MASS SPECTROMETRY: To measure mass-to-charge ratio (m/z) of ions in the gas phase. In the Proteomics Resource Center ions are typically peptides and smaller molecules.
ELECTROSPRAY IONIZATION: Technique to transfer ions from liquid phase to gas phase.
NANO FLOW LIQUID CHROMATOGRAPHY: HPLC operated at 150-300 nanoliters per minute.
TANDEM MS: Abbreviated MS/MS or MS2. Technique to isolate ions (peptides) and subject ions to fragmentation.
FRAGMENTATION: Letting the ions collide or/and react with a gas. When peptides are fragmented they typically fragment at the peptide backbone. The amino acid sequence can be deduced from the fragment ions.
PROTEOME: The complete set of proteins expressed by a genome at a given time.
PROTEOMICS: Pronounced: \ˌprō-tē-ˈō-miks\. The analysis of the expression, localizations, functions, and interactions of proteomes.
QUANTITATIVE PROTEOMICS: Comparison of peptides and/or proteins in the same or in-between multiple samples. Such experiments generally set restraint on experimental design and applied analytical techniques.
TRYPSIN: Protease that hydrolysises protein at the C-termini of the positively charged amino acids: Lysine and Arginine. Because tryptic peptides end with Lysine or Arginine these peptides are easily charged and fragment well.
IN-GEL DIGESTION: Digestion of proteins separated by gel electrophoresis. Benefits of this technique are robustness with regard to sample matrix and build-in protein separation.
IN-SOLUTION DIGESTION: Digestion is performed in solution. Benefits of this technique can be better peptide recovery and simplified sample handling. Cons: less robust to sample matrix.
STABLE ISOTOPES: Typical heavier stable (non-radioactive) isotopes often used in quantitative proteomics are 13C, 15N and 2H (deuterium).
DIMETHYL LABELING BASED QUANTITATION: Stable isotope labeled forms of formaldehyde are used to label N-termini of the peptides and the amino group of Lysine’s through reductive amination. Up to three different samples can simultaneously be compared using this technique.
SILAC BASED QUANTITATION: ‘Stable Isotope Labeling with Amino acids in Cell culture’ or – metabolic labeling of cells. One or more amino acids of a nutrient medium is substituted with heavy stable isotope labeled counterparts. Incorporation of the ‘heavy’ amino acids into the proteome is assured by the metabolism of the cells. For HeLa and 293T cells, five passages are sufficient for complete incorporation.
TMT BASED QUANTITATION: Short for ‘Tandem Mass Tags’ which is used to quantitate protein samples. TMT is a chemical tag composed of varying stable isotopes and is reacted with primary amines of peptides in samples to be compared. The quantitative measures are obtained in MS/MS experiments.
AQUA: AQUA is short for ‘Absolute quantitation’. From a protein where absolute quantitation is required selected peptides are synthesized using stable isotope labeled peptides (13C and/or15N). The identical, but heavier, peptides are spiked in known amounts into the sample to be quantitated.
LABEL FREE BASED QUANTITATION: Relative comparison of samples without the use of stable isotopes. Quantitative measures are obtained in MS experiments.
PTM ANALYSIS: Identification and/or quantitation of Post Translational Modification or proteins. Mass spectrometry is used to pinpoint many different modified amino acids.
TANDEM MS SEARCH ALGORITHM: Software algorithm that allows for automatic annotation of tandem MS spectra. Measured spectra are compared to in-silico digested and in-silico fragmented peptides in a database.
DENOVO SEQUENCING: The process of reading the order of amino acids in a peptide using fragment ions generated in a tandem MS experiment.