Protein & Peptide Sequencing

The primary amino acid sequence of peptides and proteins determines their three-dimensional structure and folding and thus their biological function. At fischer organics, we offer complete characterization using state-of-the-art technologies in two variants:

Bottom-up Data Base Search


In bottom-up database searches, proteins are first degraded using proteolytic enzymes and the resulting peptides are analyzed by LC-HR-MS/MS. High-resolution mass spectrometers such as ToF and Orbitrap Analyzer are used. The acquired mass spectra are compared with a database of known protein sequences and the protein sequence is identified. In this way, for example, potential antigens are identified as targets in pharmaceuticals.


De novo sequencing


Although protein identification by mass spectrometry is well established in databases, the method is not applicable if the protein sequence is not available in the current database. Therefore, de novo sequencing is the only method to identify novel peptides, unsequenced organisms, and antibody drugs that could not be detected by database search methods. However, de novo sequencing presents more challenges than conventional database searching, such as unclear assignments of fragment ions, insufficient product ions resulting from incomplete fragmentation leading to low sequence coverage, and difficulties in distinguishing ion series.

Our team of experts at fischer organics has many years of experience in the analysis of proteins and peptides and is your competent partner for your protein analysis.

If you have any questions or are interested in the topic of proteins and peptides, please contact us!

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