SEQUEST

Jimmy K. Eng, Ashley L. McCormack, and John R. Yates, III (1994). "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass Spectrom 5 (11): 976–989. doi:10.1016/1044-0305(94)80016-2

Preprocessing

Experimental spectrum

• Round fragment m/z to nearest integer (claim increases speed by 2X)
• Remove all ions in a 10 m/z (u) window around precursor (so that a fragment doesn't match the precursor). I assume this is +/- 5 m/z units from precursor.
• remove all but top 200 most abundant ions.
• renormalize all ions to 100 (based on the highest intensity ion, I assume)
• "The abundances of fragment ions within +/- 1 u of each other are equalized to the higher value". Does this mean that if two peaks fall into the same bin, the larger peak is taken? (makes some sense) Or does this mean that any two peaks within 1 m/z unit are given the higher intensity value (doesn't make sense).
• Immonium ions are "noted" in the experimental spectrum (what does this really mean?)

Matching

"Shared Peaks" (Sp) score

increment beta for each consecutive fragment ion matched. If the AA & immonium ion is matched, then rho is incremented. If AA is not present then rho is decreased.

• n_t = total number of predicted sequence ions
• beta increment = 0.075
• rho increment = 0.15
• (Σ i_m)n_i(1+beta)(1 + rho)/ n_t

preprocessing for Xcorr

divide spectrum into 10 equal regions and normalize the ions to value of 50.0