Protein Sequencing
Protein Sequencing - Related Videos
09:51
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Cited by 2 •
2017
A protocol for the online investigation of protein sequence-structure-dynamics relationships using Bio3D-web is presented.
08:07
Identification of Plasmodesmal Localization Sequences in Proteins In Planta
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Cited by 6 •
2017
Plant intercellular connections, the plasmodesmata (Pd), play central roles in plant physiology and plant-virus interactions. Critical to Pd transport are sorting signals that direct proteins to Pd. However, our knowledge about these sequences is still in its infancy. We describe a strategy to identify Pd localization signals in Pd-targeted proteins.
08:53
Strand-Specific Analysis of Proteins at Replicating DNA Strands by Enrichment and Sequencing of Protein-Associated Nascent DNA Method
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2025
Enrichment and sequencing of protein-associated nascent DNA (eSPAN) was developed to detect the relative abundance of a chromatin-associated protein on two replicating DNA strands, thereby revealing molecular insight into chromatin replication and its coupled processes. This protocol describes eSPAN procedures in yeast and mouse embryonic stem (ES) cells.
11:36
A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing
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Cited by 6 •
2016
We present a protocol for the functional assessment of comprehensive single-site saturation mutagenesis libraries of proteins utilizing high-throughput sequencing. Importantly, this approach uses orthogonal primer pairs to multiplex library construction and sequencing. Representative results using TEM-1 β-lactamase selected at a clinically relevant dosage of ampicillin are provided.
08:57
Amplicon Sequencing using the Long-Read Sequencing Technologies
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2025
This protocol was optimized for targeted deep sequencing of 18 drug-resistance regions in Mycobacterium tuberculosis using a long-read sequencing platform, followed by analysis with a tuberculosis-specific bioinformatics pipeline designed for long-read data.
FAQs
Tandem mass spectrometry links peptide mass measurements to sequence information through fragmentation. First, the instrument measures each peptide’s mass-to-charge ratio. It then fragments selected peptide ions, producing ion patterns that reflect the order of their amino-acid components. Interpreting these sequence-specific patterns helps provide evidence for the parent protein and can reveal differences from an expected sequence.
Enzymatic digestion converts a protein into peptides that can be measured and fragmented individually. This creates smaller molecular components for mass-to-charge analysis and generates peptide-specific ion patterns during tandem mass spectrometry. The resulting measurements provide distributed sequence evidence rather than relying on a single intact-protein signal, supporting identification and the detection of sequence differences.
Edman degradation identifies terminal amino-acid residues sequentially, removing them one at a time for analysis. Mass spectrometry instead measures peptide mass-to-charge ratios and uses tandem fragmentation to obtain sequence-specific ion patterns. The two approaches therefore derive sequence information through different chemical and analytical routes, allowing researchers to select the strategy that fits the protein-characterization objective.
A typical workflow begins by digesting the protein enzymatically into peptides. The resulting peptides are introduced for mass-to-charge measurement, after which tandem mass spectrometry fragments selected ions. Analysts interpret the resulting sequence-specific ion patterns to obtain sequence information and compare it with the expected protein composition. This workflow connects sample preparation, instrumental measurement, and chemical interpretation.
Protein sequencing can reveal sequence variants and help characterize post-translational modifications, which are molecular changes added to proteins after their initial synthesis. These findings extend analysis beyond assigning a protein name by showing whether its molecular composition differs from an expected form. Such information is useful in chemical and biomedical research and in evaluating biopharmaceutical products.
The amino-acid composition and order influence a protein’s structure and function, linking molecular analysis to biological activity. Chemical sequencing methods can therefore support characterization of proteins whose composition must be examined carefully. In biopharmaceutical quality control, sequencing contributes evidence about identity, sequence variants, and post-translational modifications, helping assess whether a product matches its intended molecular form.