Patent ID: 7247434

Claim:
A method comprising: (a) providing nucleic acid fragments, each fragment having cleavably attached thereto a mass tag; (b) separating the tagged fragments on the basis of fragment charge, sequential length, size or shape; (c) placing a charge on the tag and cleaving the tag from the fragment, where the charge is placed on the tag prior to, during, or after cleaving the tag from the fragment; and (d) characterizing each tag by mass spectrometry, wherein at least one tagged nucleic acid fragment is a compound of the formula: T ms -L-X wherein, T ms is an organic group detectable by mass spectrometry, comprising carbon, at least one of hydrogen and fluoride, and optional atoms selected from oxygen, nitrogen, sulfur, phosphorus and iodine; L is an organic group which allows a T ms -containing moiety to be cleaved from the remainder of the compound, wherein the T ms -containing moiety comprises a functional group which supports a single ionized charge state when the compound is subjected to mass spectrometry and is selected from tertiary amine, quaternary amine and organic acid; and X is a nucleic acid fragment attached to L at other than the 3′ end of the nucleic acid fragment; with the provisos that the compound is not bonded to a solid support nor has a mass of less than 250 daltons.