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Mass Spectrometry
 

FREQUENTLY ASKED QUESTIONS

What type of samples can the MALDI analyze? (top)
Peptides - Proteins - DNA - RNA - polymers - small molecules.

What should the sample concentration be? (top)
Peptide (500Da - 5000Da) = 10pmol/ul
Peptides/Protein (5kD- 25kD) = 25pmol/ul
Protein (25kD - 100kD) = 100pmol/ul
DNA (500Da - 5000Da) = 10pmol/ul
DNA (>5000Da) = 100pmol/ul

These are guidelines!!! Excessive concentration can overwhelm the matrix resulting in poor or no ionization of the sample. A volume of 10ul is generally enough for analysis.

What solvents are acceptable/unacceptable ? (top)
For MALDI, ionization of the sample is key. Excess sample AND solvents can inhibit ionization. The cleaner the sample the more likely it will ionize and be detected. Acceptable solvents are water, ACN, TFA, and other volatile solvents. Most buffers and buffer concentrations are acceptable. Excessively strong solvents should be diluted or removed with a ziptip. Unacceptable solvents are any that could inhibit ionization, including DMSO, UREA, glycerol. If you have any questions please review our sample submission page for more information or contact us.

What is a ziptip? (top)
A Ziptip is a bed of chromatography media (C18 or C4) fixed at the end of a pipet tip. It is used to clean and/or concentrate a sample. Please go to Millipore's website for more information - http://www.millipore.com/catalogue/module.do?id=C5737

Is MALDI quantitative? (top)
No, unfortunately, MALDI is not quantitative. The signal strength of a peak is a reflection of how well an analyte has ionized.

What is the difference between linear and reflector modes? (top)
In "linear mode" the average of an analyte's isotopes are averaged into one peak. The error rate in linear mode is ~0.1%. The mass range for linear mode is ~500Da - 100kDa. Linear mode is the default mode at PAN.
In "reflector mode" an analyte's individual isotopes are resolved (a monoisotope peak can be observed). The error rate in reflector mode is 0.01%. The mass range for reflector mode is ~500Da - 3000Da. Analysis in reflector mode are performed when requested.

What are the extra peaks on the mass spectrogram? (top)
Adduct peaks are very common and unavoidable in MALDI mass spec, the most common adduct peaks are the Na+(sodium = 22Da) and K+(potassium = 39Da). There are trace amounts of these molecules in everything and can never be entirely removed. The peaks are not an indication of impurity, nor should they be confused with an incorrect molecular weight.

Also, a peak that is half the MW of the M=H= is the doubly charged species of the molecule, and a peak that is twice the MW of the M+H+ is the dimer of the molecules. For more information review our sample submission page or contact us.

What format will my spectrogram come in? (top)
PDF's of the mass spec data will be emailed to you. Typically, two .pdfs for one sample provided. One .pdf will be the "full" range view of the spectrogram, and the second .pdf will be a "detailed" (zoomed in) view of the region of interest. If you would like the x-y plot also please mention that in the comments section of the order form.

What is the turn-around time? (top)
Typically, results are emailed within 72hours. Difficult to analyze samples or a large submissions may take longer.

How do I submit a sample? (top)
First, enter a mass spec order online at pan.stanford.edu. Samples and order forms can be dropped off at PAN Facility located at in the Beckman Center, B065.

Can you identify my protein? (top)
Protein identification is a service we provide under the "Protein Analytical - Mass Mapping" section. Please contact Dick Winant for more information.

Why can't I access the online "Order" page?
The server might be down. Please contact us right away if you are having any problems logging into our website. If you are trying to submit an order you can print out our Mass Spec Request Form (word or pdf) and submit this form with your samples, and we will enter the information into our database for you.