ArticleBMC genomics2012
A systematic model of the LC-MS proteomics pipeline.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed, 11 citations in OpenAlex.
- Effects of Growth Hormone Treatment and Rehabilitation in Incomplete Chronic Traumatic Spinal Cord Injury: Insight from Proteome Analysis.Journal of personalized medicine · 2020Article
- Bayesian ABC-MCMC Classification of Liquid Chromatography-Mass Spectrometry Data.Cancer informatics · 2015Article
- Modeling and systematic analysis of biomarker validation using selected reaction monitoring.EURASIP journal on bioinformatics & systems biology · 2014Article
- Modeling the next generation sequencing sample processing pipeline for the purposes of classification.BMC bioinformatics · 2013Article
- Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2011).BMC genomics · 2012Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationMass spectrometry is a complex technique used for large-scale protein profiling with clinical and pharmaceutical applications. While individual components in the system have been studied extensively, little work has been done to integrate various modules and evaluate them from a systems point of view.
resultsIn this work, we investigate this problem by putting together the different modules in a typical proteomics work flow, in order to capture and analyze key factors that impact the number of identified peptides and quantified proteins, protein quantification error, differential expression results, and classification performance. The proposed proteomics pipeline model can be used to optimize the work flow as well as to pinpoint critical bottlenecks worth investing time and resources into for improving performance. Using the model-based approach proposed here, one can study systematically the critical problem of proteomic biomarker discovery, by means of simulation using ground-truthed synthetic MS data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.