Proteomics by mass spectrometry: approaches, advances, and applications.

By John R. Yates III, C. Ruse, A. Nakorchevsky. Annual Review of Biomedical Engineering, 2009

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Multidimensional proteomics for cell biology (2015, methodology): “Most mass spectrometry-based proteomics experiments have so far used the bottom-up workflow 12 , in which proteins are identified by detecting peptides generated after protease cleavage.”
iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates* (2011, methodology): “This has been aided by the rapid progress made in several facets of proteomics technology, including improved sample preparation and labeling techniques and faster, more sensitive mass spectrometers (2).”
A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, neutral): “see [16–18]).”
A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes (2009, background): “. Metagenomic profiling data can be viewed as a sampling of the genomic sequences from many kinds of microbes living in a specific environment. Again, the incompleteness of the data makes it difficult to reconstruct the entire pathways encoded by a metagenome. Nevertheless, it is becoming routine to”