Example   Cautions and Notes   References

General Information
The convention for naming ion types is diagrammed below, Figure 1. The sequence of the oligonucleotide is written 5' -> 3'. This example oligo has an "HO-" 5' terminal group and a "-p" 3' terminal group. The most useful ion series for sequence determinations are w, y, and a-B.

Figure 1. Common Ion Types (Ref. 1)

The relationship of a, w; b, x; c, y; and d, z complimentary ion pairs is shown in Figure 2.

Figure 2. Ion Types (Ref. 2)

Here are some sequence specific issues:

• If the example oligo was specified with an "HO-" 5' terminal group and an "-OH" 3' terminal group, the b₄ fragment wouldn't be possible.
• In ion types a-d the 5' end is left as a charged ion sequence that is observed. For ion types w-z, the 3' end nucleotides are observed, up to the fragmentation site.
• For a 3' terminal "-OH" oligo, the y₁ ion would probably be missing, since there would be no phospate that would be easily ionized. Likewise, for a 5' terminal "HO-" oligo, the b₁ ion would probably be missing. If these ions are present, a proton would need to be removed from some other part of the nucleotide.

The following table shows how the various ions are listed in the output. The ion is listed for a single nucleotide with Z=1, but longer oligonucleotides and charges greater than one are shown similarly. The a-d ions are assumed to have a "HO-" 5' terminus, and the w-z ions are assumed to have a "-OH" 3' terminus.

Table 1. Ion Type Designations: (Monoisotopic mass)

Ion Type	Sequence	M/Z
M	HO-A-OH(-H+)	250.0940
a	HO-A-(-H+)	234.0991
a-B	HO-A-pf(-H+)	410.0865
b	HO-A-O(-H+)	250.0940
c	HO-A-HPO3(-H+)	314.0654
d	HO-A-p(-H+)	330.0603
d-H2O	HO-A-c(-H+)	312.0497
w	p-A-OH(-H+)	330.0603
w-H2O	c-A-OH(-H+)	312.0497
y	O-A-OH(-H+)	250.0940
z	-A-OH(-H+)	234.0991

• Alternatively, if the a ion came from a oligo that had a "p-" terminus, the ion would be listed as p-A-(-H+) and the m/z would be correspondingly greater. Similar corresponding changes would also be made for "p-" terminal b-d ions and "-p" terminal w-z ions.
• The c- indicates a cyclic phosphate with a corresponding additional mass loss -H₂O.
• The f- indicates a furanose terminal group for the a-B ions:

Some common ions of mononucleotides are given below. This style of ion names is used in some publications.

Table 2. Deoxy-Mononucleotide Ions: ( Monoisotopic mass)

base	N	pN	pN>p	pNp

These ions correspond to the nomenclature in Figure 1 as follows:

Table 3. Mononucleotide Ion Correspondence:

terminus	N	pN	pN>p	pNp
HO- 5'	b: HO-A-O(-H+)
-OH 3'	y: O-A-OH(-H+)
p- 5'		b: p-A-O(-H+)	d-H2O: p-A-c(-H+)	d: p-A-p(-H+)
-p 3'		y: O-A-p(-H+)	w-H2O: c-A-p(-H+)	w: p-A-p(-H+)

Reference to Table 1 shows that some ion types have equal m/z depending on the terminal groups. For example, in Table 1 the 5' and 3' termini are "HO-" and "-OH" respectively. So the d and w ions have the same mass and the b and y ions have the same mass. Other combinations of terminal groups give other ion equivalences.

Table 4. Ion Equivalences:

Terminal
5' \\ 3'	-OH	-p
HO-	d = w b = y	d = y a-B = w
p-	b = w	d = w b = y

For calculations of the m/z for electrospray series and ms/ms fragment ions for a known sequence use the The Nucleic Acids Mass Spec Toolbox at the University of Utah. These Web applets are very helpful in assigning peaks. The McCloskey (Ref. 1) and Murray (Ref. 2) papers are excellent introductions to spectral interpretation and are the source for the information on this help page.

Example: m/z=481.6
Set the oligo type to DNA and the 5' and 3' terminal groups to HO- and -OH, respectively. Choose "no" ion exchange. In other words, the program will not search for m/z values where Na⁺ or K⁺ ions are substituted for H⁺. Choose a maximum charge state of -1. Enter 481.6 into the Target ion m/z dialog box. Choose an uncertainty of 0.1 and press search. No results should be listed. Now switch the maximum charge state to -2 and press search again. Two possibilities should be listed, the a-B ion for CCC and the w ion for CGG. If you click on one of the entries, the isotope distribution will be plotted for that ion.

Program Notes

• In the example above one of the ions was listed as CGG. The program cannot determine the order of these bases. The true sequence could be CGG, GCG, or GGC. The results are always listed alphabetically with no implied sequence order.
• A maximum of 24 hits can be displayed. If your search produces more than 24 hits, try narrowing the m/z uncertainty, decreasing the maximum charge state, or choosing "no" ion exchange.

References:
(1) J. Ni, S. C. Pomerantz, J. Rozenski, Y. Zhang, J. A. McCloskey, "Interpretation of Oligonucleotide Mass Spectra for Determination of Sequence Using Electrospray Ionization and Tandem Mass Spectrometry,", Anal. Chem., 1996, 68(13), 1989-1999.

(2) K. K. Murray, "DNA Sequencing by Mass Spectrometry," J. Mass Spec., 1996, 31, 1203-1215.