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Proteins are macromolecules built from one or more chains of amino acids.^[1] They are dynamic entities, performing a wide range of biological functions and are essential for living organisms.^[2] The term protein was first coined by Jöns Jacob Berzelius in 1838, originated from the Greek word proteios (meaning: of first rank).^[3] Collections of proteins, or proteomes are complete sets of protein mixtures associated with a cell, a tissue or an organism.^[4] The study of modern proteins has been propelled by advances in molecular biology, analytical chemistry, and bioinformatics. The word proteomics was created by Marc Wilkins in 1995 to denote the large-scale analysis of proteomes.^[5]

Similarly, ancient proteins are complex mixtures and the term palaeoproteomics is used to characterise the study of proteomes in the past.^[6] Ancients proteins have been recovered from a wide range of archaeological materials, including bones,^[7] teeth,^[8] eggshells,^[9] leathers,^[10] parchments,^[11] ceramics,^[12] painting binders^[13] and well-preserved soft tissues like gut intestines.^[14] These preserved proteins have provided valuable information about taxonomic identification, evolution history (phylogeny), diet, health, disease, technology and social dynamics in the past.

Like modern proteomics, the study of ancient proteins has also been enabled by technological advances. Various analytical techniques, for example, amino acid profiling, racemisation dating, immunodetection, Edman sequencing, peptide mass fingerprinting, and tandem mass spectrometry have been used to analyse ancient proteins.^[15] The introduction of high-performance mass spectrometry (for example, Orbitrap) in 2000 has revolutionised the field, since the entire preserved sequences of complex proteomes can be characterised.^[16]

Over the past decade, the study of ancient proteins has evolved into a well-established field in archaeological science. However, like the research of aDNA (ancient DNA preserved in archaeological remains), it has been limited by several challenges such as the coverage of reference databases, identification, contamination and authentication.^[17] Researchers have been working on standardising sampling, extraction, data analysis and reporting for ancient proteins.^[18] Novel computational tools such as de novo sequencing^[19] and open research^[20] may also improve the identification of ancient proteomes.

History: the pioneers of ancient protein studies

Philip Abelson, Edgar Hare and Thomas Hoering

Abelson, Hare and Hoering were leading the studies of ancient proteins between the 1950s and the early 1970s.^[21] Abelson was directing the Geophysical Laboratory at the Carnegie Institute (Washington, DC) between 1953 and 1971, and he was the first to discover amino acids in fossils.^[22] Hare joined the team and specialised in amino acid racemisation (the conversion of L- to D-amino acids after the death of organisms). D/L ratios were used to date various ancient tissues such as bones, shells and marine sediments.^[23] Hoering was another prominent member, contributing to the advancement of isotopes and mass spectrometry.^[24] This golden trio drew many talented biologists, geologists, chemists and physicists to the field, including Marilyn Fogel,^[25] John Hedges^[26] and Noreen Tuross.^[27]

Ralph Wyckoff

Wyckoff was a pioneer in X-ray crystallography and electron microscopy.^[28] Using microscopic images, he demonstrated the variability and damage of collagen fibres in ancient bones and shells.^[29] His research contributed to the understanding of protein diagenesis (degradation) in the late 1960s, and highlighted that ancient amino acid profiles alone might not be sufficient for protein identification.^[30]

Margaret Jope and Peter Wesbroek

Jope and Wesbroek were leading experts in shell proteins and crystallisation.^[31] Wesbroek later established Geobiochemistry laboratory at the University of Leiden, focusing on biomineralisation and how this process facilitated protein survival.^[32] He also pioneered the use of antibodies for the study of ancient proteins in the 1970s and 1980s, utilising different immunological techniques such as Ouchterlony double immunodiffusion (interactions of antibodies and antigens in a gel).^[33]

Peggy Ostrom

Ostrom championed the use of mass spectrometry since the 1990s.^[34] She was the first to improve the sequence coverage of ancient proteins by combining different techniques such as peptide mass fingerprinting and liquid chromatography-tandem mass spectrometry (LC-MS/MS).^[35]

The biochemistry of ancient proteins

Formation & incorporation

Understanding how ancient proteins are formed and incorporated into archaeological materials are essential in sampling, evaluating contamination and planning analyses.^[6] Generally, for ancient proteins in proteinaceous tissues, notably, collagens in bones, keratins in wool, amelogenin in tooth enamel, and intracrystalline proteins in shells, they might be incorporated during the time of tissue formation.^[36]^[37]^[38] However, the formation of proteinaceous tissues is often complex, dynamic and affected by various factors such pH, metals, ion concentration, diet plus other biological, chemical and physical parameters.^[39] One of the most characterised phenomena is bone mineralisation, a process by which hydroxyapatite crystals are deposited within collagen fibres, forming a matrix.^[40] Despite extensive research, bone scaffolding is still a challenge, and the role of non-collagenous proteins (a wide range of proteoglycans and other proteins) remains poorly understood.^[41]

Another category is complex and potentially mineralised tissues, such as ancient human dental calculi and ceramic vessels. Dental calculi are defined as calcified biofilms, created and mediated by interactions between calcium phosphate ions and a wide range of oral microbial, human, and food proteins during episodic biomineralisation.^[42]^[43] Similarly, the minerals of a ceramic matrix might interact with food proteins during food processing and cooking. This is best explained by calcite deposits adhering to the inside of archaeological ceramic vessels.^[12] These protein-rich mineralised deposits might be formed during repeated cooking using hard water and scaling.^[44]

Preservation

Organic (containing carbon) biomolecules like proteins are prone to degradation.^[45] For example, experimental studies demonstrate that robust, fibrous and hydrophobic keratins such as feathers and woollen fabrics decay quickly at room temperature.^[46]^[47] Indeed ancient proteins are exceptional, and they are often recovered from extreme burial contexts, especially dry and cold environments.^[48]^[49] This is because the lack of water and low temperature may slow down hydrolysis, microbial attack and enzymatic activities.^[36]

There are also proteins whose chemical and physical properties may enable their preservation in the long term. The best example is Type 1 collagen; it is one of the most abundant proteins in skin (80-85%) and bones (80-90%) extracellular matrices.^[50] It is also mineralised, organised in a triple helix and stabilised by hydrogen bonding.^[51] Type 1 collagen has been routinely extracted from ancient bones, leathers, and parchments; these characteristics may contribute to its stability over time.^[52] Another common protein in the archaeological record is milk beta-lactoglobulin, often recovered from ancient dental calculi.^[53] Beta-lactoglobulin is a small whey protein with a molecular mass of around 18400 Da (dalton).^[54] It is resistant to heating and enzymatic degradation; structurally, it has a beta-barrel associated with binding to small hydrophobic molecules such as fatty acids, forming stable polymers.^[55]^[56]

Given that proteins vary in abundance, size, hydrophobicity (water insolubility), structure, conformation (shape), function and stability, understanding protein preservation is challenging.^[17] While there are common determinants of protein survival, including thermal history (temperature/time), burial conditions (pH/soil chemistry/water table) and protein properties (neighbouring amino acids/secondary structure/tertiary folding/proteome content), there is no clear answer and protein diagenesis is still an active research field.^[6]

Structure & damage patterns

Generally, proteins have four levels of structural complexity: quaternary (multiple polypeptides, or subunits), tertiary (the 3D folding of a polypeptide), secondary (alpha helices/beta sheets/random coils) and primary structure (linear amino acid sequences linked by peptide bonds).^[57] Ancient proteins are expected to lose their structural integrity over time, due to denaturation (protein unfolding) or other diagenetic processes.^[58]

