Peptide Sequence Analysis
Peptide Sequence Analysis - Related Videos
09:47
Analysis of Histone Antibody Specificity with Peptide Microarrays
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Cited by 21 •
2017
This manuscript describes methods for applying peptide microarray technology to specificity profiling of antibodies that recognize histones and their post-translational modifications.
07:59
A High Throughput MHC II Binding Assay for Quantitative Analysis of Peptide Epitopes
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Cited by 20 •
2014
Biochemical assays with recombinant human MHC II molecules can provide rapid, quantitative insights into immunogenic epitope identification, deletion, or design. Here, a peptide-MHC II binding assay scaled to 384-well plates is described. This cost effective format should prove useful in the fields of protein deimmunization and vaccine design and development.
07:30
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
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Cited by 21 •
2020
This method describes the steps to improve the quality and quantity of sequence data that can be obtained from formalin-fixed paraffin-embedded (FFPE) RNA samples. We describe the methodology to more accurately assess the quality of FFPE-RNA samples, prepare sequencing libraries, and analyze the data from FFPE-RNA samples.
08:16
Comparative Lesions Analysis Through a Targeted Sequencing Approach
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2019
This article describes a method to identify clonal and subclonal alterations among different specimens from a given patient. Although the experiments described here focus on a specific tumor type, the approach is broadly applicable to other solid tumors.
13:49
Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
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Cited by 6 •
2017
Biopanning bacterial display libraries is a proven technique for discovery of peptide affinity reagents, a robust alternative to antibodies. The semi-automated sorting method herein has streamlined biopanning to decrease the occurrence of false positives. Here we illustrate the thought process and techniques applied in evaluating candidates and minimizing downstream analysis.
FAQs
Enzymatic cleavage breaks a peptide or protein fragment into smaller pieces whose resulting patterns can be examined for sequence information. Comparing these fragments with composition data and mass-to-charge measurements helps researchers infer the order of amino acids rather than relying on a single measurement. This approach supports more reliable interpretation of complex peptide samples.
Mass-to-charge measurements provide molecular evidence about peptide fragments generated during analysis. When interpreted alongside amino acid composition and enzymatic cleavage patterns, these measurements help connect observed fragments to particular sequence arrangements. The combined evidence can distinguish candidate sequences and reveal sequence features relevant to peptide structure, biological activity, or protein identification.
Post-translational modifications can alter the molecular characteristics of a peptide without changing the underlying genetic sequence. By examining mass-to-charge data and comparing the results with reference databases, researchers can identify sequence features consistent with such modifications. Detecting these changes is important because they may help explain differences in structure, activity, or biological function.
A typical workflow starts by examining peptide composition, followed by enzymatic cleavage to generate interpretable fragments. Researchers then evaluate mass-to-charge measurements from mass spectrometry and compare the resulting evidence with reference databases. Together, these stages convert experimental measurements into a sequence interpretation that can support identification of the original peptide or protein fragment.
The technique is useful when related proteins share substantial sequence similarity but differ in particular peptide regions or modifications. Analysis of cleavage patterns, mass-to-charge measurements, and database matches can provide evidence for distinguishing among those candidates. This capability supports protein identification in studies of expression, disease mechanisms, and biological samples containing closely related molecules.
In biology, sequence information connects molecular structure with activity, helping researchers investigate signaling molecules, biomarkers, and therapeutic peptides. The same evidence can contribute to studies of protein expression, evolution, and disease mechanisms. In drug development, identifying sequence features and modifications helps guide the evaluation of peptides whose biological properties may have therapeutic relevance.