The three references listed below contain many hints for maintaining and optimizing ABI sequencers for low level samples. We list only a few of them here.
1.a). A regular schedule of preventative instrument maintenance beyond manufacturer specifications.
1.b). Instrument checks and system optimization before each sequencing run.
Atherton, D., Fernandez, J., DeMott, M., Andrews, L., and Mische, S.M. (1993) in Techniques in Protein Chemistry IV, (Angeletti, R.H., ed.) NY: Academic Press, pp. 409-418.
2.a) Addition of N,N-dimethylphenylthiourea (DMPTU), 0.5 mM/L, to solvent B acts as a scavenger to prevent loss of pmol amounts of PTH-amino acids on the column.
2.b) Addition of tryptophan (1.0 mmol/L) to solvent A will flatten the baseline rise attributed to DMPTU in solvent B.
2.c) Increase the percentage of analyzed sample by increasing the loop size on the PTH HPLC.
Tempst, P. and Riviere, L. (1989) Anal. Biochem. 183, 290-300.
3.a) Reduce chemical background by changing reagents and solvents weekly and by omitting DTT from S1, S2, and S3.
3.b) Use the same glass fiber filter for many peptides without reapplying Biobrene to minimize background artifacts (up to 125 cycles).
3.c) Store HPLC-collected peptides at -70oC and add additional TFA before loading.
Erdjument-Bromage, H., Geromanos, S., Choder, A., and Tempst, P. (1993) in Techniques in Protein Chemistry IV, (Angeletti, R.H., ed.) NY: Academic Press, pp 419-426.
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