Ancient proteins also tend to be fragmented, damaged and altered. Proteins can be cleaved into small fragments over time, since hydrolysis (the addition of water) breaks peptide bonds (covalent bonds between two neighbouring alpha-amino acids).^[59] In terms of post-translational modifications (changes occur after RNA translation), ancient proteins are often characterised by extensive damage such as oxidation (methionine), hydroxylation (proline), deamidation (glutamine/asparagine), citrullination (arginine), phosphorylation (serine/threonine/tyrosine), N-terminus glutamate to pyroglutamate and the addition of advanced glycation products to lysine or arginine.^[60]^[17] Among these modifications, glutamine deamidation is one of the most time-dependent processes.^[61] Glutamine deamidation is mostly a non-enzymatic process, by which glutamine is converted to glutamic acid (+0.98406 Da) via side-chain hydrolysis or the formation of a glutarimide ring.^[62] It is a slow conversion with a long half-time, depending on adjacent amino acids, secondary structures, 3D folding, pH, temperature and other factors.^[63] Bioinformatic tools are available to calculate bulk and site-specific deamidation rates of ancient proteins.^[64]

Palaeoproteomics

Overview

Palaeoproteomics is a fast-developing field that combines archaeology, biology, chemistry and heritage studies. Comparable to its high-profile sister field, aDNA analysis, the extraction, identification and authentication of ancient proteins are challenging, since both ancient DNA and proteins tend to be ultrashort, highly fragmented, extensively damaged and chemically modified.^[6]^[65]

However, ancient proteins are still one of the most informative biomolecules. Proteins tend to degrade more slowly than DNA, especially biomineralised proteins.^[37]^[66] While ancient lipids can be used to differentiate between marine, plant and animal fats^[67], ancient protein data is high-resolution with taxon- and tissue-specificities.

To date, ancient peptide sequences have been successfully extracted and securely characterised from various archaeological remains, including a 3.8 Ma (million year) ostrich eggshell,^[37] 1.77 Ma Homo erectus teeth,^[68] a 0.16 Ma Denisovan jawbone^[69] and several Neolithic (6000-5600 cal BC) pots.^[12] Hence, palaeoproteomics has provided valuable insight into past evolutionary relationships, extinct species and societies.

Extraction

Generally, there are two approaches: a digestion-free, top-down method and bottom-up proteomics. Top-down proteomics is seldom used to analyse ancient proteins due to analytical and computational difficulties.^[70] For bottom-up, or shotgun proteomics, ancient proteins are digested into peptides using enzymes, for example trypsin. Mineralised archaeological remains such as bones, teeth, shells, dental calculi and ceramics require an extra demineralisation step to release proteins from mineral matrices.^[6] This is often achieved by using a weak acid (ethylenediaminetetraacetic acid, EDTA) or cold (4 °C) hydrochloric acid (HCl) to minimise chemical modifications that may introduced during extraction.^[71]

To make ancient proteins soluble, heat, sonication, chaotropic agents (urea/guanidine hydrochloride, GnHCl), detergents or other buffers can be used.^[6] Alkylation and reduction are often included for cysteine to disrupt disulfide bonds and avoid crosslinking.^[72]

After demineralisation, protein solubilisation, alkylation and reduction, buffer exchange is needed to ensure that extracts are compatible with downstream analysis. Currently, there are three widely-used protocols for ancient proteins and gels (GASP)^[73], filters (FASP)^[74] and magnetic beads (SP3)^[75] can be used for this purpose. Once buffer exchange is completed, extracts are incubated with digestion enzymes, then concentrated, purified and desalted.

For non-mineralised archaeological materials such as parchments, leathers and paintings, demineralisation is not necessary, and protocols can be changed depending on sample preservation and sampling size.^[11]

Instrumentation and data analysis

Nowadays, palaeoproteomics is dominated by two mass spectrometry-based techniques: MALDI-ToF (matrix-assisted laser desorption/ionisation-time-of-flight) and LC-MS/MS. MALDI-ToF is used to determine the mass-to-charge (m/z) ratios of ions and their peak patterns.^[76] Digested peptides are spotted on a MALDI plate, co-crystallise with a matrix (mainly α-cyano-4-hydroxycinnamic acid, CHCA); a laser excites and ionises the matrix, then its time to travel a vacuum tube is measured and converted to a spectrum of m/z ratios and intensities.^[77]

Since only peak patterns, not entire amino acid sequences of digested peptides are characterised, peptide markers are needed for pattern matching and ancient protein identification.^[76] In archaeological contexts, MALDI-ToF has been routinely used for bones and collagens in a field known as ZooMS (zooarchaeolgy by mass spectrometry).^[7]

LC-MS/MS is another widely used approach. It is a powerful analytical technique to separate, sequence and quantify complex protein mixtures.^[78] The first step in LC-MS/MS is liquid chromatography. Protein mixtures are separated in a liquid mobile phase using a stationary column.^[79] How liquid analytes interact with a stationary phase depends on their size, charge, hydrophobicity and affinity.^[80] These differences lead to distinct elution and retention time (when a component of a mixture exit a column). After chromatographic separation, protein components are ionised and introduced into mass spectrometers.^[81] During a first mass scan (MS1), the m/z ratios of precursor ions are measured. Selected precursors are further fragmented and the m/z ratios of fragment ions are determined in a second mass scan (MS2). There are different fragmentation methods, for example, high-energy C-trap dissociation (HCD) and collision induced dissociation (CID), but b- and y-ions are frequently targeted.^[82]

Search engines and software tools are often used to process ancient MS/MS data, including MaxQuant, Mascot and PEAKS.^[83]^[84]^[85] Protein sequence data can be downloaded from public genebanks (UniProt/NCBI) and exported as FASTA files for sequencing algorithms.^[18] Recently, open search engines such as MetaMorpheus, pFind and Fragpipe have received attention, because they make it possible to identify all modifications associated with peptide spectral matches (PSMs).^[86]^[87]^[88]

De novo sequencing is also possible for the analysis of ancient MS/MS spectra. It is a sequencing technique that assembles amino acid sequences directly from spectra without reference databases.^[89] Advances in deep learning also lead to the development of multiple pipelines such as DeNovoGUI, DeepNovo2 and Casanovo.^[90]^[91]^[92] However, it may be challenging to evaluate the outputs of de novo sequences and optimisation may be required for ancient proteins to minimise false positives and overfitting.^[6]

Palaeoproteomes

Collagen Type I

The analysis of ancient bone proteomes has primarily focused on the identification of collagen type I (COL1), the dominant protein found in mineralized tissues. Collagen is highly conserved across species and comprises about 90% of organic bone compounds. Fibrillar collagens, of which COL1 is categorized, are thought to have evolved from a common metazoan ancestor, thus contributing to their abundance and importance in the fossil record.

Collagen has also been found to survive much longer than other non-collagenous proteins in fossilized specimens, and the protein remains intact beyond the degradation of ancient DNA (aDNA). Its tightly coiled triple-helical structure (consisting of two genetically identical alpha-1 chains and a third genetically distinct alpha-2 chain) and hydrophobic composition also make this protein an excellent candidate for survival, even in temperate and humid climates that support the rapid break down of organic molecules.

The taxonomic resolution of collagen has been thoroughly investigated, and it is known that amino acid substitutions can be resolved to the genus level in most medium and large mammals. Species-level identification is also possible, even in small mammal remains from high thermal climates. It is for these reasons that COL1 remains a key protein in paleoproteomics and phylogenetic investigations.

Non-collagenous proteins

The remaining 10% of organic bone molecules are non-collagenous proteins (NCPs). The most abundant NCP, osteocalcin, is a bone and dentin protein involved in bone assembly, often used as a marker for the bone formation process. Preserved osteocalcin was first detected via mass spectrometry (MALDI-MS) in 10,000 year-old bison bone and a 53,000-year-old walrus bone, revealing phylogenetic reconstruction potential beyond the temporal limits of aDNA.

More advanced proteomic techniques have enabled the investigation of additional NCPs present in the bone extracellular matrix. Though type I collagen is the longest lived protein identified in fossilized bone specimens, the identification and sequencing of NCPs may allow for a greater taxonomic resolution than collagen-based methods.

