TY - JOUR
T1 - Optimal construction of theoretical spectra for MS/MS spectra identification
AU - Fridman, Tema
AU - Protopopescu, Vladimir
AU - Hurst, Greg
AU - Borziak, Andmei
AU - Gorin, Andrey
PY - 2005
Y1 - 2005
N2 - We derive the optimal number of peaks (defined as the minimum number that provides the required efficiency of spectra identification) in the theoretical spectra as a function of (i) the experimental accuracy, σ, of the measured ratio m/z; (ii) experimental spectrum density; (iii) size of the database; (iv) number of peaks in the theoretical spectra; and (v) types of ions that the peaks represent. We show that if theoretical spectra are constructed including b and y ions alone, then for σ = 0.5, which is typical for high-throughput data, peptide chains of eight amino acids or longer can be identified based on the positions of peaks alone, at a rate of false identification below 1%. To discriminate between shorter peptides, additional (e.g., intensity-inferred) information is necessary. We derive the dependence of the probability of false identification on the number of peaks in the theoretical spectra and on the types of ions that the peaks represent. Our results suggest that the class of mass spectrum identification problems, for which more elaborate development of fragmentation rules (such as intensity model) is required, can be reduced to the problems that involve homologous peptides.
AB - We derive the optimal number of peaks (defined as the minimum number that provides the required efficiency of spectra identification) in the theoretical spectra as a function of (i) the experimental accuracy, σ, of the measured ratio m/z; (ii) experimental spectrum density; (iii) size of the database; (iv) number of peaks in the theoretical spectra; and (v) types of ions that the peaks represent. We show that if theoretical spectra are constructed including b and y ions alone, then for σ = 0.5, which is typical for high-throughput data, peptide chains of eight amino acids or longer can be identified based on the positions of peaks alone, at a rate of false identification below 1%. To discriminate between shorter peptides, additional (e.g., intensity-inferred) information is necessary. We derive the dependence of the probability of false identification on the number of peaks in the theoretical spectra and on the types of ions that the peaks represent. Our results suggest that the class of mass spectrum identification problems, for which more elaborate development of fragmentation rules (such as intensity model) is required, can be reduced to the problems that involve homologous peptides.
UR - http://www.scopus.com/inward/record.url?scp=32544437228&partnerID=8YFLogxK
U2 - 10.1089/omi.2005.9.380
DO - 10.1089/omi.2005.9.380
M3 - Article
C2 - 16402895
AN - SCOPUS:32544437228
SN - 1536-2310
VL - 9
SP - 380
EP - 390
JO - OMICS A Journal of Integrative Biology
JF - OMICS A Journal of Integrative Biology
IS - 4
ER -