# "Palaeoproteomics of Andean Camelid fibers" project
DMP

Youri van den Hurk, Elise Dufour, Séverine Zirah, Nicolas Goepfert

► To cite this version:

Youri van den Hurk, Elise Dufour, Séverine Zirah, Nicolas Goepfert. "Palaeoproteomics of Andean Camelid fibers" project DMP. MNHN. 2025. hal-05323485

HAL Id: hal-05323485

https://hal.science/hal-05323485v1

Submitted on 21 Oct 2025

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# "Palaeoproteomics of Andean Camelid fibers" project DMP

A Data Management Plan created using DMP OPIDoR, based on the "Science Europe : modèle structuré" template provided by Science Europe.

## Renseignements sur le plan

**Titre du plan** "Palaeoproteomics of Andean Camelid fibers" project DMP

**Version** Version initiale

**Objet/périmètre du plan** The objective of this plan is to keep the data safe and secure and allow for all the members to be able to use it.

**Domaines de recherche (selon classification de l'OCDE)** History and archaeology

**Langue** eng

**Date de création** 2024-01-09

**Date de dernière modification** 2024-01-19

**Identifiant** DMP_20240118

**Type d'identifiant** Identifiant local

**Licence** Creative Commons Attribution Non Commercial 4.0 International

## Renseignements sur le projet

**Titre du projet** Palaeoproteomics of Andean Camelid fibers

**Acronyme** FABRIC
Résumé

Large numbers of Pre-Hispanic Andean textile specimens were recovered during various excavations in the Mochica culture (CE 100-850) area in modern Peru. The Mochica culture was of the most flourishing cultures along Peru's northern coast. The fiber specimens found represent wool balls, spindles, textiles, and naturally mummified camelid fleeces from Peruvian archaeological sites (Huanchaquito-Las Llamas and El Brujo) curated in Peru and in the Musée d'Archéologie Nationale (MAN). These textiles are both works of art and also represent a unique biocultural archive with the potential to provide deep-time data regarding the social, cultural, ideological, and historical ecological history of the past Mochica society. Understanding the cultural choices that governed the design and usage of textiles necessitates to document the nature of the animal fibers used.

For the creation of these textiles, camelid fibers where used, which can either
derive from the domesticated llama (Lama glama) or alpaca (Vicugna pacos),
or their wild ancestors, the vicuña (Vicugna vicugna) or guanaco (Lama
guanicoe). Fiber morphology does not allow to differentiate between the four
taxa and by extension therefore limits assessments of past exploitation of
camelids in Peru.

Molecular analyses of the keratin and keratin associated proteins (KAP), which are robust and potentially species-specific proteins in animal fibers, can provide insight into the past exploitation of these four taxa. Palaeoproteomic analysis characterizes the fraction of preserved proteins and provides a molecular signature linked to taxonomic groups. Despite the paucity of references to camelids in publicly available databases, the first taxonomic markers have been produced, but more in-depth analysis is needed to optimize this work.

This project aims to undertake a bottom-up palaeoproteomic approach based on the references sequences for keratins and associated proteins derived from the genomes of the four taxa recently uploaded to NCBI. Peptides of taxonomic interest will be identified in known species fiber specimens and will subsequently be compared with the analysis undertaken on the archaeological specimens. This will allow for the reconstruction of exploitation of camelid fibers by the Mochica.

Moreover, top-down palaeoproteomic analysis will be undertaken on these
specimens as well. This will be done to overcome protein inference difficulties
as a result of multiple keratin sequences being present. This approach will
provide data regarding forms of degradation (diagenetiforms) and thus enables
us to study the diagenetic trajectory of samples through time. KAPs are
especially useful for this, due to their small size (< 100 amino acids) as well as
taxonomic interest. The data will be processed by de novo sequencing and
database search, enabling the corresponding animal species to be assigned.

