The Coming Age of Complete, Accurate, and Ubiquitous Proteomes

Slides:

Advertisements

Similar presentations

Volume 49, Issue 2, Pages (January 2013)

Advertisements

Volume 10, Issue 4, Pages (October 2009)

Altered MCM Protein Levels and Autophagic Flux in Aged and Systemic Sclerosis Dermal Fibroblasts Verónica I. Dumit, Victoria Küttner, Jakob Käppler,

Volume 138, Issue 4, Pages (August 2009)

Volume 65, Issue 2, Pages (January 2017)

Now, More Than Ever, Proteomics Needs Better Chromatography

Analytical Characteristics of Cleavable Isotope-Coded Affinity Tag-LC-Tandem Mass Spectrometry for Quantitative Proteomic Studies Cecily P. Vaughn, David.

Volume 68, Issue 1, Pages e5 (October 2017)

Volume 31, Issue 3, Pages (August 2008)

The Haystack Is Full of Needles: Technology Rescues Sugars!

Proteomics Moves into the Fast Lane

Volume 19, Issue 11, Pages (June 2017)

Hyeshik Chang, Jaechul Lim, Minju Ha, V. Narry Kim Molecular Cell

A quantitative proteomics strategy to identify SUMO-conjugated proteins. A quantitative proteomics strategy to identify SUMO-conjugated proteins. HeLa.

A, high resolution MS/MS spectrum (lower panel) of 1435

Volume 44, Issue 2, Pages (October 2011)

Volume 14, Issue 7, Pages (February 2016)

Relative quantitation of phosphopeptides from conditioned media from subtype specific breast cancer cell lines. Relative quantitation of phosphopeptides.

Top-down protein identification.

Schematic of MS1 filtering.

Significantly enriched phosphorylation motifs from up-regulated phosphopeptides by Motif-X analysis. Significantly enriched phosphorylation motifs from.

Bottom-up proteomic characterization of MALDI IMS samples.

Volume 9, Issue 5, Pages (December 2014)

Colonopshere-enriched proteins display functional interactions.

Identification of SUMO3peptides from 2D-LC-MS/MS analyses of a tryptic digest of HEK293-SUMO3 cells using DDA and DIA methods. Identification of SUMO3peptides.

MRNAs that show increased protein synthesis following UPF1 depletion are enriched for those with very long 3′UTRs. mRNAs that show increased protein synthesis.

Analysis of newly synthesized proteins by combined pulsed SILAC and click chemistry enrichment. Analysis of newly synthesized proteins by combined pulsed.

Resolution and mass accuracy of A, a peptide isotope cluster (m/z 558

Overview of the analytical workflow used in this study and a representative MS/MS spectrum.a, Overview of the analytical workflow used in this study. Overview.

Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum. Identification of chaperonin GroEL (Rv0440) with representative MS/MS spectrum.A,

Example of MS/MS spectrum of peptide FPTLTGFNR (hypothetical protein with signal peptide EAK88888; N77) from a protein digestion mixture prepared by labeling.

Distribution of the phosphoproteins based on GO analysis, including biological process (Left) and cellular component (Right). Distribution of the phosphoproteins.

Volume 8, Issue 5, Pages (September 2014)

A, Absolute ion intensities of m/z 322, 922 and 1522 as function of the transfer time. A, Absolute ion intensities of m/z 322, 922 and 1522 as function.

Comparison of mapped epitopes and peptides identified in immuno-SILAC screening of polyclonal antibodies against trypsin-digested PrESTs. Comparison of.

Is Proteomics the New Genomics?

The principle of the immuno-SILAC method.

Immuno-MS results from antibodies toward 20 different target proteins in HeLa cell lysates. Immuno-MS results from antibodies toward 20 different target.

Bar plot representation of the transcriptomic changes in Δsaci_ptp and Δsaci_pp2a. Bar plot representation of the transcriptomic changes in Δsaci_ptp and.

Shotgun Proteomics in Neuroscience

Analytical metrics of yeast proteome analysis using the Q-OT-qIT (Fusion) as compared with qIT-OT (Orbitrap Elite) and Q-OT (Q-Exactive) hybrids. Analytical.

Dorota F. Zielinska, Florian Gnad, Jacek R. Wiśniewski, Matthias Mann

Summary of intralaboratory and interlaboratory variation for metrics for three LTQ and three LTQ-Orbitrap instruments in six replicate analyses of a tryptic.

Stability and variation of metrics over a range of sample injection amounts. Stability and variation of metrics over a range of sample injection amounts.

Performance metrics for triplicate analyses of a tryptic digest of the CPTAC yeast reference proteome on four LTQ-Orbitraps at three different sites in.

Comparison of proteomics and RNA‐Seq data.

Illustration of chromatography metric C-2A applied to LC-MS/MS data from three Thermo LTQ systems in analyses of yeast proteome samples in CPTAC Study.

Proteins in Plant Brassinosteroid Signaling

Volume 65, Issue 4, Pages e4 (February 2017)

Classification of the 1458 identified proteins into molecular functions. Classification of the 1458 identified proteins into molecular functions. The pie.

Top-down analysis of intact bovine carbonic anhydrase II by LTQ Orbitrap Velos. Top-down analysis of intact bovine carbonic anhydrase II by LTQ Orbitrap.

Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. Enlargements of 2-D gels visualized by Coomassie Brilliant Blue staining. In.

Influence of MS measurement conditions on the deviation factors between the estimated and measured concentrations of 46 proteins in neuro2a cells.A, QSTAR.

Yun Wah Lam, Angus I. Lamond, Matthias Mann, Jens S. Andersen

Label-free pyQms quantification of metabolites and peptides.

Barrier Function at HMR

Schematic of AIMS-to-MRM experiment.

Statistical evaluation of CD56+ NK cell subset data.

The average median S.D. and PEV reduction after applying different normalization methods compared with raw data. The average median S.D. and PEV reduction.

Volume 61, Issue 2, Pages (January 2016)

Differential protein, mRNA, lncRNA and miRNA regulation by p53.

Brandon Ho, Anastasia Baryshnikova, Grant W. Brown Cell Systems

Maria S. Robles, Sean J. Humphrey, Matthias Mann Cell Metabolism

Volume 15, Issue 2, Pages (April 2016)

Volume 43, Issue 3, Pages (August 2011)

Volume 2, Issue 3, Pages (March 2016)

Volume 32, Issue 2, Pages (February 2010)

Volume 7, Issue 6, Pages e3 (December 2018)

Navigating the Deubiquitinating Proteome with a CompPASS

SCX chromatography at low pH permits strong enrichment of phosphopeptides of distinct solution charge states.A, the number of phosphopeptides (blue triangles)

Presentation transcript:

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 583-590 (February 2013) DOI: 10.1016/j.molcel.2013.01.029 Copyright © 2013 Elsevier Inc. Terms and Conditions

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 2013 49, 583-590DOI: (10.1016/j.molcel.2013.01.029) Copyright © 2013 Elsevier Inc. Terms and Conditions

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 2013 49, 583-590DOI: (10.1016/j.molcel.2013.01.029) Copyright © 2013 Elsevier Inc. Terms and Conditions

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 2013 49, 583-590DOI: (10.1016/j.molcel.2013.01.029) Copyright © 2013 Elsevier Inc. Terms and Conditions