Other complex mixtures

Proteomic analysis has also been applied to other fossilized and ancient materials. The examination of damaged artifacts through the sequencing of their keratin peptides has allowed researchers to discriminate between horn and hoof remains of important species used at archeological sites. The keratin of textiles and animal skins worn by Ötzi, the Iceman, were also identified using peptide mass fingerprinting (PMF) from the ancient samples and from reference species. Immune response proteins have illuminated the presence of infections and diseases in multiple studies of mummified human remains. Additionally, the identification of egg proteins, caseins, whey globulins, and other proteinaceous materials used as binders in the paint of historical artworks has allowed for a better understanding of proper conservation methods.

Analytical challenges

Dinosaur collagen

A 2007 paleontology study reported the alleged discovery of endogenous collagen peptides in 68 mya Tyrannosaurus rex fossils. This claim purported survival beyond experimental decay rates, leading to controversy in the emerging field. The same team again reported finding similar collagen peptide sequence matches in 2009 from 80 mya hadrosaur fossils belonging to Brachylophosaurus canadensis.

Subsequent studies have reanalyzed the original T. rex sequence data to infer that the sample was predominantly laboratory contaminants, soil bacteria, and bird-like hemoglobin and collagen; the former protein is typically only seen in relatively recent samples. Another exceptionally preserved hadrosaur from the Hell Creek Formation (USA), yielded none of the previous findings despite extensive testing, and only the presence of protein breakdown products were detected.

Further experimentation demonstrated that contamination from other specimens present in the T. rex lab cannot be ruled out. Every peptide that was considered unique to both dinosaurs in the 2009 study could be matched to modern ostrich with much greater confidence than could be placed on their own, unique identifications.

While there have been several methods described to support the authenticity of paleoproteomics, including immunological or amino acid composition and racemization data, both of these approaches have limitations and are known to yield false-positive reactions in fossils. Great care must be taken to rule out contamination by determining whether sequences differ from those of all extant taxa present in the laboratory environments. Deamidation has also been proposed as an effective method for distinguishing between endogenous and contaminating NCPs, when extraction protocols may permit for this evaluation. This kind of research has almost the same goals with projects focused on studying the impact of differential therapeutic treatments on the hippocampus proteome of depressed mice but also has tremendously different sets of instruments. ^{[citation needed]}

Future directions

Paleoproteomics is still a young field, with most complex proteomes only being discovered in the last decade. Current proteomic methods greatly suffer from the fact that it is not a true form of sequencing, relying on probability-matching against expected results. While several MS methods are being employed to increase the robustness of retrievable data, these techniques also increase the sensitivities to contamination.