This project therefore has the potential to both answer historical questions as
well as biomolecular questions relating to the rapidly evolving field of
palaoproteomic analysis. Moreover, the results of this study can provide a
valuable contribution to the identification of illegal trade in vicuña fiber.
**Sources de financement**

* Region Ile de France : FABRIC

* CNRS :

**Date de début** 2023-12-01

**Date de fin** 2024-11-30

**Partenaires**

* Archéozoologie, archéobotanique, Sociétés, pratiques et environnements (200918448T)

* Molécules de Communication et Adaptation des Microorganismes (201119722U)

* Archéologie des Amériques (200012755U)

**Produits de recherche :**

1. From raw material to finished product: selection and dyeing of camelid fibers in pre-Hispanic Andean textiles (Jeu de données)

**Contributeurs**
<table><thead><tr><td>Nom</td><td>Affiliation</td><td>Rôles</td></tr></thead><tbody><tr><td>Dufour Elise</td><td>UMR 7209 AASPE</td><td><ul><li>Coordinateur de projet</li><li>Responsable des questions éthiques</li></ul></td></tr><tr><td>Goepfert Nicolas</td><td>UMR 8096 ARCHAM</td><td></td></tr><tr><td>van den Hurk Youri</td><td></td><td><ul><li>Personne contact pour les données</li><li>Responsable de la documentation des données</li><li>Responsable de la production ou de la collecte des données</li><li>Responsable de la protection des données</li><li>Responsable de la qualité des données</li><li>Responsable des questions éthiques</li><li>Responsable du dépôt et de la diffusion des données</li><li>Responsable du plan</li><li>Responsable du stockage des données</li><li>Responsable du traitement et de l'analyse des données</li><li>Responsable juridique</li></ul></td></tr><tr><td>Zirah Séverine</td><td>UMR 7245 MCAM</td><td><ul><li>Responsable de la conservation à long terme des données</li><li>Responsable de la documentation des données</li><li>Responsable de la protection des données</li><li>Responsable de la qualité des données</li><li>Responsable du dépôt et de la diffusion des données</li><li>Responsable du stockage des données</li><li>Responsable du traitement et de l'analyse des données</li><li>Responsable juridique</li></ul></td></tr></tbody></table>

## Budget

<table><thead><tr><td>Type de coût (Titre)</td><td>Montant</td><td>Etape du cycle de vie</td></tr></thead><tbody><tr><td>Frais d'utilisation du plateau technique (2 forfait Maxis 10 days)</td><td>2400 EUR</td><td>Coûts liés à la collecte/production des données - FABRIC</td></tr></tbody></table>
# 1. Description des données et collecte ou réutilisation de données existantes

## 1.1 Description générale du produit de recherche

<table><tr><td>Nom</td><td>From raw material to finished product: selection and dyeing of camelid fibers in pre-Hispanic Andean textiles</td></tr><tr><td>Description</td><td>One paper detailing the results of LC-MS/MS analysis on the archaeological specimens will be the aimed research product of this project. This will provide valuable information into the past exploitation of camelids by the Mochica culture in ancient Peru.</td></tr><tr><td>Type</td><td>Jeu de données</td></tr><tr><td>Mots clés (texte libre)</td><td>palaeproteomics, South American Camelids, Archaeology</td></tr><tr><td>Langue</td><td>eng</td></tr><tr><td>Date de publication</td><td>2024-01-18</td></tr><tr><td>Contient des données personnelles ?</td><td>Non</td></tr><tr><td>Contient des données sensibles ?</td><td>Non</td></tr><tr><td>Prend en compte des aspects éthiques ?</td><td>Non</td></tr></table>

## 1.2 Est-ce que des données existantes seront réutilisées ?

**Justification**

Existing data generated by Azemárd et al. (2021) will be used to compare the LC-MS/MS results of archaeological specimens against. Additionally, references sequences for keratins and associated proteins derived from the genomes of the four taxa recently uploaded to NCBI will be generated.

Also, the genomes available for South American camelids in NCBI (Fan et al., 2020) will be used to establish a list of potential protein sequences, which will be used in a database search to assign LC-MS/MS data to peptide and protein sequences.

There will be no costs associated with re-using this data

Azémard, C., Dufour, E., Zazzo, A., Wheeler, J.C., Goepfert, N., Marie, A. and Zirah, S, 2021. Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking. *J Proteomics*, 16, 231, 104040. doi: 10.1016/j.jprot.2020.104040.

