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Related Experiment Video

Updated: Jul 11, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Finding haplotypic signatures in proteins.

Jakub Vašíček^1,2, Dafni Skiadopoulou^1,2, Ksenia G Kuznetsova^1,2

¹Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.

|November 3, 2023

Summary

This summary is machine-generated.

Protein haplotypes, arising from genetic variations, impact proteomic searches. This study found that multiple amino acid substitutions can occur in single peptides, affecting protein identification and highlighting the need for improved error estimation in proteomics.

Keywords:

bioinformatics haplotype post-translational modification protein proteogenomics

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Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

Area of Science:

Genomics
Proteomics
Bioinformatics

Background:

Haplotypes, nonrandom allele distributions, are crucial in genetic studies.
Protein-coding genes can produce distinct protein haplotypes due to allele combinations.
Current proteomic searches do not account for protein haplotypes, obscuring their impact.

Purpose of the Study:

To investigate how common genetic haplotypes influence the proteomic search space.
To assess the feasibility of matching peptides with multiple amino acid substitutions in proteomic data.
To understand the discoverability of haplotype-specific peptides.

Main Methods:

Analysis of common genetic haplotypes and their encoded protein variations.
Investigating co-occurrence of amino acid substitutions within peptides after tryptic digestion.
Matching identified peptides against a public mass spectrometry dataset.

Main Results:

12.42% of discoverable amino acid substitutions encoded by common haplotypes can co-occur in peptides.
352 spectra matched to multivariant peptides, covering 6.37% of identified amino acid substitutions.
Reliability assessment of matches for complex proteomic searches remains challenging.

Conclusions:

Refined error rate estimation procedures are necessary for complex proteomic searches involving protein haplotypes.
Advancements in analyzing protein haplotypes will enhance proteomics' ability to reveal consequences of common variation.
Future proteomics studies will offer new insights into genetic variation's impact across tissues and time.