User:Hannes Röst/Mass spectrometry-based proteomics

Mass spectrometry-based proteomics refers to the application of mass spectrometry to identify and quantify proteins in complex biological samples.

History
History of Proteomics:
 * Enzymes (Anselme Payen)
 * Sumner
 * Tiselius
 * Pauling

See also:
 * History of biochemistry
 * Protein
 * History of molecular biology
 * History_of_molecular_biology -- most relevant ...

Sample preparation

 * Sample preparation Trypsin, Sample preparation in mass spectrometry

Mass spectrometric Methods
Historic methods (all before MS): see Proteomics


 * Bottom-up proteomics
 * Top-down proteomics

Other Methods

 * AMT, SWATH-MS etc

MS2-based (tag-based) quantification

 * iTRAQ
 * ICAT
 * TMT

MS1-based (stable isotope-based) labels

 * SILAC

Label-free quantification

 * MS1 or MS2

Analysis software

 * SEQUEST
 * Mascot (software)
 * Trans-Proteomic Pipeline
 * OpenMS
 * ProteoWizard
 * Gpm (proteomics)

Standards

 * Minimum information about a proteomics experiment

Applications

 * See Protein_mass_spectrometry
 * See Proteomics
 * See Biomarker

Sub-cellular localization

 * Surface
 * Secreted proteins Secretome, Secretomics
 * other organelles ?
 * plasma proteome (see Blood proteins)

Tissue proteomics

 * Neuroproteomics

Native peptides

 * MHC proteome

Protein degradation

 * Pulse chase

International efforts
maybe Proteomics ??
 * Human Protein Atlas
 * Human proteome project