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@@ Line 2: / Line 2: @@
 [[Protein]]s are [[macromolecule]]s built from one or more chains of [[amino acid]]s.<ref>{{Cite book | vauthors = Nelson DL, Cox MM   |url= http://worldcat.org/oclc/1325116516 |title=Lehninger Principles of Biochemistry |date=2021 |isbn=978-1-319-32239-7 |oclc=1325116516}}</ref> They are dynamic entities, performing a wide range of biological functions and are essential for living [[organism]]s.<ref>{{Cite book |url=https://link.springer.com/book/10.1007/978-0-387-68480-2 |title=Fundamentals of Protein Structure and Function |year=2007 |language=en |doi=10.1007/978-0-387-68480-2|isbn=978-0-387-26352-6 }}</ref> The term protein was first coined by [[Jöns Jacob Berzelius]] in 1838, originated from the Greek word ''proteios'' (meaning: of first rank).<ref>{{cite journal | vauthors = Cristea IM, Gaskell SJ, Whetton AD | title = Proteomics techniques and their application to hematology | journal = Blood | volume = 103 | issue = 10 | pages = 3624–3634 | date = May 2004 | pmid = 14726377 | doi = 10.1182/blood-2003-09-3295 }}</ref> Collections of proteins, or [[proteome]]s are complete sets of protein mixtures associated with a [[Cell (biology)|cell]], a [[Tissue (biology)|tissue]] or an [[organism]].<ref>{{cite journal | vauthors = Chen CH | title = Review of a current role of mass spectrometry for proteome research | journal = Analytica Chimica Acta | volume = 624 | issue = 1 | pages = 16–36 | date = August 2008 | pmid = 18706308 | doi = 10.1016/j.aca.2008.06.017 }}</ref> The study of modern proteins has been propelled by advances in [[molecular biology]], [[analytical chemistry]], and [[bioinformatics]]. The word [[proteomics]] was created by [[Marc Wilkins (geneticist)|Marc Wilkins]] in 1995 to denote the large-scale analysis of [[Proteome|proteomes]].<ref>{{cite journal | vauthors = Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL | title = Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it | journal = Biotechnology & Genetic Engineering Reviews | volume = 13 | issue = 1 | pages = 19–50 | date = 1996 | pmid = 8948108 | doi = 10.1080/02648725.1996.10647923 }}</ref>
-Similarly, [[Ancient protein|ancient proteins]] are complex mixtures and the term palaeoproteomics is used to characterise the study of [[Proteome|proteomes]] in the past.<ref name=":0">{{cite journal | vauthors = Warinner C, Korzow Richter K, Collins MJ | title = Paleoproteomics | journal = Chemical Reviews | volume = 122 | issue = 16 | pages = 13401–13446 | date = August 2022 | pmid = 35839101 | pmc = 9412968 | doi = 10.1021/acs.chemrev.1c00703 }}</ref> Ancients proteins have been recovered from a wide range of archaeological materials, including [[Bone|bones]],<ref>{{cite journal | vauthors = Buckley M, Collins M, Thomas-Oates J, Wilson JC | title = Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry | journal = Rapid Communications in Mass Spectrometry | volume = 23 | issue = 23 | pages = 3843–3854 | date = December 2009 | pmid = 19899187 | doi = 10.1002/rcm.4316 | bibcode = 2009RCMS...23.3843B }}</ref> [[Tooth|teeth]],<ref>{{cite journal | vauthors = Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SK, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MT, Olsen JV, Lordkipanidze D, Willerslev E | display-authors = 6 | title = Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny | journal = Nature | volume = 574 | issue = 7776 | pages = 103–107 | date = October 2019 | pmid = 31511700 | doi = 10.1038/s41586-019-1555-y | pmc = 6894936 | bibcode = 2019Natur.574..103C }}</ref> [[Eggshell|eggshells]],<ref>{{cite journal | vauthors = Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, Clarke J, Legendre LJ, Boano R, Sicheritz-Pontén T, Magee J, Zhang G, Bunce M, Collins MJ, Miller G | display-authors = 6 | title = Ancient proteins resolve controversy over the identity of <i>Genyornis</i> eggshell | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 119 | issue = 43 | pages = e2109326119 | date = October 2022 | pmid = 35609205 | doi = 10.1073/pnas.2109326119 | s2cid = 249045755 }}</ref> [[Leather|leathers]],<ref>{{Cite journal | vauthors = Elnaggar A, Osama A, Anwar AM, Ezzeldin S, Abou Elhassan S, Ebeid H, Leona M, Magdeldin S | display-authors = 6 |date=2022-11-09 |title=Paleoproteomic profiling for identification of animal skin species in ancient Egyptian archaeological leather using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) |url=https://doi.org/10.1186/s40494-022-00816-0 |journal=Heritage Science |volume=10 |issue=1 |pages=182 |doi=10.1186/s40494-022-00816-0 | s2cid = 253399828 |issn=2050-7445}}</ref> [[Parchment|parchments]],<ref name=":1">{{Cite journal | vauthors = Fiddyment S, Teasdale MD, Vnouček J, Lévêque É, Binois A, Collins MJ |date=2019-06-07 |title=So you want to do biocodicology? A field guide to the biological analysis of parchment |journal=Heritage Science |language=en |volume=7 |issue=1 |pages=35 |doi=10.1186/s40494-019-0278-6 |s2cid=195245888 |issn=2050-7445}}</ref> [[Ceramic|ceramics]],<ref name=":2">{{cite journal | vauthors = Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, Lucquin A, Spindler L, Anvari J, Stroud E, Biehl PF, Speller C, Boivin N, Mackie M, Jersie-Christensen RR, Olsen JV, Collins MJ, Craig OE, Rosenstock E | display-authors = 6 | title = Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers | journal = Nature Communications | volume = 9 | issue = 1 | pages = 4064 | date = October 2018 | pmid = 30283003 | doi = 10.1038/s41467-018-06335-6 | pmc = 6170438 | bibcode = 2018NatCo...9.4064H }}</ref> painting binders<ref>{{cite journal | vauthors = Dallongeville S, Garnier N, Rolando C, Tokarski C | title = Proteins in Art, Archaeology, and Paleontology: From Detection to Identification | journal = Chemical Reviews | volume = 116 | issue = 1 | pages = 2–79 | date = January 2016 | pmid = 26709533 | doi = 10.1021/acs.chemrev.5b00037 }}</ref> and well-preserved soft tissues like [[Gastrointestinal tract|gut intestines]].<ref>{{cite journal | vauthors = Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Tecchiati U, Putzer A, Palazoglu M, Meissen J, Lösch S, Rausch P, Baines JF, Kim BJ, An HJ, Gostner P, Egarter-Vigl E, Malfertheiner P, Keller A, Stark RW, Wenk M, Bishop D, Bradley DG, Fiehn O, Engstrand L, Moritz RL, Doble P, Franke A, Nebel A, Oeggl K, Rattei T, Grimm R, Zink A | display-authors = 6 | title = The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals | journal = Current Biology | volume = 28 | issue = 14 | pages = 2348–2355.e9 | date = July 2018 | pmid = 30017480 | doi = 10.1016/j.cub.2018.05.067 | pmc = 6065529 }}</ref> These preserved proteins have provided valuable information about [[Taxonomy|taxonomic identification]], evolution history ([[Phylogenetic tree|phylogeny]]), diet, health, disease, technology and social dynamics in the past.
+Similarly, [[Ancient protein|ancient proteins]] are complex mixtures and the term palaeoproteomics is used to characterise the study of [[Proteome|proteomes]] in the past.