Using replicated human serum samples, we applied an error model for proteomic differential expression profiling for a high-resolution liquid chromatography-mass spectrometry (LC-MS) platform. The detailed noise analysis presented here uses an experimental design that separates variance caused by sample preparation from variance due to analytical equipment. An analytic approach based on a two-component error model was applied, and in combination with an existing data driven technique that utilizes local sample averaging, we characterized and quantified the noise variance as a function of mean peak intensity. The results indicate that for processed LC-MS data a constant coefficient of variation is dominant for high intensities, whereas a model for low intensities explains Poisson-like variations. This result leads to a quadratic variance model which is used for the estimation of sample preparation noise present in LC-MS data.

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Zinc fingers are usually associated with proteins that interact with DNA. Yet in two oocyte-specific Xenopus proteins, TFIIIA and p43, zinc fingers are used to bind 5S RNA. One of these, TFIIIA, also binds the 5S RNA gene. Both proteins have nine zinc fingers that are nearly identical with respect to size and spacing. We have determined the relative affinities of groups of zinc fingers from TFIIIA for both 5S RNA and the 5S RNA gene. We have also determined the relative affinities of groups of zinc fingers from p43 for 5S RNA. The primary protein regions for RNA and DNA interaction in TFIIIA are located at opposite ends of the molecule. All zinc fingers from TFIIIA participate in binding 5S RNA, but zinc fingers from the C terminus have the highest affinity. N-terminal zinc fingers are essential for binding the 5S RNA gene. In contrast, zinc fingers at the amino terminus of p43 are essential for binding 5S RNA.The zinc finger motif was first postulated for the repeated amino acid sequence found in the transcription factor TFIIIA (4,20). TFIIIA has nine adjacent zinc fingers near the amino terminus of the protein that enable it to bind to the 60-bp internal promoter of the 5S RNA gene (11,30). Each zinc finger consists of approximately 30 amino acids shaped by coordination of a zinc atom to invariant cysteine and histidine residues. Proteins that contain TFIIIA-like zinc fingers are by analogy usually assumed to be transcription factors. Yet TFIIIA is atypical of most zinc finger proteins because it binds specifically to RNA as well as DNA (12,23). RNA-binding zinc finger proteins may be more prevalent than is currently recognized, since many of the putative zinc finger proteins have been identified through sequence homology and their functions are unknown (6,7,18,35