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FAQ proteomics

Learn more about proteomics techniques and data analysis

We collected a number of papers that provide a general overview on proteomics techniques and more specific fields of proteomics and data analysis.

General overview on mass spectrometry and proteomics techniques

Paper title: "Mass Spectrometry." (Nature Milestones, 2015) Link
Historical overview on key technical developments in mass spectrometry as well as chemical and biological applications.

Paper title: "Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present." (Analytical and Bioanalytical Chemistry, 2012) Link
Very good review with focus on the major technical and conceptual developments in proteomics since 2007.

Paper title: "Next-generation proteomics: towards an integrative view of proteome dynamics." (Nature Reviews, 2013) Link
Very good review on MS-based proteomics techniques.

Paper title: "A researcher’s guide to mass spectrometry-based proteomics." (Proteomics, 2016) Link
Describes the basic MS principles, including electric current, ion optics, ion traps, quadrupole mass filters, and Orbitrap FT-analyzers.

Paper title: "Mass-spectrometric exploration of proteome structure and function." (Nature, 2016) Link
Review on achievements of mass-spectrometry-based proteomics and remaining challenges.


Paper title: "Rapid, optimized interactomic screening." (Nat. Methods, 2015) Link
The paper provides information on the influence of the buffer composition on the detection of interaction partners in a IP experiment.

SILAC labeling

Paper title: "Global analysis of cellular protein translation by pulsed SILAC." (Proteomics, 2009) Link
Introduction to pulsed stable isotope labeling (pSILAC) in cell culture with two heavy isotope labels to directly quantify protein translation on a proteome-wide scale.

Paper title: "SILAC Mouse for Quantitative Proteomics Uncovers Kindlin-3 as an Essential Factor for Red Blood Cell Function." (Cell, 2008) Link
Description of completely label mice with a diet to quantitatively compare proteomes from knockout mice and thereby determine protein functions under complex in vivo conditions.

Paper title: "Global Protein Expression Profiling of Zebrafish Organs Based on in Vivo Incorporation of Stable Isotopes." (J. Proteome Res., 2014) Link
Description of SILAC zebrafish as a “spike-in” reference to generate a protein atlas of nine organs.


Paper title: "Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate." (Nat. Communications, 2015) Link
Study on proteome phosphorylation in response to TNF-α stimulation.

Data analysis

Paper title: "MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification." (Nat. Biotech., 2008) Link
Introduction to MaxQuant, an integrated suite of algorithms specifically developed for high-resolution, quantitative MS data.

Paper title: "Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment." (J. Proteome Res., 2011) Link
Description of the peptide search engine Andromeda based on probabilistic scoring.

Paper title: "The Perseus computational platform for comprehensive analysis of (prote)omics data." (Nat. Methods, 2016) Link
Description of the Perseus software platform to support biological and biomedical researchers in interpreting protein quantification, interaction, and post-translational modification data.