<ref name=":0">{{cite journal | vauthors = Warinner C, Korzow Richter K, Collins MJ | title = Paleoproteomics | journal = Chemical Reviews | volume = 122 | issue = 16 | pages = 13401–13446 | date = August 2022 | pmid = 35839101 | pmc = 9412968 | doi = 10.1021/acs.chemrev.1c00703 }}</ref> Ancients proteins have been recovered from a wide range of archaeological materials, including [[Bone|bones]],<ref name=":6">{{cite journal | vauthors = Buckley M, Collins M, Thomas-Oates J, Wilson JC | title = Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry | journal = Rapid Communications in Mass Spectrometry | volume = 23 | issue = 23 | pages = 3843–3854 | date = December 2009 | pmid = 19899187 | doi = 10.1002/rcm.4316 | bibcode = 2009RCMS...23.3843B }}</ref> [[Tooth|teeth]],<ref>{{cite journal | vauthors = Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, Fotakis AK, Lyon D, Moreno-Mayar JV, Bukhsianidze M, Rakownikow Jersie-Christensen R, Mackie M, Ginolhac A, Ferring R, Tappen M, Palkopoulou E, Dickinson MR, Stafford TW, Chan YL, Götherström A, Nathan SK, Heintzman PD, Kapp JD, Kirillova I, Moodley Y, Agusti J, Kahlke RD, Kiladze G, Martínez-Navarro B, Liu S, Sandoval Velasco M, Sinding MS, Kelstrup CD, Allentoft ME, Orlando L, Penkman K, Shapiro B, Rook L, Dalén L, Gilbert MT, Olsen JV, Lordkipanidze D, Willerslev E | display-authors = 6 | title = Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny | journal = Nature | volume = 574 | issue = 7776 | pages = 103–107 | date = October 2019 | pmid = 31511700 | doi = 10.1038/s41586-019-1555-y | pmc = 6894936 | bibcode = 2019Natur.574..103C }}</ref> [[Eggshell|eggshells]],<ref>{{cite journal | vauthors = Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, Clarke J, Legendre LJ, Boano R, Sicheritz-Pontén T, Magee J, Zhang G, Bunce M, Collins MJ, Miller G | display-authors = 6 | title = Ancient proteins resolve controversy over the identity of <i>Genyornis</i> eggshell | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 119 | issue = 43 | pages = e2109326119 | date = October 2022 | pmid = 35609205 | doi = 10.1073/pnas.2109326119 | s2cid = 249045755 }}</ref> [[Leather|leathers]],<ref>{{Cite journal | vauthors = Elnaggar A, Osama A, Anwar AM, Ezzeldin S, Abou Elhassan S, Ebeid H, Leona M, Magdeldin S | display-authors = 6 |date=2022-11-09 |title=Paleoproteomic profiling for identification of animal skin species in ancient Egyptian archaeological leather using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) |url=https://doi.org/10.1186/s40494-022-00816-0 |journal=Heritage Science |volume=10 |issue=1 |pages=182 |doi=10.1186/s40494-022-00816-0 | s2cid = 253399828 |issn=2050-7445}}</ref> [[Parchment|parchments]],<ref name=":1">{{Cite journal | vauthors = Fiddyment S, Teasdale MD, Vnouček J, Lévêque É, Binois A, Collins MJ |date=2019-06-07 |title=So you want to do biocodicology? A field guide to the biological analysis of parchment |journal=Heritage Science |language=en |volume=7 |issue=1 |pages=35 |doi=10.1186/s40494-019-0278-6 |s2cid=195245888 |issn=2050-7445}}</ref> [[Ceramic|ceramics]],<ref name=":2">{{cite journal | vauthors = Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, Lucquin A, Spindler L, Anvari J, Stroud E, Biehl PF, Speller C, Boivin N, Mackie M, Jersie-Christensen RR, Olsen JV, Collins MJ, Craig OE, Rosenstock E | display-authors = 6 | title = Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers | journal = Nature Communications | volume = 9 | issue = 1 | pages = 4064 | date = October 2018 | pmid = 30283003 | doi = 10.1038/s41467-018-06335-6 | pmc = 6170438 | bibcode = 2018NatCo...9.4064H }}</ref> painting binders<ref>{{cite journal | vauthors = Dallongeville S, Garnier N, Rolando C, Tokarski C | title = Proteins in Art, Archaeology, and Paleontology: From Detection to Identification | journal = Chemical Reviews | volume = 116 | issue = 1 | pages = 2–79 | date = January 2016 | pmid = 26709533 | doi = 10.1021/acs.chemrev.5b00037 }}</ref> and well-preserved soft tissues like [[Gastrointestinal tract|gut intestines]].<ref>{{cite journal | vauthors = Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Tecchiati U, Putzer A, Palazoglu M, Meissen J, Lösch S, Rausch P, Baines JF, Kim BJ, An HJ, Gostner P, Egarter-Vigl E, Malfertheiner P, Keller A, Stark RW, Wenk M, Bishop D, Bradley DG, Fiehn O, Engstrand L, Moritz RL, Doble P, Franke A, Nebel A, Oeggl K, Rattei T, Grimm R, Zink A | display-authors = 6 | title = The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals | journal = Current Biology | volume = 28 | issue = 14 | pages = 2348–2355.e9 | date = July 2018 | pmid = 30017480 | doi = 10.1016/j.cub.2018.05.067 | pmc = 6065529 }}</ref> These preserved proteins have provided valuable information about [[Taxonomy|taxonomic identification]], evolution history ([[Phylogenetic tree|phylogeny]]), diet, health, disease, technology and social dynamics in the past.
 Like modern proteomics, the study of ancient proteins has also been enabled by technological advances. Various analytical techniques, for example, amino acid profiling, [[racemisation]] dating, immunodetection, [[Edman degradation|Edman sequencing]], [[peptide mass fingerprinting]], and [[tandem mass spectrometry]] have been used to analyse ancient proteins.<ref>{{cite journal | vauthors = Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, de Barros Damgaard P, Gutenbrunner P, Dunne J, Hammann S, Roffet-Salque M, Ilardo M, Moreno-Mayar JV, Wang Y, Sikora M, Vinner L, Cox J, Evershed RP, Willerslev E | display-authors = 6 | title = Ancient Biomolecules and Evolutionary Inference | journal = Annual Review of Biochemistry | volume = 87 | issue = 1 | pages = 1029–1060 | date = June 2018 | pmid = 29709200 | doi = 10.1146/annurev-biochem-062917-012002 | s2cid = 14004952 }}</ref> The introduction of high-performance [[mass spectrometry]] (for example, [[Orbitrap]]) in 2000 has revolutionised the field, since the entire preserved sequences of complex proteomes can be characterised.<ref>{{cite journal | vauthors = Hendy J | title = Ancient protein analysis in archaeology | journal = Science Advances | volume = 7 | issue = 3 | date = January 2021 | pmid = 33523896 | doi = 10.1126/sciadv.abb9314 | pmc = 7810370 | bibcode = 2021SciA....7.9314H }}</ref>
-Over the past decade, the study of ancient proteins has evolved into a well-established field in archaeological science. However, like the research of [[Ancient DNA|aDNA]] (ancient DNA preserved in archaeological remains), it has been limited by several challenges such as the coverage of reference databases, identification, contamination and authentication.<ref name=":3">{{cite book | vauthors = Hendy J, van Doorn N, Collins M | chapter = Proteomics |date=2020 | title =Archaeological Science: An Introduction |pages=35–69 | veditors = Britton K, Richards MP |place=Cambridge |publisher=Cambridge University Press |doi=10.1017/9781139013826.003 |isbn=978-0-521-19522-5 | s2cid = 241941528 }}</ref> Researchers have been working on standardising sampling, extraction, data analysis and reporting for ancient proteins.<ref>{{cite journal | vauthors = Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ | title = A guide to ancient protein studies | journal = Nature Ecology & Evolution | volume = 2 | issue = 5 | pages = 791–799 | date = May 2018 | pmid = 29581591 | doi = 10.1038/s41559-018-0510-x | s2cid = 256704765 | url = https://eprints.whiterose.ac.uk/129160/1/Hendy_et_al_Final_Revised_Manuscript.pdf }}</ref> Novel computational tools such as [[De novo peptide sequencing|de novo sequencing]]<ref>{{Cite journal | vauthors = Yilmaz M, Fondrie WE, Bittremieux W, Nelson R, Ananth V, Oh S, Noble WS |date=2023-01-04 |title=Sequence-to-sequence translation from mass spectra to peptides with a transformer model | journal = bioRxiv |language=en |pages=2023.01.03.522621 |doi=10.1101/2023.01.03.522621|s2cid=255441838 }}</ref> and open research<ref>{{cite journal | vauthors = Chi H, Liu C, Yang H, Zeng WF, Wu L, Zhou WJ, Wang RM, Niu XN, Ding YH, Zhang Y, Wang ZW, Chen ZL, Sun RX, Liu T, Tan GM, Dong MQ, Xu P, Zhang PH, He SM | display-authors = 6 | title = Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine | journal = Nature Biotechnology | volume = 36 | issue = 11 | pages = 1059–1061 | date = October 2018 | pmid = 30295672 | doi = 10.1038/nbt.4236 | s2cid = 52930101 }}</ref> may also improve the identification of ancient proteomes.
