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Bioinformatics of the Brain

various biological materials such as cerebrospinal fluid (CSF), serum, plasma

and brain tissue. However, finding robust biomarkers that meet expectations

for these diseases remains a challenging aspect of the field of proteomics. In a

significant portion of studies, further analysis of biomarker candidates cannot

be performed due to sample size and technical difficulties in the sample collec-

tion procedures, device and informatics analysis, and thus candidate markers

cannot progress to the clinic.

Constructing a strong study design is one of the main challenges, and a

successful proteomic study requires choosing the most appropriate one among

many methods and instruments that have their own strengths and weaknesses

[3, 4]. Recently, bioinformatics tools used in the evaluation of big data have

become widespread, making it easier to interpret many data sets together

and visualize these data [7, 8]. In this context, integrating various proteomic

approaches with each other and with other omics platforms has the potential

to find biomarker panels that are more clinically reliable and robust.

10.3

The Importance of Sample Selection for Proteomics

Research

Sample selection and preparation in a proteomics study affects the entire pro-

cess, from the first step to the last step of the workflow. Despite the great se-

lectivity and sensitivity of MS approaches, a major drawback is that abundant

proteins obscure low-abundance proteins during analysis, preventing their de-

tection. Accordingly, the biggest effort spent in the sample preparation process

is to reduce sample complexity. However, this difficulty cannot be overcome

by a single method but can be achieved with a combination of several methods

[9, 10]. An ideal sample preparation procedure that will increase the analy-

sis power of MS and reveal the highest protein coverage therefore requires

meticulousness in every aspect. The most commonly used samples to investi-

gate neurodegenerative diseases include brain tissue, serum/plasma, and CSF

[11–13]. In this context, knowing some of the characteristics of the samples

planned to be examined that will shape the study design and choosing the

method accordingly will make the study valuable.

10.4

Shotgun Proteomics

To date, various methods such as ELISA, western-blot, 2D-PAGE, 2D-DIGE,

protein microarray and mass spectrometry techniques have been used for pro-

tein analysis in brain research [4, 14]. However, the evolution and widespread