Understanding Information Processes at the Proteomics Level

Abstract

All living organisms are composed of proteins. Proteins are large, complex molecules made of long chains of amino acids. Twenty different amino acids are usually found in proteins. Proteins are produced on protein-synthesizing machinery directed by codons made of three deoxyribonucleic acid (DNA) bases. DNA is an information storage macromolecule. With the fast advancement of DNA sequencing technology, more and more genomes have been sequenced. Sequence analysis of this exploding genomic information has revealed a lot of novel genes for which molecular and/or biological functions are to be determined. The huge genomic information stored in DNA and genes is stationary and heritable. At cellular level, genomic information flows selectively from DNA to messenger RNA (mRNA) through transcription and from mRNA to proteins through translation for biological functions, such as response to changes in the environment. Different large-scale, high-throughput studies have been performed to investigate the information flow, e.g., transcriptomic profiling using microarray or RNAseq technologies. As a complementary approach to genomics and transcriptomics, proteomics has been fast developing to investigate gene expression at protein levels including quantitative changes, posttranslational modifications, and interactions with other molecules. These protein-level events represent a global view of information processing at the proteomics level. In this chapter, we focus on the description of technological and biological aspects of the information flow from the static ge nome to the dynamic proteome through gene transcription, protein translation, posttranslational modification, and protein interactions.

Keywords

Shotgun Proteomics Tandem Affinity Purification Initiator tRNA Cytidine Triphosphate Boronate Affinity Chromatography 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

1-DE

one-dimensional electrophoresis

2-D-DIGE

two-dimensional fluorescence difference gel electrophoresis

2-D

two-dimensional

2-DE

two-dimensional electrophoresis

3-D

three-dimensional

AD

activating domain

ATP

adenosine triphosphate

BD

binding domain

CID

collision-induced dissociation

CTP

cytidine triphosphate

DE

differential evolution

DIGE

difference in gel electrophoresis

DNA

deoxyribonucleic acid

ECD

electron-capture dissociation

EF-G

elongation factor G

EF

elongation factor

ER

endoplasmic reticulum

ESI

electrospray ionization

ETD

electron-transfer dissociation

FT-ICR

Fourier-transform ion cyclotron resonance

FT

Fourier transform

GDP

guanosine diphosphate

GTP

guanosine triphosphate

HILIC

hydrophilic interaction chromatography

HPLC

high-performance liquid chromatography

ICAT

isotope-coded affinity tag

IEF

isoelectric focusing

IEX

ion exchange

IF

initiation factor

IMAC

ion-affinity chromatography

IPG

immobilized pH gradient

LC-MS

liquid chromatography-mass spectrometry

LC

liquid chromatography

LTQ

linear ion trap

MALDI

matrix assisted laser desorption/ionization

MOC

metal oxide chromatography

MS/MS

tandem mass spectrometry

MS

mass spectrometry

NHS

N-hydroxysuccinimidyl

NanoESI

nanoelectrospray ionization

PAGE

polyacrylamide gel electrophoresis

PNGase F

N-glycosidase F

PTM

posttranslational modification

QTOF

quadrupole TOF

QTRAP

quadrupole ion-trap

RF

releasing factor

RNA

ribonucleic acid

RNAseq

next-gen sequencing

RP

reversed-phase

SCX

strong cation exchange

SDS-PAGE

sodium dodecyl sulfate-polyacrylamide gel electrophoresis

SDS

sodium dodecyl sulfate

SILAC

stable-isotope labeling with amino acids in cell culture

TAP

tandem affinity purification

TOF-TOF

tandem time-of-flight

TOF

time-of-flight

UTP

uridine triphosphate

dsDNA

double-strand DNA

iTRAQ

isobaric tags for relative and absolute quantitation

mRNA

messenger RNA

pI

isoelectric point

tRNA

transfer RNA

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Copyright information

© Springer-Verlag 2014

Authors and Affiliations

  1. 1.Alkali Soil Natural Environmental Science CenterNortheast Forestry UniversityHarbinChina
  2. 2.Department of BiologyUniversity of FloridaGainesvilleUSA

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