Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

TY - JOUR

T1 - Assessment of different screening methods for selecting palaeontological bone samples for peptide sequencing

AU - Presslee, Samantha

AU - Penkman, Kirsty

AU - Fischer, Roman

AU - Richards-Slidel, Eden

AU - Southon, John

AU - Hospitaleche, Carolina Acosta

AU - Collins, Matthew

AU - MacPhee, Ross

N1 - © 2020 Elsevier B.V. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy.

PY - 2021/1/6

Y1 - 2021/1/6

N2 - Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. Significance: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.

AB - Ancient proteomics is being applied to samples dating further and further back in time, with many palaeontological specimens providing protein sequence data for phylogenetic analysis as well as protein degradation studies. However, fossils are a precious material and proteomic analysis is destructive and costly. In this paper we consider three different techniques (ATR-FTIR, MALDI-ToF MS and chiral AA analysis) to screen fossil material for potential protein preservation, aiming to maximise the proteomic information recovered and saving costly time consuming analyses which may produce low quality results. It was found that splitting factor and C/P indices from ATR-FTIR were not a reliable indicator of protein survival as they are confounded by secondary mineralisation of the fossil material. Both MALDI-ToF MS and chiral AA analysis results were able to successfully identify samples with surviving proteins, and it is suggested that one or both of these analyses be used for screening palaeontological specimens. Significance: This study has shown both chiral amino acid analysis and MALDI-ToF MS are reliable screening methods for predicting protein survival in fossils. Both these methods are quick, cheap, minimally destructive (1 mg and 15 mg respectively) and can provide crucial additional information about the endogeneity of the surviving proteins. It is hoped that the use of these screening methods will encourage the examination of a wide range of palaeontological specimens for potential proteomic analysis. This in turn will give us a better understanding of protein survival far back in time and under different environmental conditions.

KW - ATR-FTIR

KW - Chiral AA analysis

KW - Collagen

KW - MALDI-ToF MS

KW - Palaeoproteomics

UR - http://www.scopus.com/inward/record.url?scp=85091673792&partnerID=8YFLogxK

U2 - 10.1016/j.jprot.2020.103986

DO - 10.1016/j.jprot.2020.103986

M3 - Article

C2 - 32941991

AN - SCOPUS:85091673792

SN - 1874-3919

VL - 230

JO - JOURNAL OF PROTEOMICS

JF - JOURNAL OF PROTEOMICS

M1 - 103986

ER -