Liquid chromatography mass spectrometry-based proteomics: biological and technological as\-pects
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Publication:542945
DOI10.1214/10-AOAS341zbMATH Open1220.62139arXiv1101.1154WikidataQ34983181 ScholiaQ34983181MaRDI QIDQ542945FDOQ542945
Authors: Yuliya V. Karpievitch, Ashoka D. Polpitiya, Gordon A. Anderson, Richard D. Smith, Alan R. Dabney 
Publication date: 20 June 2011
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used, significant challenges remain, and there are many opportunities for statisticians to make important contributions. In the most widely used "bottom-up" approach to proteomics, complex mixtures of proteins are first subjected to enzymatic cleavage, the resulting peptide products are separated based on chemical or physical properties and analyzed using a mass spectrometer. The two fundamental challenges in the analysis of bottom-up MS-based proteomics are as follows: (1) Identifying the proteins that are present in a sample, and (2) Quantifying the abundance levels of the identified proteins. Both of these challenges require knowledge of the biological and technological context that gives rise to observed data, as well as the application of sound statistical principles for estimation and inference. We present an overview of bottom-up proteomics and outline the key statistical issues that arise in protein identification and quantification.
Full work available at URL: https://arxiv.org/abs/1101.1154
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Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)
Cites Work
- Statistical significance for genomewide studies
- Classifier technology and the illusion of progress
- Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology
- Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection
- DNA microarray experiments: biological and technological aspects
- The influence of vector filtering on the matching precision of stereo images
- Recognising online spatial activities using a bioinformatics inspired sequence alignment approach
- Theory and mathematical methods in bioinformatics
Cited In (19)
- Feature extraction for proteomics imaging mass spectrometry data
- Statistically appraising process quality of affinity isolation experiments
- International Competition on Mass Spectrometry Proteomic Diagnosis
- A nested mixture model for protein identification using mass spectrometry
- Efficient interpretation of tandem mass tags in top-down proteomics
- A mixed-effects model for incomplete data from labeling-based quantitative proteomics experiments
- A likelihood-based scoring method for peptide identification using mass spectrometry
- Multiple Testing Issues in Discriminating Compound-Related Peaks and Chromatograms from High Frequency Noise, Spikes and Solvent-Based Noise in LC - MS Data Sets
- A review of statistical methods for protein identification using tandem mass spectrometry
- Analyzing LC-MS/MS data by spectral count and ion abundance: two case studies
- Generalized linear and mixed models for label-free shotgun proteomics
- Calibration using constrained smoothing with applications to mass spectrometry data
- Mathematical tools and statistical techniques for proteomic data mining
- Bayesian hierarchical model for protein identifications
- Bayesian identification of protein differential expression in multi-group isobaric labelled mass spectrometry data
- An insight into high-resolution mass-spectrometry data
- Minimax Quasi-Bayesian Estimation in Sparse Canonical Correlation Analysis via a Rayleigh Quotient Function
- Estimation and inference in metabolomics with nonrandom missing data and latent factors
- Modeling proteolysis from mass spectrometry proteomic data
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