Skip to main content Skip to secondary navigation
Pro tip

How to get in touch with the SUMS experts

Have a question about a potential mass spec project?
Not sure exactly who to talk with at SUMS?

fill out this form and a SUMS scientist will reach out to you

Sample Preparation & Autosampler Vials for ESI-MS

Main content start

Guidelines for sample preparation:


  1. Use appropriate solvents for the ESI-MS system. 
    a.  Appropriate solvents include:
         •  Acetonitrile
         •  Methanol
         •  Water

       b.  If your compound is not sufficiently soluble in one of the above, you can first dissolve it in DMSO, but you must dilute the DMSO to 0.1%
            or less in the sample you run.  Samples for loop injection can be dissolved first in acetone or chloroform then diluted at least 1:20 in

       c.  Appropriate modifiers include volatile organic acids and buffers at 1% concentration or less
            •  Acetic acid
•  Formic acid
•  TFA (trifluoroacetic acid)
•  Ammonium acetate

       d.  If your sample solution contains a high percent organic, use caution when running LC-MS methods.  A large volume (>5uL) of injected
            sample containing mostly organic solvent may result in:
            •  Column breakthough, where the sample elutes undetected in the solvent front.  Lower injection volumes may allow sufficient mixing
                 of the sample with the mobile phase, but take care to avoid
            •  Sample or buffer precipitation, where when any sample component is not soluble in the initial mobile phase composition.

       e.  Never use mineral acids like HCl or sulfuric acid which can damage stainless steel instrument components.

       f.  Avoid detergents which can suppress ionization of your sample

       g.  Avoid non-volatile buffers like sodium phosphate which can suppress ionization and clog the electrospray source.

 2.   Ensure your samples are completely in solution, and that they will not precipitate out under the analysis conditions.  Note that the
       autosampler chamber is chilled, approx. 5°C.

 3.   Use appropriate concentrations for the LC-MS system

If none of the options listed above will work for your sample, please talk with Allis or Theresa.  Inappropriate solvents or modifiers can damage the physical components of the LC-MS system, resulting is system downtime and expensive repairs.

Autosampler vials
Purpose Description Unit Manufacturer Manufacturer P/N VWR P/N
General use – vials & caps Glass 2 mL clear vials with write-on spot, PTFE/silicone septa, blue caps Pk 100 Agilent 5182-0865  
Limited sample volume (<300 uL) vials  Polypropylene limited volume vials, narrow opening   Pk 100 National Scientific C4013-11 66030-982
Limited sample volume (<300 uL) – caps Caps for narrow opening vials (8-425) Pk 100 National Scientific C4013-60A 66030-420

Critical alerts regarding autosampler vials:

*Do NOT use limited volume vial inserts in the ESI-MS instrument!  These will physically damage the autosampler, resulting in a service call and days of instrument downtime.

*Do NOT reuse autosampler vials!  Used septa are prone to coring and bits of the septa get lodged in the flow path, blocking the flow and rendering the instrument unusable.  The cents per vial that are saved are not worth the damage to the instrument and the aggravation caused to all who use and maintain the instrument.  (Not to mention the contamination risk to your experiments and data integrity!) 

Because these issues are entirely preventable and traceable, repair costs for repeat incidents, approximately $400, will be charged to the user responsible.