Fan, R., Gu, Z., Guang, X., Marin, J.C., Varas, v., Gonzalez, B.A., Wheeler, J.C., Hu, Y., Li, E., Sun, X., Yang, X., Zhang, C., Gao, W., He, J., Munch, K., Corbett-Detig, R., Barbato, M., Pan, S., Zhan, X., Bruford, M. and Dong, C., 2020. Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. *Genome Biol* 21, 159. https://doi.org/10.1186/s13059-020-02080-6

**Données réutilisées**

* Caractérisation protéomique et isotopique de fibres textiles animales en contexte archéologique (FIBRES) :
* Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca : https://doi.org/10.1186/s13059-020-02080-6

## 1.3 Comment seront produites/collectées les nouvelles données ?
<table><tr><td>Nom de la méthode</td><td>LC-MS/MS</td></tr><tr><td>Description</td><td>The sample preparation and analysis will be done within two research units: AASPE (UMR 7209 CNRS-MNHN) which conserves the collection of archaeological hair and textile specimens imported from Peru, and MCAM (UMR 7245 CNRS-MNHN), which contains the facilities for biochemistry and mass spectrometry experiments.<br>The archaeological Mochica culture textile specimens will be sampled, aiming to retrieve 2 mg of sample per identified fiber specimen per textile specimen (one specimen might hold multiple kinds of fiber). These specimens will subsequently be washed with milliQ water and a 2:1 chloroform methanol solution, to extract contaminants. These specimens will subsequently be pre-treated and the fibers will be extracted upon incubation under stirring for 3 days at 50°C in 3 mL 25mM Tris-HCl, 2.4 M thiourea, 5M urea (pH 8.5), and dithiothreitol (DTT, 100 mM). The protein extract will be reduced with DTT (5 mM) and alkylated using iodoacetamide (20 mM) and then submitted to ultrafiltration with 0.5 mL centrifugal filter devices with a 3 kDa cut-off, permitting to exchange the extraction buffer with ammonium bicarbonate 50 mM pH 8. The retained fraction will then split in two: (1) half will be used for top-down proteomics (second round of ultrafiltration with a 30 kDa to remove the high Mw proteins. The filtrate will be submitted to LC-MS); (2) the second half will be split in two again: (2a) half will be used for bottom-up proteomics (overnight digestion with trypsin), (2b) the second half will be used for middle-down proteomics (overnight digestion with Endo-AspN).<br>The (1) top-down, (2a) bottom-up and (2b) middle-down samples will be analysed by ultra-high-performance liquid chromatography - mass spectrometry (UHPLC-MS) on an Ultimate 3000-RSLC system (Thermo Scientific) connected to an electrospray ionization - quadrupole-time of flight (ESI-Q-TOF) instrument (Maxis II ETD, Bruker Daltonics). For bottom-up and middle-down samples, data-dependent LC-MS/MS data will be generated. For top-down analysis, we will perform LC-MS, data-dependent LC-MS/MS and targeted LC-MS/MS using collision induced dissociation (CID) and/or electron transfer dissociation (ETD) acquisitions.<br>The LC-MS/MS data be generated for bottom-up and middle-down samples will be analysed using PEAKS DB Studio software version 7.5 (BioInformatics Solutions) and BYONIC software, to assist database-assisted de novo sequencing. PEAKS and BYONIC searches will be performed against a home-made database, constructed from the proteomic and genomic data collected in NCBI for South American camelids. A list of diagnostic peptides potentially distinguishing between Camelidae species will be made based on the literature, alignments of the available sequences, PEAKS, and BYONIC results. For top-down proteomics, protein inference and annotation of MS/MS spectra will be conducted using the dedicated tool Biotools (Bruker).</td></tr></table>

<table><tr><td>Nature des données</td><td>Données expérimentales</td></tr><tr><td>Equipements, plateaux techniques utilisés</td><td><ul><li>Plateau Technique de Spectrométrie de Masse Bio-organique du Muséum national d'Histoire naturelle : PtSMB</li></ul></td></tr><tr><td>Coûts</td><td><ul><li>Frais d'utilisation du plateau technique : 2,400 EUR</li></ul></td></tr></table>

## 2. Documentation et qualité des données

### 2.1 Quelles métadonnées et quelle documentation (par exemple mode d'organisation des données) accompagneront les données ?

