Mass Spec Services


One of the most powerful tools available to the mass spectrometrist is MS/MS. 

Whereas fragmentation is virtually absent in electrospray mass spectrometry, it can be

deliberately induced by MS/MS techniques. Tandem MS employs collision-induced

dissociation (CID) to fragment a precursor ion.  For a sample mixture (even after

chromatography, a mixture of different species can be present), the first quadrupole

mass analyzer (Q1 in the QSTART XL) generates a spectrum of ions. The ion of

interest is then selectively allowed to progress into the collision cell (Q2), containing an

inert gas typically argon, which is allowed to collide with the selected ion.  This induces

fragmentation, caused by collision-induced dissociation (CID) and the resulting ions are

then analyzed as product ions. Sequence as well as other structural information can be

derived from these fragments. Tandem MS/MS can be used to elucidate the structure

of a variety of small to medium sized molecules, including organic molecules, lipids and

fatty acids, peptides, carbohydrates, oligonucleotides, as well as DNA and RNA

adducts, etc.

In the past a few years, researchers have begun to use mass spectrometry to

determine peptide sequence. Improvements in machinery sensitivity as well as

software now allows for the confirmation of peptide sequence with virtual certainty. 

When fragmented, a series of ions are produced, termed a, b, and c ions for those with

N-terminal charge and termed x, y and z ions for those fragments with C-terminal

charge.  The b and y ions are the ions generated when the fragments are due to the

cleavage at the peptide bond, whereas the a, c, x, and z ions are generated when

cleavages occur on the N-terminal side of the peptide bond carbon (a and x) C-terminal

side of the peptide bond amine (c and z).  These ions are then matched up with known

amino acids and amino acid fragments, and the mass difference between consecutive

ions reveals the identities of the consecutive amino acids.  From this map, an accurate

peptide sequence can be determined.

The QSTART XL is so accurate in determining mass of the various CID fragments, that

with the exception of leucine and isoleucine, two amino acids with identical molecular

weights, all other amino acids can be differentiated.  Even glutamine, with a mass of

128.0586 and lysine, with a mass of 128.0950, can be differentiated.  Similarly, various

amino acid modifications can be determined due to the gentle nature of ESI (versus

MALDI, which tends to remove some modifications, such as phosphates).  These

include phosphorylation, glycosylation, acylation, nitronation, and many others.


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