+Over the past decade, the study of ancient proteins has evolved into a well-established field in archaeological science. However, like the research of [[Ancient DNA|aDNA]] (ancient DNA preserved in archaeological remains), it has been limited by several challenges such as the coverage of reference databases, identification, contamination and authentication.<ref name=":3">{{cite book | vauthors = Hendy J, van Doorn N, Collins M | chapter = Proteomics |date=2020 | title =Archaeological Science: An Introduction |pages=35–69 | veditors = Britton K, Richards MP |place=Cambridge |publisher=Cambridge University Press |doi=10.1017/9781139013826.003 |isbn=978-0-521-19522-5 | s2cid = 241941528 }}</ref> Researchers have been working on standardising sampling, extraction, data analysis and reporting for ancient proteins.<ref name=":8">{{cite journal | vauthors = Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ | title = A guide to ancient protein studies | journal = Nature Ecology & Evolution | volume = 2 | issue = 5 | pages = 791–799 | date = May 2018 | pmid = 29581591 | doi = 10.1038/s41559-018-0510-x | s2cid = 256704765 | url = https://eprints.whiterose.ac.uk/129160/1/Hendy_et_al_Final_Revised_Manuscript.pdf }}</ref> Novel computational tools such as [[De novo peptide sequencing|de novo sequencing]]<ref>{{Cite journal | vauthors = Yilmaz M, Fondrie WE, Bittremieux W, Nelson R, Ananth V, Oh S, Noble WS |date=2023-01-04 |title=Sequence-to-sequence translation from mass spectra to peptides with a transformer model | journal = bioRxiv |language=en |pages=2023.01.03.522621 |doi=10.1101/2023.01.03.522621|s2cid=255441838 }}</ref> and open research<ref>{{cite journal | vauthors = Chi H, Liu C, Yang H, Zeng WF, Wu L, Zhou WJ, Wang RM, Niu XN, Ding YH, Zhang Y, Wang ZW, Chen ZL, Sun RX, Liu T, Tan GM, Dong MQ, Xu P, Zhang PH, He SM | display-authors = 6 | title = Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine | journal = Nature Biotechnology | volume = 36 | issue = 11 | pages = 1059–1061 | date = October 2018 | pmid = 30295672 | doi = 10.1038/nbt.4236 | s2cid = 52930101 }}</ref> may also improve the identification of ancient proteomes.
 == History: the pioneers of ancient protein studies ==
@@ Line 46: / Line 46: @@
 Palaeoproteomics is a fast-developing field that combines [[archaeology]], [[biology]], [[chemistry]] and [[heritage studies]]. Comparable to its high-profile sister field, [[Ancient DNA|aDNA]] analysis, the extraction, identification and authentication of ancient proteins are challenging, since both ancient DNA and proteins tend to be ultrashort, highly fragmented, extensively damaged and chemically modified.<ref name=":0" /><ref>{{Cite journal |last=Orlando |first=Ludovic |last2=Allaby |first2=Robin |last3=Skoglund |first3=Pontus |last4=Der Sarkissian |first4=Clio |last5=Stockhammer |first5=Philipp W. |last6=Ávila-Arcos |first6=María C. |last7=Fu |first7=Qiaomei |last8=Krause |first8=Johannes |last9=Willerslev |first9=Eske |last10=Stone |first10=Anne C. |last11=Warinner |first11=Christina |date=2021-02-11 |title=Ancient DNA analysis |url=https://www.nature.com/articles/s43586-020-00011-0 |journal=Nature Reviews Methods Primers |language=en |volume=1 |issue=1 |pages=1–26 |doi=10.1038/s43586-020-00011-0 |issn=2662-8449}}</ref>
-However, ancient proteins are still one of the most informative biomolecules. Proteins tend to degrade more slowly than DNA, especially biomineralised proteins.<ref name=":4" /><ref>{{Cite journal |last=Allentoft |first=Morten E. |last2=Collins |first2=Matthew |last3=Harker |first3=David |last4=Haile |first4=James |last5=Oskam |first5=Charlotte L. |last6=Hale |first6=Marie L. |last7=Campos |first7=Paula F. |last8=Samaniego |first8=Jose A. |last9=Gilbert |first9=M. Thomas P. |last10=Willerslev |first10=Eske |last11=Zhang |first11=Guojie |last12=Scofield |first12=R. Paul |last13=Holdaway |first13=Richard N. |last14=Bunce |first14=Michael |date=2012-12-07 |title=The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils |url=https://pubmed.ncbi.nlm.nih.gov/23055061/ |journal=Proceedings. Biological Sciences |volume=279 |issue=1748 |pages=4724–4733 |doi=10.1098/rspb.2012.1745 |issn=1471-2954 |pmc=3497090 |pmid=23055061}}</ref> While ancient lipids can be used to differentiate between marine, plant and animal fats<ref>{{Citation |last=Craig |first=Oliver E. |title=Residue Analysis |date=2020 |url=https://www.cambridge.org/core/books/archaeological-science/residue-analysis/3FB49B57DFAE9D1DCE387797D9317EF0 |work=Archaeological Science: An Introduction |pages=70–98 |editor-last=Britton |editor-first=Kate |place=Cambridge |publisher=Cambridge University Press |isbn=978-0-521-19522-5 |access-date=2023-02-21 |last2=Saul |first2=Hayley |last3=Spiteri |first3=Cynthianne |editor2-last=Richards |editor2-first=Michael P.}}</ref>, ancient protein data is high-resolution with taxon- and tissue-specificities.
+However, ancient proteins are still one of the most informative biomolecules. Proteins tend to degrade more slowly than DNA, especially biomineralised proteins.<ref name=":4" /><ref>{{Cite journal |last=Allentoft |first=Morten E. |last2=Collins |first2=Matthew |last3=Harker |first3=David |last4=Haile |first4=James |last5=Oskam |first5=Charlotte L. |last6=Hale |first6=Marie L. |last7=Campos |first7=Paula F. |last8=Samaniego |first8=Jose A. |last9=Gilbert |first9=M. Thomas P. |last10=Willerslev |first10=Eske |last11=Zhang |first11=Guojie |last12=Scofield |first12=R. Paul |last13=Holdaway |first13=Richard N. |last14=Bunce |first14=Michael |date=2012-12-07 |title=The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils |url=https://pubmed.ncbi.nlm.nih.gov/23055061/ |journal=Proceedings. Biological Sciences |volume=279 |issue=1748 |pages=4724–4733 |doi=10.1098/rspb.2012.1745 |issn=1471-2954 |pmc=3497090 |pmid=23055061}}</ref> While ancient [[Lipid|lipids]] can be used to differentiate between marine, plant and animal fats<ref>{{Citation |last=Craig |first=Oliver E. |title=Residue Analysis |date=2020 |url=https://www.cambridge.org/core/books/archaeological-science/residue-analysis/3FB49B57DFAE9D1DCE387797D9317EF0 |work=Archaeological Science: An Introduction |pages=70–98 |editor-last=Britton |editor-first=Kate |place=Cambridge |publisher=Cambridge University Press |isbn=978-0-521-19522-5 |access-date=2023-02-21 |last2=Saul |first2=Hayley |last3=Spiteri |first3=Cynthianne |editor2-last=Richards |editor2-first=Michael P.}}</ref>, ancient protein data is high-resolution with taxon- and tissue-specificities.
 To date, ancient peptide sequences have been successfully extracted and securely characterised from various archaeological remains, including a 3.8 Ma (million year) ostrich eggshell,<ref name=":4" /> 1.77 Ma ''[[Homo erectus]]'' teeth,<ref>{{Cite journal |last=Welker |first=Frido |last2=Ramos-Madrigal |first2=Jazmín |last3=Gutenbrunner |first3=Petra |last4=Mackie |first4=Meaghan |last5=Tiwary |first5=Shivani |last6=Rakownikow Jersie-Christensen |first6=Rosa |last7=Chiva |first7=Cristina |last8=Dickinson |first8=Marc R. |last9=Kuhlwilm |first9=Martin |last10=de Manuel |first10=Marc |last11=Gelabert |first11=Pere |last12=Martinón-Torres |first12=María |last13=Margvelashvili |first13=Ann |last14=Arsuaga |first14=Juan Luis |last15=Carbonell |first15=Eudald |date=2020 |title=The dental proteome of Homo antecessor |url=https://www.nature.com/articles/s41586-020-2153-8 |journal=Nature |language=en |volume=580 |issue=7802 |pages=235–238 |doi=10.1038/s41586-020-2153-8 |issn=1476-4687}}</ref> a 0.16 Ma [[Denisovan]] jawbone<ref>{{Cite journal |last=Chen |first=Fahu |last2=Welker |first2=Frido |last3=Shen |first3=Chuan-Chou |last4=Bailey |first4=Shara E. |last5=Bergmann |first5=Inga |last6=Davis |first6=Simon |last7=Xia |first7=Huan |last8=Wang |first8=Hui |last9=Fischer |first9=Roman |last10=Freidline |first10=Sarah E. |last11=Yu |first11=Tsai-Luen |last12=Skinner |first12=Matthew M. |last13=Stelzer |first13=Stefanie |last14=Dong |first14=Guangrong |last15=Fu |first15=Qiaomei |date=2019 |title=A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau |url=https://www.nature.com/articles/s41586-019-1139-x. |journal=Nature |language=en |volume=569 |issue=7756 |pages=409–412 |doi=10.1038/s41586-019-1139-x |issn=1476-4687}}</ref> and several Neolithic (6000-5600 cal BC) pots.<ref name=":2" /> Hence, palaeoproteomics has provided valuable insight into past evolutionary relationships, extinct species and societies.
@@ Line 59: / Line 59: @@
 For non-mineralised archaeological materials such as parchments, leathers and paintings, demineralisation is not necessary, and protocols can be changed depending on sample preservation and sampling size.<ref name=":1" />
-=== Instrumentation ===
+=== Instrumentation and data analysis ===
