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Journal of Systems Biology & Proteome Research
|
Volume 2
J u n e 2 5 - 2 7 , 2 0 1 8 | D u b l i n , I r e l a n d
MASS SPECTROMETRY
AND PROTEOMICS
International Conference on
Sameh Magdeldin et al., J Syst Biol Proteome Res 2018, Volume 2
HIGH THROUGHPUT PROTEOMIC
ANALYSIS USING DIFFERENT OFFGEL
FRACTIONATION PANELS
Sameh Magdeldin
1,2
, Aya Osama
3
and
Tadashi Yamamoto
4
1
Children Cancer Hospital, Egypt
2
Suez Canal University, Egypt
3
Al-Azhar University, Egypt.
4
Niigata University, Japan
O
FFGEL fractionation of mouse kidney protein lysate and its tryptic pep-
tide digest has been examined in this study for better understanding the
differences between protein and peptide fractionation methods and attaining
maximum recruitment of this modern methodology for in-depth proteomic
analysis. With the same initial protein/peptide load for both fractionation
methods, protein OFFGEL fractionation showed a preponderance in terms of
protein identification, fractionation efficiency, and focusing resolution, while
peptide OFFGEL was better in recovery, number of peptide matches, and
protein coverage. This result suggests that the protein fractionation method
is more suitable for shotgun analysis while peptide fractionation suits well
quantitative peptide analysis [isobaric tags for relative and absolute quanti-
tation (iTRAQ) or tandem mass tags (TMT)]. Taken together, utilization of the
advantages of both fractionation approaches could be attained by coupling
both methods to be applied on complex biological tissue. A typical result is
shown in this article by identification of 8262 confident proteins of whole
mouse kidney under stringent condition. We therefore consider OFFGEL frac-
tionation as an effective and efficient addition to both label-free and quantita-
tive label proteomics workflow.
samehmagd@yahoo.com