<table><tr><td>Description</td><td>Good laboratory practices will be applied and followed throughout the project. For metadata, all relevant information of each experiment (date, procedures, conditions, observations etc.) will be documented rigorously in notebooks or electronic notebooks and progress reports, in order to allow for data re-use and experimental reproduction. All of this information will be included in any publications reporting the data, to permit use and reproducibility by the scientific community.</td></tr><tr><td>Code langue des métadonnées</td><td>eng</td></tr></table>

### 2.2 Quelles seront les méthodes utilisées pour assurer la qualité scientifique des données ?

<table><tr><td>Description</td><td>Experimental data will be controlled by at least two independent experiments (ideally three). Instruments used to obtain the palaeoproteomic data, e.g. LC-MS/MS spectrometer, will be subjected to routine calibration. Peer review of the data acts as the final stage of validation.</td></tr></table>
# 3. Exigences légales et éthiques, code de conduite

## 3.1 Quelles seront les mesures appliquées pour assurer la protection des données à caractère personnel ?

**Description** No personal data will be collected or compiled as part of this project.

## 3.2 Comment les autres questions juridiques, comme la titularité ou les droits de propriété intellectuelle sur les données, seront-elles abordées ? Quelle est la législation applicable en la matière ?

**Description** Intellectual property and ownership of data will be managed according to the rules of each partner institution, and consensus will be obtained among partners. Data will be shared between partners upon request, and each institution will control the means by which the data are shared. All related data will be made available to the community following the publication of the results.

## 3.3 Quels sont les aspects éthiques à prendre en compte lors de la collecte des données ?

**Description** Besides open transparency in the work undertaken by the various partners of the project, no other ethical aspects are recognized as part of this project.

# 4. Traitement et analyse des données

## 4.1 Comment et avec quels moyens seront traitées les données ?

**Description** See section 1.3 for a detailed description on how the data will be generated and processed.

**Equipements, plateaux techniques**
* Plateau Technique de Spectrométrie de Masse Bio-organique du Muséum national d'Histoire naturelle : PtSMB

# 5. Stockage et sauvegarde des données pendant le processus de recherche

## 5.1 Comment les données seront-elles stockées et sauvegardées tout au long du projet ?
**Besoins de stockage**

Access to the data storage space is protected by personal identification and password for each member. The Data storage servers of IT support of MNHN and CNRS guarantee local redundancy of data. Duplicates, or even triplicates, of the data will be produced and stored on external hard drives to ensure the safe keeping of the data.

**Volume estimé des données** 1

**Unité** To

**Equipements, plateaux techniques**

* Molécules de Communication et Adaptation des Microorganismes (MCAM) : UMR 7245 CNRS-MNHN

**Mesures prises pour la sécurité des données**

see above

# 6. Partage des données et conservation à long terme

## 6.1 Comment les données seront-elles partagées ?

**Modalités de partage**

The raw LC-MS/MS data and protein/peptide identification results will be deposited in the ProteomeXchange Consortium via the PRIDE partner repository (https://www.proteomexchange.org/).

If the study permits to reconstruct the sequence of proteins from South American camelids (type I and type II keratins, keratin associated proteins), the sequences will be deposited on NCBI (https://www.ncbi.nlm.nih.gov/protein/).

These data will be shared and made freely available upon publication of the project. A data embargo might be requested after completion of the project, if the final findings have not been published yet.

For French partners, all publications will be deposited into the open archive HAL (https://hal.archives-ouvertes.fr). In addition, open access journals will be preferred for publication of the results.

**Potentiel de réutilisation**

It has the potential to be reused by others analysing South American Camelid fibers, from both archaeological as well a modern zoological perspective

**Entrepôt/Catalogue de données**

* ProteomeXchange : https://www.proteomexchange.org/ ()
* National Center for Biotechnology Information (NCBI) : https://www.ncbi.nlm.nih.gov/ ()

## 6.2 Comment les données seront-elles conservées à long terme ?

**Justification**

For long-term storage, the raw LC-MS and LC-MS/MS data will be stored on a dedicated NAS server in the MCAM unit. The LC-MS/MS data will also be available from ProteomeXchange.

**Volume estimé des données** 1

**Unité** To

**Date de début** 2024-01-01

**Date de fin** 2030-12-31