-Nowadays, palaeoproteomics is dominated by two mass spectrometry-based techniques: [[Matrix-assisted laser desorption/ionization|MALDI-ToF]] (matrix-assisted laser desorption/ionisation-time-of-flight) and [[Liquid chromatography–mass spectrometry|LC-MS/MS]]. MALDI-ToF is used to determine the mass-to-charge (m/z) ratios of ions and their peak patterns.<ref>{{Cite journal |last=Richter |first=Kristine Korzow |last2=Codlin |first2=Maria C. |last3=Seabrook |first3=Melina |last4=Warinner |first4=Christina |date=2022-05-17 |title=A primer for ZooMS applications in archaeology |url=https://pnas.org/doi/full/10.1073/pnas.2109323119 |journal=Proceedings of the National Academy of Sciences |language=en |volume=119 |issue=20 |pages=e2109323119 |doi=10.1073/pnas.2109323119 |issn=0027-8424 |pmc=PMC9171758 |pmid=35537051}}</ref> Digested peptides are spotted on a MALDI plate, co-crystallise with a matrix (mainly [[Α-Cyano-4-hydroxycinnamic acid|α-cyano-4-hydroxycinnamic acid]], CHCA); a laser excites and ionises the matrix, then its time to travel a vacuum tube is measured and converted to a spectrum of m/z ratios and intensities.<ref>{{Citation |last=Hosseini |first=Samira |title=Principles and Mechanism of MALDI-ToF-MS Analysis |date=2017 |url=https://doi.org/10.1007/978-981-10-2356-9_1 |work=Fundamentals of MALDI-ToF-MS Analysis: Applications in Bio-diagnosis, Tissue Engineering and Drug Delivery |pages=1–19 |editor-last=Hosseini |editor-first=Samira |place=Singapore |publisher=Springer |language=en |doi=10.1007/978-981-10-2356-9_1 |isbn=978-981-10-2356-9 |access-date=2023-02-21 |last2=Martinez-Chapa |first2=Sergio O. |editor2-last=Martinez-Chapa |editor2-first=Sergio O.}}</ref>
+Nowadays, palaeoproteomics is dominated by two mass spectrometry-based techniques: [[Matrix-assisted laser desorption/ionization|MALDI-ToF]] (matrix-assisted laser desorption/ionisation-time-of-flight) and [[Liquid chromatography–mass spectrometry|LC-MS/MS]]. MALDI-ToF is used to determine the [[Mass-to-charge ratio|mass-to-charge (m/z) ratios]] of [[Ion|ions]] and their peak patterns.<ref name=":9">{{Cite journal |last=Richter |first=Kristine Korzow |last2=Codlin |first2=Maria C. |last3=Seabrook |first3=Melina |last4=Warinner |first4=Christina |date=2022-05-17 |title=A primer for ZooMS applications in archaeology |url=https://pnas.org/doi/full/10.1073/pnas.2109323119 |journal=Proceedings of the National Academy of Sciences |language=en |volume=119 |issue=20 |pages=e2109323119 |doi=10.1073/pnas.2109323119 |issn=0027-8424 |pmc=PMC9171758 |pmid=35537051}}</ref> Digested peptides are spotted on a MALDI plate, co-crystallise with a matrix (mainly [[Α-Cyano-4-hydroxycinnamic acid|α-cyano-4-hydroxycinnamic acid]], CHCA); a laser excites and ionises the matrix, then its time to travel a vacuum tube is measured and converted to a spectrum of m/z ratios and intensities.<ref>{{Citation |last=Hosseini |first=Samira |title=Principles and Mechanism of MALDI-ToF-MS Analysis |date=2017 |url=https://doi.org/10.1007/978-981-10-2356-9_1 |work=Fundamentals of MALDI-ToF-MS Analysis: Applications in Bio-diagnosis, Tissue Engineering and Drug Delivery |pages=1–19 |editor-last=Hosseini |editor-first=Samira |place=Singapore |publisher=Springer |language=en |doi=10.1007/978-981-10-2356-9_1 |isbn=978-981-10-2356-9 |access-date=2023-02-21 |last2=Martinez-Chapa |first2=Sergio O. |editor2-last=Martinez-Chapa |editor2-first=Sergio O.}}</ref>
+Since only peak patterns, not entire amino acid sequences of digested peptides are characterised, peptide markers are needed for pattern matching and ancient protein identification.<ref name=":9" /> In archaeological contexts, MALDI-ToF has been routinely used for bones and collagens in a field known as [[ZooMS]] (zooarchaeolgy by mass spectrometry).<ref name=":6" />
-LC-MS/MS is another widely used approach. It is a powerful analytical technique to separate, sequence and quantify complex protein mixtures.<ref>{{Cite journal |last=Patterson |first=Scott D. |last2=Aebersold |first2=Ruedi H. |date=2003 |title=Proteomics: the first decade and beyond |url=https://www.nature.com/articles/ng1106z |journal=Nature Genetics |language=en |volume=33 |issue=3 |pages=311–323 |doi=10.1038/ng1106 |issn=1546-1718}}</ref> The first step in LC-MS/MS is liquid chromatography. Protein mixtures are separated in a liquid mobile phase using a stationary column.<ref>{{Citation |last=Akash |first=Muhammad Sajid Hamid |title=High Performance Liquid Chromatography |date=2020 |url=https://doi.org/10.1007/978-981-15-1547-7_14 |work=Essentials of Pharmaceutical Analysis |pages=175–184 |editor-last=Akash |editor-first=Muhammad Sajid Hamid |place=Singapore |publisher=Springer Nature |language=en |doi=10.1007/978-981-15-1547-7_14 |isbn=978-981-15-1547-7 |access-date=2023-02-21 |last2=Rehman |first2=Kanwal |editor2-last=Rehman |editor2-first=Kanwal}}</ref> How liquid analytes interact with a stationary phase depends on their size, charge, hydrophobicity and affinity.<ref>{{Cite book |last=Niessen |first=W. M. A. |url=https://www.worldcat.org/oclc/1329091536 |title=Liquid chromatography--mass spectrometry. |date=2006 |isbn=0-429-11680-2 |edition=3rd |location=Boca Raton |oclc=1329091536}}</ref> These differences lead to distinct elution and retention time (when a component of a mixture exit a column). After chromatographic separation, protein components are ionised and introduced into mass spectrometers.<ref>{{Cite journal |last=Seger |first=Christoph |last2=Salzmann |first2=Linda |date=2020-08-01 |title=After another decade: LC–MS/MS became routine in clinical diagnostics |url=https://www.sciencedirect.com/science/article/pii/S0009912020301053 |journal=Clinical Biochemistry |series=Advancement and Applications of Mass Spectrometry in Laboratory Medicine |language=en |volume=82 |pages=2–11 |doi=10.1016/j.clinbiochem.2020.03.004 |issn=0009-9120}}</ref> During a first mass scan (MS1), the m/z ratios of precursor ions are measured. Selected precursors are further fragmented and the m/z ratios of fragment ions are determined in a second mass scan (MS2). There are different fragmentation methods, for example, high-energy C-trap dissociation (HCD) and collision induced dissociation (CID), but b- and y-ions are frequently targeted.<ref>{{Cite book |url=https://www.worldcat.org/oclc/960910529 |title=Encyclopedia of spectroscopy and spectrometry |date=2016 |others=John C. Lindon, George E. Tranter, David W. Koppenaal |isbn=978-0-12-803225-1 |edition=3rd |location=Kidlington, Oxford, United Kingdom |oclc=960910529}}</ref>
+LC-MS/MS is another widely used approach. It is a powerful analytical technique to separate, sequence and quantify complex protein mixtures.<ref>{{Cite journal |last=Patterson |first=Scott D. |last2=Aebersold |first2=Ruedi H. |date=2003 |title=Proteomics: the first decade and beyond |url=https://www.nature.com/articles/ng1106z |journal=Nature Genetics |language=en |volume=33 |issue=3 |pages=311–323 |doi=10.1038/ng1106 |issn=1546-1718}}</ref> The first step in LC-MS/MS is liquid chromatography. Protein mixtures are separated in a liquid mobile phase using a stationary column.<ref>{{Citation |last=Akash |first=Muhammad Sajid Hamid |title=High Performance Liquid Chromatography |date=2020 |url=https://doi.org/10.1007/978-981-15-1547-7_14 |work=Essentials of Pharmaceutical Analysis |pages=175–184 |editor-last=Akash |editor-first=Muhammad Sajid Hamid |place=Singapore |publisher=Springer Nature |language=en |doi=10.1007/978-981-15-1547-7_14 |isbn=978-981-15-1547-7 |access-date=2023-02-21 |last2=Rehman |first2=Kanwal |editor2-last=Rehman |editor2-first=Kanwal}}</ref> How liquid analytes interact with a stationary phase depends on their size, charge, hydrophobicity and affinity.<ref>{{Cite book |last=Niessen |first=W. M. A. |url=https://www.worldcat.org/oclc/1329091536 |title=Liquid chromatography--mass spectrometry. |date=2006 |isbn=0-429-11680-2 |edition=3rd |location=Boca Raton |oclc=1329091536}}</ref> These differences lead to distinct [[elution]] and retention time (when a component of a mixture exit a column). After chromatographic separation, protein components are ionised and introduced into mass spectrometers.<ref>{{Cite journal |last=Seger |first=Christoph |last2=Salzmann |first2=Linda |date=2020-08-01 |title=After another decade: LC–MS/MS became routine in clinical diagnostics |url=https://www.sciencedirect.com/science/article/pii/S0009912020301053 |journal=Clinical Biochemistry |series=Advancement and Applications of Mass Spectrometry in Laboratory Medicine |language=en |volume=82 |pages=2–11 |doi=10.1016/j.clinbiochem.2020.03.004 |issn=0009-9120}}</ref> During a first mass scan (MS1), the m/z ratios of precursor ions are measured. Selected precursors are further fragmented and the m/z ratios of fragment ions are determined in a second mass scan (MS2). There are different fragmentation methods, for example, high-energy C-trap dissociation (HCD) and [[Collision-induced dissociation|collision induced dissociation]] (CID), but b- and y-ions are frequently targeted.<ref>{{Cite book |url=https://www.worldcat.org/oclc/960910529 |title=Encyclopedia of spectroscopy and spectrometry |date=2016 |others=John C. Lindon, George E. Tranter, David W. Koppenaal |isbn=978-0-12-803225-1 |edition=3rd |location=Kidlington, Oxford, United Kingdom |oclc=960910529}}</ref>
