ArticleJournal of the American Society for Mass Spectrometry2005
Guidelines for the routine application of the peptide hits technique.
Article in Journal of the American Society for Mass Spectrometry, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
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- Label-free protein quantitation using weighted spectral counting.Methods in molecular biology (Clifton, N.J.) · 2012Article
- Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.BMC genomics · 2011Article
- Improving proteome coverage on a LTQ-Orbitrap using design of experiments.Journal of the American Society for Mass Spectrometry · 2011Article
- Response of porcine intestinal in vitro organ culture tissues following exposure to Lactobacillus plantarum JC1 and Salmonella enterica serovar Typhimurium SL1344.Applied and environmental microbiology · 2010Article
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- Insights into aging through measurements of the Drosophila proteome as a function of temperature.Mechanisms of ageing and development · 2010Article
- Global effects of inactivation of the pyruvate kinase gene in the Mycobacterium tuberculosis complex.Journal of bacteriology · 2009Article
- Shotgun proteomics in neuroscience.Neuron · 2009Article
- Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics.Briefings in functional genomics & proteomics · 2009Review
- Proteomic analysis of nuclear factors binding to an intronic enhancer in the myelin proteolipid protein gene.Journal of neurochemistry · 2008Article
- Phenotypic and proteomic characterization of multiply antibiotic-resistant variants of Salmonella enterica serovar Typhimurium selected following exposure to disinfectants.Applied and environmental microbiology · 2008Article
- Proteomic analysis of Schistosoma mansoni egg secretions.Molecular and biochemical parasitology · 2007Article
- Protein abundance ratios for global studies of prokaryotes.Proteomics · 2007Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A set of guidelines has been developed for using the peptide hits technique (PHT) as a semi-quantitative screening tool for the identification of proteins that change in abundance in a complex mixture. The dataset that formed the basis for these experiments was created using a cell lysate derived from the yeast Saccharomyces cerevisiae, spiked at various levels with serum albumin (BSA), and analyzed by LC/MS/MS and SEQUEST. Knowing that the level of only one protein (BSA) actually changed in the mixture allowed for the development and refinement of the necessary bioinformatics and statistical analyses, e.g., principal component analysis (PCA), normalization, and analysis of variation (ANOVA). As expected, the number of BSA peptide hits changed in proportion to the amount of BSA added to the sample. PCA was able to clearly distinguish between the spiked samples and the untreated sample, indicating that PCA may be able to classify samples, e.g., healthy versus diseased, in future experiments. The use of an endogenous "housekeeping" protein was found to be superior to the use of total hits for data normalization prior to analysis. An ANOVA based model readily identified BSA as a protein of interest, that is, one likely to be changing from amongst the background proteins, indicating that an ANOVA model may be able to identify individual proteins in target or biomarker discovery experiments. General guidelines based on these combined observations are set forth for future analyses and the rapid screening for candidate proteins of interest.
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