Peptide Identification Method—De Novo Sequence Analysis

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Peptide Identification Method—De Novo Sequence Analysis

For the first time, the De Novo Sequencing contains sequencing a novel genome. And it needs professional unit of sequencing reads. Because of the read lenght, read depth, and flexible paired-end insert sizes, we choose de novo sequencing as the most ideal method. The accuracy of raw read can make the confident and efficient and high-quality production.

Body: In contrast to another popular peptide identification approach, the peptide de novo sequencing has an obvious advantage of working for both database and novel peptides. Using difference between two fragmentions to calculate the mass of an amino acid residue on the peptide backbone is the main purpose of de novo sequencing. The residue can be usually determined by the mass. De novo sequencing are being used because in the sequence database, the sequence determination of a protein can not be found. In the process of de novo sequencing, the amino acid sequence is deduced without the prior awareness of the DNA or protein sequence. A careful experimental design is needed by the de novo sequencing of an intact protein, as well as the combination of different analysis an evalution of data.

Follows are the condition, in which the de novo peptide and protein sequencing can be used:
the design to find out the partial amino acid sequences’ NDA primers; cloning and DNA/mRNA sequencing; the sequences for the monoclonal antibody variable regions; full characterization of immunoglobulins purified from immunized organism or from hybridoma cells; for proteomics projects and protein identification on organisms where genome sequences are not available; for bioactive peptides with modified and unusual amino acids.

Following factors are always included in a de-novo protein sequencing project: using specific proteases, when protein cleavage into peptides; de-novo protein sequencing using SPITC labeling with 4-sulfophenyl isothiocyanate and MS/MS peptide fragmentation. N-terminal peptide sequencing by MALDI-ISD.
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