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{{Under construction|placedby=}}[[File:High_resolution_ancient_protein.png|thumb|A timeline of key ancient protein analysis since the 1950s.]]
[[File:High_resolution_ancient_protein.png|thumb|A timeline of key ancient protein analysis since the 1950s.]]
[[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>
[[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>


Revision as of 04:46, 22 February 2023

A timeline of key ancient protein analysis since the 1950s.

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]

Applications

Palaeoproteomes

Bones

Ancient bones are one of the most well-characterised and iconic palaeoproteomes. Ancient bone proteomes have been sequenced from hominins, humans, mammoths, moas and now extinct rhinoceros.[93][94][95][96][97][98][99] Fibrillar collagens are the most abundant proteins in modern bones; similarly, Type 1 and III collagens are also common in the archaeological record.[36] While modern bones contain about 10% of non-collagenous proteins (NCPs), various NCPs have been recorded, including osteocalcin, biglycan and lumican.[97] Generally, NCPs are excellent targets for studying evolution history, since they have higher turnover rates than bones.[36] Given the abundance of ancient bone proteomes, a bottom-up proteomic workflow known as SPIN (Species by Proteome INvestigation) is available for the high-throughput analysis of 150 million mammalian bones.[100]

Teeth

Tooth enamel is one of the hardest and most mineralised tissues in the human body, since it is mainly composed of hydroxyapatite crystals.[101] While an enamel proteome is small, ancient amelogenins and other ameloblast-relevant proteins are often well-preserved in a mineralised, closed system.[36] Ancient enamel proteins are useful when aDNA or other proteins do not survive, and they have been analysed to understand extinct species and evolution.[102][103]

Shells

Archaeological shells also contain rich palaoproteomes.[104] Like tooth enamel, They are more or less close systems that isolate proteins from water or other forces of degradation.[6] Strathiocalcin-1 and -2 are securely identified in 3.8 Ma ostrich eggshell samples at the site of Laetoli in Tazania.[37] These C-type lectins are associated with biomineralisation, and they are also found in extinct big bird shells collected from Australia.[9]  

Given the age of the ostrich eggshell, it was verified by a combination of six methods: analytical replication (same samples analysed in different labs), amino acid racemisation (D/L ratios), carry-over analysis (pre- and after-injection washes to evaluation the extent of carry-over in mass spectrometers), various damage patterns (deamidation/oxidation/phosphorylation/amidation/decomposition) and aDNA studies.[37] These independent procedures ensure the authenticity of the oldest peptide sequences.

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

While palaeoproteomics is a useful tool for a wide array of research questions, there are some analytical challenges that prevent the field from reaching its potential. The first issue is preservation. Mineral-binding seems to stabilise proteins, but this is a complex, dynamic process that has not been systematically investigated in different archaeological and burial contexts.[17][37]

Destructive sampling is another problem that can cause irreparable damage to archaeological materials. Although minimally-destructive or non-destructive sampling methods are being developed for parchments, bones, mummified tissues and leathers, it is unclear if they are suitable for other types of remains such as dental calculi, ceramics and food crusts.[105][106][107]

It is equally difficult to extract mineral-bound proteins due to their low abundance, extensive degradation, and often strong intermolecular interactions (hydrogen bonding, dispersion, ion-dipole and dipole-dipole interactions) with mineral matrice.[108] Ancient proteins also vary in preservation states, hydrophobicity, solubility and optimum pH values; methodological development is still required to maximise protein recovery.[109][110]

Ancient protein identification is still a challenge, because database search algorithms are not optimised for low-intensity and damaged ancient proteins, increasing the probabilities of false positive and false negatives.[17] There is also the issue of the dark proteome (unknown protein regions that cannot be sequenced); approximately 44-54% of proteins in eukaryotes such as animals and plants are dark.[111] Reference databases are also biassed towards model organisms such as yeasts and mouses,[112] and current sequence data may not cover all archaeological materials.  

Lastly, while cytosine deamination (cytosine being converted to uracil over time that causes misreadings) has been widely used in the authentication of aDNA, there are no standardised procedures to authenticate ancient proteins.[65][113][114] This authentication issue is highlighted by the claim identification of 78 Ma Brachylophosaurus canadensis (hadrosaur) and 68 Ma Tyrannosaurus rex collagen peptides.[115][116] The lack of post-translational modifications and subsequent experimental studies demonstrate that these sequences may be derived from bacterial biofilms, the cross-contamination of control samples or modern laboratory procedures.[117]

