Functional Proteomics

Running Head: FUNCTIONAL PROTEOMICS
FUNCTIONAL PROTEOMICS
Name of the Student
Name of the University
Author Note

FUNCTIONAL PROTEOMICS1
COMPARE AND CONTRAST THE WAYS IN WHICH PROTEOMICS STUDIES
ARE PERFORMED IN CURRENT LITERATURE AS OPPOSED TO THESE
PERFORMED TEN YEARS AGO.
ABBREVIATIONS: MS, Mass spectrometry; ESI, Electron spray ionization; MALDI.,
Matrix-assisted laser desorption/ionization; Q-Q-ToF, hybrid quadruple time-of-flight; ToF-
ToF, tandem time-of-flight; HPLC, high pressure liquid chromatography; MALDI-TOF,
Matrix associated laser ionization –time of flight; PMF, peptide mass fingerprinting; LC-
MS/MS, liquid chromatography coupled with tandem mass spectrometry; PMF, peptide mass
fingerprinting; DIGE, differential in gel electrophoresis; Mud PIT, multidimensional protein
identification technology; RP, reverse phase, iTRAQ, isbaric tag for relative and absolute
quantification ; DDA ,data dependent acquisition; MRM ,multiple reaction monitoring; SCX ,
strong action exchanger; SWATH ,Sequential window acquisition of all theoretical mass
spectra; ICAT, isotope- coded affinity tag;
KEYWORDS: shot gun proteomics/ Mass analyzer/ label free quantitative method/ Mass
spectrometry.
TOTAL NUMBER OF WORDS: 2009
ABSTRACT
Proteome are the modified forms of the collection of protein. Proteomics is the study
of proteins on a large scale. A proteome is also defined as a protein set that is being produced
in an organism. It is used for the identification of the patterns of the protein expression at a
particular time in trigger to a certain stimulus, along with this it also helps in the
determination of the protein networks that are functional that is exists at the stage of the
whole organism, tissue or cell. The comparative analysis of the protein which are at a normal
stage to the proteins that are present in the cancerous cell in order to determine the
biomarkers that are proteinaceous in nature and are linked with cancerous cells. The most
important tool for performing proteomics is Mass spectrometry and it is being used for a long
time. It helps in the determination of the polypeptide mass and their features or the type of the
post translational modifications. However, the shotgun proteomics and the detection of the

FUNCTIONAL PROTEOMICS2
protein based on MS are very confined to tiny molecules that are also thermostable until there
was evolution of the techniques like the matrix-assisted laser desorption or ionization
(MALDI) and electrospray ionization (ESI). This further stimulated the invention of the mass
analysers and a number of complicated instruments like, the hybrid quadruple time-of-flight
(Q-Q-ToF) and the tandem time-of-flight (ToF-ToF). Thus this review highlights on the way
proteomics studies have evolved along with the advancements of the technology in the field
of proteomics in the last 10 years.
SIGNIFICANCE OF THE PAPER:
This report analyses the advancements and development in the field of proteomics
from the last 10 years. It shows a huge range of technologies that are associated with
proteomic and which has been used because of their higher resolution and accuracy. It gives
information about the recent ways in which the research of proteomics is conducted, the
obstacles and the profits benefits of the study in clinical proteomics.
INTRODUCTION
Previously, the formation of polypeptide was done manually and the complete
analysis of the protein was very critical and troublesome. The analysis of the protein needs
the dissociation of maximum number of peptides from a number of digested part of the target
protein along with the help of the proteases that has certain specific properties that have the
ability to gather the matched fragments that cover up the complete sequence (Sarbu, Ghiulai
and Zamfir 2014). The protein sequencing is done using the Edman Degradation. There are
certain specialist advances such as the use of the novel valves to manage the harsh chemicals,
the beginning of the HPLC or high pressure liquid chromatography, and the use of
immobilization of the sample which were all added in the first gas phase that helps to
increase the susceptibility and also allowed the automatic collection of data and their analysis
(Sun, Chen and Yao 2013). On the other hand, the instruments that are used in the present