+Search engines and software tools are often used to process ancient MS/MS data, including MaxQuant, [[Mascot (software)|Mascot]] and PEAKS.<ref>{{Cite journal |last=Tyanova |first=Stefka |last2=Temu |first2=Tikira |last3=Cox |first3=Juergen |date=2016 |title=The MaxQuant computational platform for mass spectrometry-based shotgun proteomics |url=https://www.nature.com/articles/nprot.2016.136 |journal=Nature Protocols |language=en |volume=11 |issue=12 |pages=2301–2319 |doi=10.1038/nprot.2016.136 |issn=1750-2799}}</ref><ref>{{Cite journal |last=Hirosawa |first=Makoto |last2=Hoshida |first2=Masaki |last3=Ishikawa |first3=Masato |last4=Toya |first4=Tomoyuki |date=1993 |title=MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming |url=http://dx.doi.org/10.1093/bioinformatics/9.2.161 |journal=Bioinformatics |volume=9 |issue=2 |pages=161–167 |doi=10.1093/bioinformatics/9.2.161 |issn=1367-4803}}</ref><ref>{{Cite journal |last=Ma |first=Bin |last2=Zhang |first2=Kaizhong |last3=Hendrie |first3=Christopher |last4=Liang |first4=Chengzhi |last5=Li |first5=Ming |last6=Doherty-Kirby |first6=Amanda |last7=Lajoie |first7=Gilles |date=2003-10-30 |title=PEAKS: powerful software for peptidede novo sequencing by tandem mass spectrometry |url=https://onlinelibrary.wiley.com/doi/10.1002/rcm.1196 |journal=Rapid Communications in Mass Spectrometry |language=en |volume=17 |issue=20 |pages=2337–2342 |doi=10.1002/rcm.1196 |issn=0951-4198}}</ref> Protein sequence data can be downloaded from public genebanks ([[UniProt]]/[[National Center for Biotechnology Information|NCBI]]) and exported as FASTA files for sequencing algorithms.<ref name=":8" /> Recently, open search engines such as MetaMorpheus, pFind and Fragpipe have received attention, because they make it possible to identify all modifications associated with peptide spectral matches (PSMs).<ref>{{Cite journal |last=Solntsev |first=Stefan K. |last2=Shortreed |first2=Michael R. |last3=Frey |first3=Brian L. |last4=Smith |first4=Lloyd M. |date=2018-05-04 |title=Enhanced Global Post-translational Modification Discovery with MetaMorpheus |url=https://pubs.acs.org/doi/10.1021/acs.jproteome.7b00873 |journal=Journal of Proteome Research |language=en |volume=17 |issue=5 |pages=1844–1851 |doi=10.1021/acs.jproteome.7b00873 |issn=1535-3893}}</ref><ref>{{Cite journal |last=Sun |first=Jinshuai |last2=Shi |first2=Jiahui |last3=Wang |first3=Yihao |last4=Wu |first4=Shujia |last5=Zhao |first5=Liping |last6=Li |first6=Yanchang |last7=Wang |first7=Hong |last8=Chang |first8=Lei |last9=Lyu |first9=Zhitang |last10=Wu |first10=Junzhu |last11=Liu |first11=Fengsong |last12=Li |first12=Wenjun |last13=He |first13=Fuchu |last14=Zhang |first14=Yao |last15=Xu |first15=Ping |date=2019-12-06 |title=Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue |url=https://pubs.acs.org/doi/10.1021/acs.jproteome.9b00376 |journal=Journal of Proteome Research |language=en |volume=18 |issue=12 |pages=4189–4196 |doi=10.1021/acs.jproteome.9b00376 |issn=1535-3893}}</ref><ref>{{Cite journal |last=Geiszler |first=Daniel J. |last2=Kong |first2=Andy T. |last3=Avtonomov |first3=Dmitry M. |last4=Yu |first4=Fengchao |last5=Leprevost |first5=Felipe da Veiga |last6=Nesvizhskii |first6=Alexey I. |date=2021-01-01 |title=PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results |url=https://www.mcponline.org/article/S1535-9476(20)35132-X/abstract |journal=Molecular & Cellular Proteomics |language=English |volume=20 |doi=10.1074/mcp.TIR120.002216 |issn=1535-9476 |pmid=33568339}}</ref>
+[[De novo peptide sequencing|De novo sequencing]] is also possible for the analysis of ancient MS/MS spectra. It is a sequencing technique that assembles amino acid sequences directly from spectra without reference databases.<ref>{{Cite journal |last=Tran |first=Ngoc Hieu |last2=Zhang |first2=Xianglilan |last3=Xin |first3=Lei |last4=Shan |first4=Baozhen |last5=Li |first5=Ming |date=2017 |title=De novo peptide sequencing by deep learning |url=https://pnas.org/doi/full/10.1073/pnas.1705691114 |journal=Proceedings of the National Academy of Sciences |language=en |volume=114 |issue=31 |pages=8247–8252 |doi=10.1073/pnas.1705691114 |issn=0027-8424 |pmc=PMC5547637 |pmid=28720701}}</ref> Advances in deep learning also lead to the development of multiple pipelines such as DeNovoGUI, DeepNovo2 and Casanovo.<ref>{{Cite journal |last=Muth |first=Thilo |last2=Weilnböck |first2=Lisa |last3=Rapp |first3=Erdmann |last4=Huber |first4=Christian G. |last5=Martens |first5=Lennart |last6=Vaudel |first6=Marc |last7=Barsnes |first7=Harald |date=2014-02-07 |title=DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra |url=https://pubs.acs.org/doi/10.1021/pr4008078 |journal=Journal of Proteome Research |language=en |volume=13 |issue=2 |pages=1143–1146 |doi=10.1021/pr4008078 |issn=1535-3893 |pmc=PMC3923451 |pmid=24295440}}</ref><ref>{{Cite journal |last=Qiao |first=Rui |last2=Tran |first2=Ngoc Hieu |last3=Xin |first3=Lei |last4=Chen |first4=Xin |last5=Li |first5=Ming |last6=Shan |first6=Baozhen |last7=Ghodsi |first7=Ali |date=2021 |title=Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices |url=https://www.nature.com/articles/s42256-021-00304-3 |journal=Nature Machine Intelligence |language=en |volume=3 |issue=5 |pages=420–425 |doi=10.1038/s42256-021-00304-3 |issn=2522-5839}}</ref><ref>{{Cite journal |last=Yilmaz |first=Melih |last2=Fondrie |first2=William |last3=Bittremieux |first3=Wout |last4=Oh |first4=Sewoong |last5=Noble |first5=William S. |date=2022-06-28 |title=De novo mass spectrometry peptide sequencing with a transformer model |url=https://proceedings.mlr.press/v162/yilmaz22a.html |journal=Proceedings of the 39th International Conference on Machine Learning |language=en |publisher=PMLR |pages=25514–25522}}</ref> However, it may be challenging to evaluate the outputs of de novo sequences and optimisation may be required for ancient proteins to minimise false positives and overfitting.<ref name=":0" />
 === '''Palaeoproteomes''' ===

v t e Omics
Genomics	Cognitive genomics Computational genomics Comparative genomics Functional genomics Genome project Human Genome Project Metagenomics Human Microbiome Project Pangenomics Personal genomics Population genomics Social genomics Structural genomics
Bioinformatics	Biochip Cheminformatics Chemogenomics Connectomics Human Connectome Project Epigenomics Human Epigenome Project Glycomics Immunomics Lipidomics Metabolomics Microbiomics Nutrigenomics Paleopolyploidy Pharmacogenetics Pharmacogenomics Systems biology Toxicogenomics Transcriptomics
Structural biology	Proteomics Human proteome project Call-map proteomics Structure-based drug design Expression proteomics
Research tools	2-D electrophoresis Mass spectrometer Electrospray ionization Matrix-assisted laser desorption ionization Matrix-assisted laser desorption ionization-time of flight mass spectrometer Microfluidic-based tools Isotope affinity tags Chromosome conformation capture
Organizations	DNA Data Bank of Japan (JP) European Molecular Biology Laboratory (EU) National Institutes of Health (USA) Wellcome Sanger Institute (UK)
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