Future directions

Despite significant analytical challenges, palaeoproteomics is constantly evolving and adopting new technology. Latest high-performance mass spectrometry, for example, TimsToF (trapped ion mobility-time-of-flight) in a DIA mode (data independent acquisition) may help with the separation, selection and resolution of ancient MS/MS data.[6] Novel extraction protocols such as DES (Deep Eutectic Solvent)-assisted procedures may increase the numbers and types of extracted palaeoproteomes.[118] Identification tools are also improving thanks to progress of bioinformatics, machine learning and artificial intelligence.[119]

Useful tools

Public depositories for raw data

Reference databases

De novo programmes

See also

Further reading

Wikipedia pages

References

  1. ^ Nelson DL, Cox MM (2021). Lehninger Principles of Biochemistry. ISBN 978-1-319-32239-7. OCLC 1325116516.
  2. ^ Fundamentals of Protein Structure and Function. 2007. doi:10.1007/978-0-387-68480-2. ISBN 978-0-387-26352-6.
  3. ^ Cristea IM, Gaskell SJ, Whetton AD (May 2004). "Proteomics techniques and their application to hematology". Blood. 103 (10): 3624–3634. doi:10.1182/blood-2003-09-3295. PMID 14726377.
  4. ^ Chen CH (August 2008). "Review of a current role of mass spectrometry for proteome research". Analytica Chimica Acta. 624 (1): 16–36. doi:10.1016/j.aca.2008.06.017. PMID 18706308.
  5. ^ Wilkins MR, Sanchez JC, Gooley AA, Appel RD, Humphery-Smith I, Hochstrasser DF, Williams KL (1996). "Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it". Biotechnology & Genetic Engineering Reviews. 13 (1): 19–50. doi:10.1080/02648725.1996.10647923. PMID 8948108.
  6. ^ a b c d e f g h i Warinner C, Korzow Richter K, Collins MJ (August 2022). "Paleoproteomics". Chemical Reviews. 122 (16): 13401–13446. doi:10.1021/acs.chemrev.1c00703. PMC 9412968. PMID 35839101.
  7. ^ a b Buckley M, Collins M, Thomas-Oates J, Wilson JC (December 2009). "Species identification by analysis of bone collagen using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry". Rapid Communications in Mass Spectrometry. 23 (23): 3843–3854. Bibcode:2009RCMS...23.3843B. doi:10.1002/rcm.4316. PMID 19899187.
  8. ^ Cappellini E, Welker F, Pandolfi L, Ramos-Madrigal J, Samodova D, Rüther PL, et al. (October 2019). "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny". Nature. 574 (7776): 103–107. Bibcode:2019Natur.574..103C. doi:10.1038/s41586-019-1555-y. PMC 6894936. PMID 31511700.
  9. ^ a b Demarchi B, Stiller J, Grealy A, Mackie M, Deng Y, Gilbert T, et al. (October 2022). "Ancient proteins resolve controversy over the identity of Genyornis eggshell". Proceedings of the National Academy of Sciences of the United States of America. 119 (43): e2109326119. doi:10.1073/pnas.2109326119. PMID 35609205. S2CID 249045755.
  10. ^ Elnaggar A, Osama A, Anwar AM, Ezzeldin S, Abou Elhassan S, Ebeid H, et al. (2022-11-09). "Paleoproteomic profiling for identification of animal skin species in ancient Egyptian archaeological leather using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)". Heritage Science. 10 (1): 182. doi:10.1186/s40494-022-00816-0. ISSN 2050-7445. S2CID 253399828.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  11. ^ a b Fiddyment S, Teasdale MD, Vnouček J, Lévêque É, Binois A, Collins MJ (2019-06-07). "So you want to do biocodicology? A field guide to the biological analysis of parchment". Heritage Science. 7 (1): 35. doi:10.1186/s40494-019-0278-6. ISSN 2050-7445. S2CID 195245888.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  12. ^ a b c Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, et al. (October 2018). "Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers". Nature Communications. 9 (1): 4064. Bibcode:2018NatCo...9.4064H. doi:10.1038/s41467-018-06335-6. PMC 6170438. PMID 30283003.
  13. ^ Dallongeville S, Garnier N, Rolando C, Tokarski C (January 2016). "Proteins in Art, Archaeology, and Paleontology: From Detection to Identification". Chemical Reviews. 116 (1): 2–79. doi:10.1021/acs.chemrev.5b00037. PMID 26709533.
