Glossary


EPFL-PCF EPFL-Proteomics Core Facility
FSB School of Basic Sciences – Faculté des Sciences de Base
FSV School of Life Sciences – Faculté des Sciences de la Vie
ISREC Institut Suisse de Recherche Expérimentale sur le Cancer
UNIL Université de Lausanne

HPLC High Performance Liquid Chromatography
IEX Ion Exchange
LC Liquid Chromatography
LC-MS Liquid Chromatography coupled to Mass Spectrometry
nLC Nano-Liquid Chromatography
rpHPLC Reverse Phase HPLC
SAX Strong Anion Exchange
SCX Strong Cation Exchange

CAD Collisionnally Activated Dissociation (same as CID)
CID Collision Induced Dissociation (sane as CAD)
Deconvolution Action of extracting the molecular mass from the distribution of multiply charged ions of the molecule of interest.
ECD Electron Capture Dissociation
ES-MS or ESI-MS ElectroSpray (Ionization) Mass Spectrometry
IS or TIS Timed Ion Selector for parent ion selection in MALDI PSD and TOF/TOF experiments
ISD In-Source Decay
LID Laser Induced Dissociation
LIFT-TOF Second Ion Source in the TOF-TOF instrument
MALDI-TOF Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight
MS Mass Spectrometry
MS(n) or Tandem MS Multistage ion fragmentation capability with n≥2
PSD Post-Source Decay
SORI-CAD Sustained Off-Resonance Irradiation-CAD

Proteomics is the analysis of complete complements of proteins, and includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and, ultimately, their function (Stanley Fields).
PTM Post-Translational Modification(s) ex: glycosylation, phosphorylation, etc…
PMF Peptide Mass Fingerprint.
‘Shotgun Proteomics’ refers to the direct analysis of complex protein mixtures to rapidly generate a global profile of the protein complement within the mixture. This approach has been facilitated by the use of multidimensional protein identification technology (MudPIT), which incorporates multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) and database-searching algorithms.

“An Automated Multidimensional Protein Identification Technology for shotgun proteomics” Wolters D. et al., Anal. Chem. 2001 35 (23): 5683-5690.
“Shotgun proteomics: tools for the analysis of complex biological systems.” Wu and MacCoss Curr. Opin. Mol. Ther. 2002 4 (3):242-50.

MudPIT A term introduced by John Yates and stands for Multidimensional Protein Identification Technology which incorporates multidimensional high-pressure liquid chromatography (LC/LC), tandem mass spectrometry (MS/MS) and database-searching algorithms. The MudPIT approach relies heavily on specific database-search engines and other bioinformatics tools to facilitate the interpretation.

“Large-scale analysis of the yeast proteome by multidimensional protein identification technology.” Washburn MP, Wolters D, Yates JR 3rd Nat. Biotechnol. 2001 Mar;19(3):242-7.

Top-Down This term refers to approaches that attempt to determine the structure of the protein directly on the protein itself without breaking it into pieces by digestion. The Top-Down approach makes use of mass spectrometers capable of isolating ions of the protein and breaking them into fragments of interpretable size that bear sequence information. The Top-Down approach relies also heavily on specific database-search engines to facilitate the interpretation.

“Proteomics by FTICR mass spectrometry: top down and bottom up.” Bogdanov B and Smith RD. Mass Spectrom Rev. 2005 Mar-Apr;24(2):168-200. Review.

Bottom-Up This term refers to approaches that have been developed for the identification of proteins and the in-depth characterization of their structure. The term Bottom-Up reflects the reconstruction of the primary structure of the proteins from the little pieces of sequences of the peptides that could either be identified in databases or derived from the analysis of their mass spectra. Bottom-up approaches are often applied on protein mixtures in comparative proteomics using the MudPIT methodology.

“Proteomics by FTICR mass spectrometry: top down and bottom up.” Bogdanov B and Smith RD. Mass Spectrom Rev. 2005 Mar-Apr;24(2):168-200. Review.