ProLuCID: An improved SEQUEST-like algorithm with enhanced sensitivity and specificity

AbstractProLuCID, a new algorithm for peptide identification using tandem mass spectrometry and protein sequence databases has been developed. This algorithm uses a three tier scoring scheme. First, a binomial probability is used as a preliminary scoring scheme to select candidate peptides. The binomial probability scores generated by ProLuCID minimize molecular weight bias and are independent of database size. A modified cross-correlation score is calculated for each candidate peptide identified by the binomial probability. This cross-correlation scoring function models the isotopic distributions of fragment ions of candidate peptides which ultimately results in higher sensitivity and specificity than that obtained with the SEQUEST XCorr. Finally, ProLuCID uses the distribution of XCorr values for all of the selected candidate peptides to compute a Z score for the peptide hit with the highest XCorr. The ProLuCID Z score combines the discriminative power of XCorr and DeltaCN, the standard parameters for assessing the quality of the peptide identification using SEQUEST, and displays significant improvement in specificity over ProLuCID XCorr alone. ProLuCID is also able to take advantage of high resolution MS/MS spectra leading to further improvements in specificity when compared to low resolution tandem MS data. A comparison of filtered data searched with SEQUEST and ProLuCID using the same false discovery rate as estimated by a target-decoy database strategy, shows that ProLuCID was able to identify as many as 25% more proteins than SEQUEST. ProLuCID is implemented in Java and can be easily installed on a single computer or a computer cluster.This article is part of a Special Issue entitled: Computational Proteomics

The localization of thiamine pyrophosphatase activity in the acinar cells of stimulated and non-stimulated sublingual glands of the rat

The distribution of thiamine pyrophosphatase (TPPase) activity in the acinar cells of the rat sublingual gland has been studied at various stages of the secretory cycle following stimulated secretion. The rats were stimulated to secrete by an intraperitoneal injection of isoproterenol and pilocarpine. In non-stimulated glands, TPPase activity is detected mainly in 3–4 cisternae at the inner concave side of the Golgi complex and in some adjacent condensing vacuoles as in other cells. In the acinar cells 1 to 2 h after stimulation, however, reaction product for the same enzyme activity is detected in the cisternae at the outer aspect, as well as the inner aspect, of the Golgi complex and even in the cisternae of the endoplasmic reticulum (ER). About 4 h after stimulation, TPPase activity becomes concentrated in 3–4 disternae at the inner concave side of the Golgi complex as in the acinar cells under non-stimulated conditions. Morphological observations of the acinar cells 1 to 2 h after the stimulation have indicated that the reorganization of the Golgi complex and ER is a major event which occurs at this stage. It is possible that this cellular event is related to the occurrence of TPPase activity in those sites which normally show negative reaction in non-stimulated state.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47402/1/418_2004_Article_BF00492557.pd