Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping.
A derivatization reaction, guanidination, was recently reported that increases MALDI-TOF MS sensitivity toward lysine-terminated peptides. Its application conveys sequence information that can be used as a parameter in peptide mass mapping database searches. This paper presents a systematic study of the impact of guanidination on proteomic analysis of an entire bacterial organelle. Sixty-two 2-D gel isolated proteins from Caulobacter crescentus stalks were studied. A novel computer algorithm, Prodigies, was developed to analyze the data. Absolute confidence limits associated with protein assignments were established using Monte Carlo simulations of database searches. The advantages of guanidination are illustrated using both experimental and theoretical data.
Karty
Jonathan A
JA
Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA.
Ireland
Marcia M E
MM
Brun
Yves V
YV
Reilly
James P
JP
D000465:Algorithms; D001426:Bacterial Proteins / Q000032:analysis*; D016935:Caulobacter crescentus / Q000737:chemistry*; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D019791:Guanidine; D009010:Monte Carlo Method; D010449:Peptide Mapping; D010455:Peptides / Q000737:chemistry; D020539:Sequence Analysis, Protein; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
D001426:Bacterial Proteins; D010455:Peptides; D019791:Guanidine