1. The Coming Age of Complete, Accurate, and Ubiquitous Proteomes
Matthias Mann, Nils A. Kulak, Nagarjuna Nagaraj, Jürgen Cox 
Molecular Cell 
Volume 49, Issue 4, Pages (February 2013)
DOI: /j.molcel
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2. Figure 1
Shotgun Proteomics Workflow for Complete Proteome Measurements
The first three steps pertain to sample preparation and on-line peptide separation. Steps 4–7 represent electrospray ionization of peptides, analysis in the mass spectrometer (quadrupole-Orbitrap analyzer), resulting in survey scans of the eluting peptides as well as high-resolution fragment spectra. Computational proteomics makes up the remaining steps of the pipeline, including bioinformatic and systems biological interpretation of the results (shown for the MaxQuant framework).
Molecular Cell  , DOI: ( /j.molcel )
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3. Figure 2 The Complete Yeast Proteome
(A) Comparison of shotgun proteomics results against tandem affinity tagging (TAP) or green fluorescent protein (GFP) tagging experiments. (Reprinted from de Godoy et al. [2008].)
(B) Streamlined system for rapid analysis of nearly the entire yeast proteome. (Adapted from Nagaraj et al. [2012], American Society for Biochemistry and Molecular Biology.)
(C) Median fold changes for heat shock proteins (red) and nucleolar proteins (blue). Error bars represent the SD from quantification with a yeast spike-in SILAC standard. (Reprinted from Nagaraj et al. [2012].)
Molecular Cell  , DOI: ( /j.molcel )
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4. Figure 3 Single-Run Analysis of the Human Proteome
(A) Eleven different cell lines were measured by single 4 hr LC MS/MS runs. Numbers of identified proteins are indicated with (blue) or without (green) “matching between runs” in the MaxQuant environment.
(B) Dynamic range of the single-run proteome spans more than six orders of magnitude, but 90% of the MS signals of the identified proteins are within three orders of magnitude.
(C) Binned histogram of estimated protein copy numbers. Significantly enriched protein categories compared to the entire proteome abundance distribution are annotated (calculated by 1D enrichment [Cox and Mann, 2012]).
Molecular Cell  , DOI: ( /j.molcel )
Copyright © 2013 Elsevier Inc. Terms and Conditions