Sample Preparation

Sample preapration is crucial for obtaining good results in mass spectrometry.  There are several general factors namely, purity, concentration, salt content, solvent used and the nature of compound.  Below, please find the guidelines to different services.

Call us at (617) 384-9585 if you have any questions regarding sample preparation.  As a rule of thumb, avoid the use of detergents (especially non-ionic detergents), nonvolatile salts, TFA (>0.10%) and other additives.  A table of salts and buffers which are incompatible with mass spectrometry and their levels is downloadable below.  If salts must be used, stick with a volatile salt like 10 mM ammonium acetate. If you have salts/TFA in your hydrophobic sample, a customized LC-MS method can be developed that diverts salts to waste for the first 2 minutes.  We recommend a ZiptipTM cleanup for hydrophobic samples prior to analysis.  Some samples like oligonucleotides are particularly susceptible to salt interference and must be thoroughly desalted prior to analysis with techniques like MALDI-TOF MS.

Fee For Service

sample preparation


General Information

Each sample MUST be submitted with a submission sheet with all fields filled out.  Unless otherwise requested, all samples will be carried out by ESI before other ionization techniques will be performed.  Users wishing to submit for MALDI analysis should consult the laboratory personnel before submitting samples.  If you have a sensitive compound (air/moisture etc), please consult the laboratory staff to schedule an appointment.  Please call us at (617) 384-9585 if you have any questions about the process and we will be happy to help you.

Submission Sheets 

To assist our personnel optimizing experimental conditions, proposed compound structure should be provided.  An internal and an external form are available.  For those have a Harvard 33 digit billing code, please use the internal form.  All others should use the external form.  Forms can be found here:  Forms  

Submission Process
  • There is one "In" tray, located on top of the mailboxes against the wall as you enter the facility. 
  • Sample vials may be taped to the sheets (if stable in room temp.) or placed in the tray on the top shelf in the fridge next to the mailboxes. 
  • All samples MUST be labeled. 
  • Samples should be submitted and fully-dissolved (in suitable solvents) in chromatography auto-injector vials (available in the stockroom) at an appropriate concentration (~0.1 mg/mL). 
  • Partial solubility is not acceptable. 
  • Solid sample placed in vials may be submitted ONLY if the sample is not stable in liquid solvents and please identify a solvent that will dissolve your sample completely on the submission sheet.

 

sampleprep

 

Open Access

SAMPLE PREPARATION

General Information

Four instruments are available for Open Access use:
  • Agilent 6210 Time-of-Flight LC/MS
  • Agilent 6890 GC/MS
  • Waters Micro Mx MALDI-TOF 
  • Agilent 1200 HPLC with DAD

Open Access (OA) provides a "Do It Yourself" mechanism for users to acquire mass spectra. Sample information is entered into a login Interface by the user. For LC-MS, samples are prepared in auto injector vials and placed in the instrument's auto injector rack as instructed by the login system. Data are printed out after each sample has been analyzed. You can also log in a batch of samples.  Samples must be in solution and in a volatile solvent for ESI or MALDI ionization.  The solvent system used on the open access HPLC is water and acetonitrile.  If your analyte does not stay in solution under these conditins, please consult with us.

No more than tens of picomoles of sample should enter the instrument. It should be ensured that there is absolutely no particulate/undissolved matter in the sample, so as not to clog the autosampler and other tubing, including the ESI spray needle. Please make sure that your concentration is not too high.  This will produce a number of problems including producing poor signal and poor mass accuracy.  On the ESI-TOF, for example, concentration higher than about 10 μM will start saturating the detector producing a broad peak and poor mass accuracy.  In addition, you will form non-covalent dimers and trimers if the concentration is high, instead of the typical molecular ion.  These are all reasons to stay within the recommended concentration range.

  • You may contaminate the ion source of the instrument.
  • To discourage overloading, a service charge will be applied to your account if the instrument needs to be cleaned because of high concentration used in your sample.  Signal in mass spectrometry is concentration dependent, and thus depends on the molecular weight (g/mole) of your analyte. However, as a rule of thumb, please keep your concentration around 10-20 μM.  This corresponds to 0.01 mg/ml for a molecule of 500 g/mole molecular weight.
  • For protein samples (yes we run accurate mass on proteins  beteen 8 kDa-67 kDa!), please have the protein in solution and at a concentration of approximately 10-20 μM.
  • Make sure that there are no non-ionic detergents in the samples such as TWEEN, Thesit, Triton-X etc.  These contain polyethylene glycol which causes strong interference through the abundant formation of ions for all the polymeric ions.
  • If your samples are in an organic solvent like chloroform, methanol or acetonitrile, be sure to avoid the use of plastics since these contain plasticizers which also cause high background problems.