Analysis of Post-translational Modifications by LC-MS/MS - LC-MS/MS in Proteomics: Methods and Applications - page 96

MS analysis ( 10 ) . Collision-induced dissociation (CID) remains
the fragmentation method of choice for most proteomic appli-
cations. However, CID results in preferential fragmentation of
the most facile bonds, and in the case of modified peptides, this
is often the covalent bond linking the modification to the pep-
tide backbone. Consequently, when peptides containing a PTM
undergo CID, neutral loss of the modification is often the most
abundant fragmentation product, leading to ambiguity in pin-
pointing the site of modification. Preferential loss of the PTM
is thought to be due to the large amount of energy transferred to
the analyte during collisional activation, which is randomized over
many vibrational degrees of freedom before dissociation takes
place. Vibrational dissipation of this excess translational energy
results in dissociation of the weakest bonds, often at the bulky side
chains containing the modification. Phosphopeptides are notori-
ously problematic in this regard. While CID has been invaluable
in characterizing sites of phosphorylation on specific proteins ( 11 )
and also in large-scale proteomic studies ( 12 , 13 ) , CID results pri-
marily in neutral loss of the phosphate group, observed as a loss
either of 80 Da (HPO 3 )orof98Da(H 3 PO 4 ,

-elimination)
( 14 ) . As the primary fragmentation pathway is loss of this phos-
phate moiety, the production of sequence-determining b- and y-
fragment ions may be limited, making sequence analysis of the
peptides difficult ( Fig. 5.2 ) . Unlike phosphorylated serine and
threonine residues, phosphorylated tyrosine residues are much
more stable to the neutral loss of H 3 PO 4 , simplifying identifi-
cation. While glycosylated and sulfated peptides also characteristi-
cally exhibit this loss of functional group following CID, it would
be incorrect to state that this is a universal issue for PTM anal-
ysis. Peptides containing many PTMs, including acetylation and
methylation, can also be readily characterized using CID ( 15 ) .
Alternate fragmentation mechanisms such as electron capture
and electron transfer dissociation (ECD and ETD, respectively)
do not promote analyte fragmentation by transfer of vibrational
energy, rather they enable radical-initiated bond cleavage follow-
ing the transfer of electrons ( Fig. 5.2 ) . Labile PTMs are there-
fore typically maintained on the peptide backbone ions during
fragmentation. Specific sites of modification, particularly glycosy-
lation and phosphorylation, can thus be more accurately identi-
fied using these alternate tandem MS strategies ( 16 - 19 ) . How-
ever, the utility of ETD decreases with a decrease in charge
state, with a shift toward non-dissociative electron transfer for
peptides with a precursor ion charge of less than 3, as is most
often generated by tryptic peptides. This results in an intact elec-
tron transfer product species, [M+2H] + • , and limited informa-
tive fragment ion generation ( 20 ) . The application of a short
burst of collisional dissociation after the ETD reaction, termed
ETcaD ( 20 ) (supplemental activation with CID post-ETD) or

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