experiments quickly and will work with researchers to ensure sample degradation does not impact data quality. However, most staff run instrumentation requires significant startup times and are frequently used in multiple configurations. Therefore, “while you wait” analysis of samples should not be the expectation. If you require rush analysis for papers, presentations etc., contact staff members at least one business day before the sample will be ready. The staff member will arrange a mutually acceptable time when we will be available and have the instrument prepared for the sample. Consistent abuse of the rush sample will result in a minimum 1 hr additional staff charge to account for instrument setup and lost staff output. Air sensitive samples should be loaded in a 2mL vial under nitrogen. IMSERC has had the best success when the 2 mL vial is placed in another vial with the cap wrapped in parafilm. Usually, we will request two samples be provided to allow method development. Consult a staff member before submitting this type of sample for the first time to arrange a time to analyze the samples and design a protocol for your specific sample. Temperature sensitive samples can be stored in your lab (if LN2 temperatures are needed) or in the IMSERC refrigerator. Please note where the samples are located on the sample submission form.

    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.

    6. Mixtures, Proteins, and 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 and Contaminants

    Most mass spectrometry techniques detect materials in the µM 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.

    7. 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 (Less than 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 them and 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
    • Immediately cap solvents when not in use
    • 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.

    8. General Submission Tips and Special Considerations

    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.

    Contact IMSERC before submitting your sample for any special considerations, so that we may accomodate you as best we can.

      Special Considerations:
        Do you have more than 5 samples?
        Do you have air sensitive samples or sample that need special handling?
        Do you have time sensitive or Rush samples?

    9. Submit Samples... Where?

    Unless other arrangements have been made, all samples must be submitted both online in NUcore and submitting a hard copy in the “Sample Submission” box located in Tech BG70. A blue tray for your sample(s) is located near the entrace for room temperature samples, in front of the submission box. Addtional blue trays are kept in a refriegertor and freezer if needed, the freezer/fridge is located near the back of the MS lab in BG70.

    Submitting a Sample for Accurate Mass Verification in NUcore

    1. Set up and account in NUCore

      Please remember to follow NUcore sample submission instructions and request a NUcore account if needed, below.

      Account request for NU User
    2. Contact an IMSERC staff member

      Remember to please contact an IMSERC staff member before your initial submission to validate that your sample is suitable for mass spec analysis.

    3. Ship or drop off samples

      Ship or drop off samples in the MS lab (BG70) in IMSERC. Samples can be placed in the blue tray near the south entrace when entering the lab. For temperature sensitive compunds, samples may be placed in a blue tray stored in the refrigerator located at the back of the lab. If you store your samples here please indicate this on your sample submission form in the notes section.

      Please ensure you print your submission from NUcore when submitting your samples. You will typically be emailed/contacted within 2 business days with data or to set.

      Please consult a member from the mass spec team for analysis of large number of samples, when new method development is required, or if you need your data before a specified deadline, before submitting your samples.

      10. 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 be 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.