Brain Proteomics

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molecular networks of diseases and a graphical map of biological processes

and pathways.

STRING database, which contains protein information of a wide variety

of organisms from the human proteome to Blastomyces parvus, is the most

preferred address for displaying known and predicted protein-protein interac-

tions. Although this platform offers limited color and features for PPI, the

existing network can be exported. However, the fact that each program or

tool allows importing files in different formats for processing can sometimes

increase the workload.

The recently introduced STRINGApp tool also provides ease of trans-

ferring the network and enrichment results performed on STRING to Cy-

toscape and allows more analysis opportunities [29]. Additionally, following

the Perseus software platform (https://maxquant.net/perseus/) used for both

statistical analysis and data visualization, a new network module, PerseusNet,

was recently introduced to facilitate graph analysis of proteome interaction

[30].

Moreover, the use of R and Python programming languages with various

interfaces has ensured researchers with great flexibility in this process. In

this context, the use of programming languages has become more common in

recent studies. Studies explaining how to visualize proteomic data using these

programming languages are also very useful for scientists who do not have

programming experience. See Ref [27, 31] for more information.

10.6

Proteomic Studies on Neurological Diseases

Alzheimer’s and Parkinson’s diseases, which cause progressive neurodegen-

eration, affect a significant portion of the elderly population worldwide.

Schizophrenia is a psychiatric disease that seriously affects both the individ-

ual and the people around him. However, it may include neurological findings

in which physical damage to the brain tissue can be observed. Further in-

vestigation of these three diseases, which seriously affect public health, with

proteomic approaches is very interesting as it can provide depth at the molec-

ular level regarding the definitions and treatment practices of these diseases.

Here we review recent proteomic studies in a variety of, but not all, clinical

samples and animal models.

10.6.1

Alzheimer’s Disease (AD)

AD is a neurodegenerative disease characterized by progressive cognitive im-

pairment. Amyloid β (Aβ) peptide accumulation and neurofibrillary tangles

due to tau hyperphosphorylation, seen in advanced stages, are the two known

basic pathological features of the disease. Although clinical symptoms and