Mass-ladder

The 1.2% agarose gel is prepared using agarose (usb) and 10 x TAE (Tris-Acetate-EDTA) pH 8.3 buffer (Invitrogen). Ethidium Bromide (Sigma) as marker and Low DNA Mass Ladder (Invitrogen) are used in agarose gel analysis. 

Load appropriate DNA ladder in a well adjacent to the DNA samples (e.g., 4 pi of high mass ladder. Life Technology). 

Quantitative DNA ladder (High DNA Mass Ladder, Invitrogen, catalog no. 10496-016). 

The utility of any mass spectrometric sequencing method that relies on consecutive backbone cleavages depends on the formation of a mass ladder. The sequence information is obtained by determining the mass difference between successive peaks in the mass spectrum. In the case of oligodeoxynucleotides, the expected mass differences between successive peaks will correspond to the loss of dC = 289.25 u, dT = 304.26 u, dA = 313.27 u and dG = 329.27 u (all values are atomic mass-based). With oligoribo-nucleotides, the mass differences will be rC = 305.25 u, rU = 306.26 u, rA = 329.27 u and rG = 345.27 u (all values are atomic mass-based). 

Sequence determination of oligonucleotides by an analysis of the failure sequences is an extremely simple and straightforward method. The mass spectrum will contain a series of peaks that corresponds to the final product and to each one of the failure sequences, each of which differs in mass by the appropriate nucleotide residue value. The sequence of the oligonucleotide is determined in the 5 to 3 direction from the mass ladder of the synthesis failure products. 

Figure 18.1. A mass spectrum containing a peptide mass ladder. The peptide sequence is determined from...

From the ladder diagram it appears that we may safely assume that the concentrations of H2L+ and L are significantly smaller than that for HL, allowing us to simplify the mass balance equation to... 

Schliiter et al. have isolated the beltene derivative 20, which was developed as byproduct when synthesizing the ladder-type polymer 21 by a repeated Diels-Alder reaction (Fig. 11). The monomer 19 can act both as diene and as dienophil [41]. The iterative Diels-Alder method is however limited by the decreasing solubility of the products of higher molecular masses. 

Figure 14.6 Representative mass spectrum showing ladder of a bisglycosylated glycopeptide obtained from screening of a glycopeptide library for the mannose binding protein. The nonanoic acid (Non) and tridecanoic acid (Tri) encode for Ser(Man) (Sm) and Asn(Man) (Nm), respectively.

McMahon, T.B. Thermochemical Ladders Scaling the Ramparts of Gaseous Ion Energetics. Int. J. Mass Spectrom. 2000, 200, 187-199. 

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