Elucidation of cross-species proteomic effects in human and hominin bone proteome identification through a bioinformatics experiment

BMC Evolutionary Biology
F Welker

Abstract

The study of ancient protein sequences is increasingly focused on the analysis of older samples, including those of ancient hominins. The analysis of such ancient proteomes thereby potentially suffers from "cross-species proteomic effects": the loss of peptide and protein identifications at increased evolutionary distances due to a larger number of protein sequence differences between the database sequence and the analyzed organism. Error-tolerant proteomic search algorithms should theoretically overcome this problem at both the peptide and protein level; however, this has not been demonstrated. If error-tolerant searches do not overcome the cross-species proteomic issue then there might be inherent biases in the identified proteomes. Here, a bioinformatics experiment is performed to test this using a set of modern human bone proteomes and three independent searches against sequence databases at increasing evolutionary distances: the human (0 Ma), chimpanzee (6-8 Ma) and orangutan (16-17 Ma) reference proteomes, respectively. Incorrectly suggested amino acid substitutions are absent when employing adequate filtering criteria for mutable Peptide Spectrum Matches (PSMs), but roughly half of the mutable PSMs were not recovered. As...Continue Reading

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Citations

Jun 7, 2019·Proteomics·Mary Higby SchweitzerWenxia Zheng
Nov 15, 2019·Nature·Frido WelkerEnrico Cappellini
May 3, 2019·Nature·Fahu ChenJean-Jacques Hublin
Apr 10, 2020·Nature·Frido WelkerEnrico Cappellini
Nov 16, 2020·Journal of Proteomics·Carine FromentCatherine Mollereau
Jun 18, 2021·Forensic Science International. Genetics·Glendon J ParkerZachary C Goecker
May 25, 2021·Genome Biology and Evolution·K D AhlquistKelsey E Witt
Dec 18, 2021·Journal of Proteome Research·Elena R SchroeterMary H Schweitzer

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Software Mentioned

PEAKS
Geneious
PEAKS SPIDER
RAxML
Homo
PepNovo
Byonic
house R script
MASCOT
biomaRt

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