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Peptide Synthesis > MALDI-MS
Peptides & MALDI-MS
Mass spectrometry of an aliquot of each peptide pool is routinely carried out on a
Micromass TofSpec SE mass spectrometer that is operated in positive ion mode and that is
equipped with a nitrogen laser (337 nm), a reflectron, delayed extraction and a post
acceleration detector. The reflectron and delayed extraction feature significantly
improves mass accuracy. Typically, 40 µl of the peptide pool is mixed with 200 µL of a
suspension of alpha-cyano-4-hydroxy cinnamic acid (CHCA) matrix and data are acquired
first in reflectron mode. Linear mode data are acquired also when multiple ions are
observed that may partially result from post source decay in the mass spectrometer (which
is possible only in reflectron mode) rather than from side products that are present in
the peptide pool. Data acquired in linear mode will provide an "average" mass
for the singly protonated species (MH+) that will reflect the natural abundance
of C12 and C13 isotopes. In contrast, data acquired in reflectron
mode will provide monoisotopic resolution below 2,000-2,500 Da and average masses above
this range. When monoisotopic resolution is achieved, the first peak in the cluster will
usually correspond to the MH+ species that contains only the C12
isotope and whose predicted mass will be the monoisotopic MH+ mass given on the
predicted mass tabulation sheet included in the peptide data package. MALDI-MS is carried
out routinely with external calibration which should provide an average mass error of less
than ±0.1%. If higher mass accuracy is needed, a 20 pmol or larger aliquot of the
reverse-phase desalted or purified peptide should be submitted to our mass spectrometry
section for ESMS analysis where mass accuracies of ±0.005% may be achieved for a 1000 Da
peptide. In this instance the
ESMS sample submission form should
specifically request a high mass accuracy determination. (More
Information on MALDI-MS)
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