Brain Proteomics

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studies present extensive proteomic data, including a large number of differ-

entially expressed proteins. However, the results of these analysis may vary

depending on the biological materials, instruments, sample preparation and

analysis methods to be selected [1, 4, 5]. The diversity in the studies is too

great to explain each method and summarize the studies here. Therefore, the

scope of this study is only limited to the presentation of shotgun proteomics .

In the following headings, information will be given about the programs used

to process the raw data, and then the databases and tools used to visualize the

data in these studies. A significant portion of these tools are utilized to per-

form enrichment analyses that reveal the biological significance of identified

proteins. These analyses classify proteins and reveal possible molecular mech-

anisms in which the proteins play a role. Some other informatics tools pro-

vide networks depicting protein interactions and these will also be mentioned.

Finally, MS-based proteomic studies using these technologies in the investi-

gation of neurodegenerative diseases will be discussed. We believe that this

chapter will provide important clues about new developments for those who

want to carry out research in the field of proteomics using high-throughput

technologies.

10.2

The Importance of Proteomics in Brain Research

The field of proteomics, which brings together different disciplines and aims

to analyses all proteins in a given sample, has made great progress in the

last decade. During this period, advances in methodological, technological,

and bioinformatics greatly facilitated researchers’ efforts to uncover how the

brain proteome is dynamically regulated. Proteins, as functional molecules of

the cell, exhibit a highly dynamic profile. The fact that the human brain is

more difficult to obtain than other tissues has made mass spectrometry-based

proteomics studies, which provide the opportunity for large-scale analysis,

very valuable compared to gel electrophoresis and antibody-dependent pro-

tein analyses that provide limited information. In this regard, MS systems,

which have a high scanning speed and allow the measurement of thousands of

proteins and peptides even in complex biological samples, contribute to the

creation of proteome catalogs of the nervous system and the discovery of pro-

cesses related to neurological diseases. Moreover, these catalogs are important

data sources for understanding protein-protein, protein-DNA or protein-small

molecule interactions [6].

Therefore, large-scale proteomic studies conducted to understand the

molecular pathophysiology of the human brain encourage researchers to de-

velop early diagnosis and treatment strategies for neurodegenerative diseases

such as Alzheimer’s and Parkinson’s for the near future. For this purpose, there

are various studies in which comprehensive protein profiles are obtained in