  14. ^ Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, et al. (July 2018). "The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals". Current Biology. 28 (14): 2348–2355.e9. doi:10.1016/j.cub.2018.05.067. PMC 6065529. PMID 30017480.
  15. ^ Cappellini E, Prohaska A, Racimo F, Welker F, Pedersen MW, Allentoft ME, et al. (June 2018). "Ancient Biomolecules and Evolutionary Inference". Annual Review of Biochemistry. 87 (1): 1029–1060. doi:10.1146/annurev-biochem-062917-012002. PMID 29709200. S2CID 14004952.
  16. ^ Hendy J (January 2021). "Ancient protein analysis in archaeology". Science Advances. 7 (3). Bibcode:2021SciA....7.9314H. doi:10.1126/sciadv.abb9314. PMC 7810370. PMID 33523896.
  17. ^ a b c d e Hendy J, van Doorn N, Collins M (2020). "Proteomics". In Britton K, Richards MP (eds.). Archaeological Science: An Introduction. Cambridge: Cambridge University Press. pp. 35–69. doi:10.1017/9781139013826.003. ISBN 978-0-521-19522-5. S2CID 241941528.
  18. ^ a b Hendy J, Welker F, Demarchi B, Speller C, Warinner C, Collins MJ (May 2018). "A guide to ancient protein studies" (PDF). Nature Ecology & Evolution. 2 (5): 791–799. doi:10.1038/s41559-018-0510-x. PMID 29581591. S2CID 256704765.
  19. ^ Yilmaz M, Fondrie WE, Bittremieux W, Nelson R, Ananth V, Oh S, Noble WS (2023-01-04). "Sequence-to-sequence translation from mass spectra to peptides with a transformer model". bioRxiv: 2023.01.03.522621. doi:10.1101/2023.01.03.522621. S2CID 255441838.
  20. ^ Chi H, Liu C, Yang H, Zeng WF, Wu L, Zhou WJ, et al. (October 2018). "Comprehensive identification of peptides in tandem mass spectra using an efficient open search engine". Nature Biotechnology. 36 (11): 1059–1061. doi:10.1038/nbt.4236. PMID 30295672. S2CID 52930101.
  21. ^ Abelson PH (1 July 1956). "Paleobiochemistry". Scientific American. Retrieved 2023-02-19.
  22. ^ "National Academy of Sciences: Abstracts of Papers Presented at the Annual Meeting April 26-28, 1954, Washington, D.C". Science. 119 (3096): 576–588. April 1954. doi:10.1126/science.119.3096.576. PMID 17777440.
  23. ^ Wehmiller J, Hare PE (September 1971). "Racemization of amino acids in marine sediments". Science. 173 (4000): 907–911. Bibcode:1971Sci...173..907W. doi:10.1126/science.173.4000.907. PMID 17751312. S2CID 17286901.
  24. ^ Abelson PH, Hoering TC. Carbon Isotope Fractionation in Formation of Amino Acids by Photosynthetic Organisms. OCLC 678738249.
  25. ^ Hare PE, Fogel ML, Stafford Jr TW, Mitchell AD, Hoering TC (May 1991). "The isotopic composition of carbon and nitrogen in individual amino acids isolated from modern and fossil proteins". Journal of Archaeological Science. 18 (3): 277–292. doi:10.1016/0305-4403(91)90066-X. ISSN 0305-4403.
  26. ^ Hedges JI, Hare PE (February 1987). "Amino acid adsorption by clay minerals in distilled water". Geochimica et Cosmochimica Acta. 51 (2): 255–259. Bibcode:1987GeCoA..51..255H. doi:10.1016/0016-7037(87)90237-7. ISSN 0016-7037.
  27. ^ Tuross N, Fogel ML, Hare PE (1988-04-01). "Variability in the preservation of the isotopic composition of collagen from fossil bone". Geochimica et Cosmochimica Acta. 52 (4): 929–935. Bibcode:1988GeCoA..52..929T. doi:10.1016/0016-7037(88)90364-X. ISSN 0016-7037.
  28. ^ Wyckoff RW, Mccaughey WF, Doberenz AR (November 1964). "The amino acid composition of proteins from pleistocene bones☆". Biochimica et Biophysica Acta (BBA) - General Subjects. 93 (2): 374–377. doi:10.1016/0304-4165(64)90387-3. PMID 14251315.
  29. ^ Akiyama M, Wyckoff RW. The Total Amino Acid Content of Fossil Pecten Shells*. OCLC 678746870.
  30. ^ Wyckoff RW, Doberenz AR (February 1965). "The Electron Microscopy of Rancho La Brea Bone". Proceedings of the National Academy of Sciences of the United States of America. 53 (2): 230–233. Bibcode:1965PNAS...53..230W. doi:10.1073/pnas.53.2.230. PMC 219495. PMID 14294054.
  31. ^ Jope M (1967-02-01). "The protein of brachiopod shell—I. Amino acid composition and implied protein taxonomy". Comparative Biochemistry and Physiology. 20 (2): 593–600. doi:10.1016/0010-406X(67)90271-X. ISSN 0010-406X.
  32. ^ Westbroek P (1992). Life as a geological force : dynamics of the earth. W.W. Norton. ISBN 0-393-30817-0. OCLC 26700519.
  33. ^ de Jong EW, