Protein Sequence Identification
Protein Sequence Identification - Related Videos
08:07
Identification of Plasmodesmal Localization Sequences in Proteins In Planta
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Cited by 7 •
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.
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
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Cited by 6 •
2022
The protocol described here provides detailed instructions on how to analyze genomic regions of interest for microprotein-coding potential using PhyloCSF on the user-friendly UCSC Genome Browser. Additionally, several tools and resources are recommended to further investigate sequence characteristics of identified microproteins to gain insight into their putative functions.
08:51
Identification of Mouse and Human Antibody Repertoires by Next-Generation Sequencing
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Cited by 4 •
2019
Here, we describe protocols for the analysis and visualization of the structure and constitution of whole antibody repertoires. This involves the acquisition of vast sequences of antibody RNA using next-generation sequencing.
08:25
Identification of Circular RNAs using RNA Sequencing
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Cited by 30 •
2019
Circular RNAs (circRNAs) are non-coding RNAs that may have roles in transcriptional regulation and mediating interactions between proteins. Following assessment of different parameters for construction of circRNA sequencing libraries, a protocol was compiled utilizing stranded total RNA library preparation with RNase R pre-treatment and is presented here.
06:34
Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
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Cited by 29 •
2016
Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and molecular techniques (16S rRNA gene sequencing) permit the identification of rare bacterial pathogens in routine diagnostics. The goal of this protocol lies in the combination of both techniques which leads to more accurate and reliable data.
FAQs
Mass spectrometry provides two complementary types of evidence: measured peptide masses and fragmentation patterns that reveal information about peptide composition and sequence. These measurements generate sequence-related data that can be compared with reference entries through sequence alignment. Agreement between the experimental signals and a database sequence strengthens the assignment, while mismatches can indicate a related protein or a chemically modified form.
Residue composition provides a chemical profile of the amino acids present, while peptide bonds define how those residues are connected in the protein chain. Conserved motifs are recurring sequence features shared among related proteins and can help distinguish biologically similar candidates. Considering these properties together gives identification more chemical and structural context than relying on a single measured feature.
Post-translational modifications alter the chemical characteristics of a protein or its peptides and therefore may influence measured sequence evidence. A candidate sequence must be considered alongside possible modification-related differences rather than treated as an unmodified reference automatically. Including these features helps researchers assess whether an observed molecular pattern is consistent with the proposed protein and improves interpretation of identification confidence.
A typical workflow begins with experimental measurement of peptide masses or fragmentation patterns. The resulting sequence information is then compared with reference protein entries, commonly through sequence alignment. Researchers evaluate how well the measured evidence matches candidate sequences, considering residue features, conserved motifs, and possible modifications. The final interpretation connects the strongest sequence-supported candidate with the sample under study.
Protein sequence identification supports protein characterization and structural studies by connecting chemical measurements with molecular sequence information. It also contributes to pathway analysis, where identified proteins help clarify biological relationships, and to quality control, where sequence evidence can help evaluate a protein sample. These uses make the approach relevant whenever researchers need to interpret protein composition or molecular identity.
Comparing sequence-related measurements across samples can help researchers examine molecular changes associated with different experimental or clinical conditions. Sequence features, conserved motifs, and post-translational modifications provide chemical context for interpreting those differences. The method does not merely name a protein; it can also support characterization of altered molecular forms and help relate observed patterns to broader biochemical investigations.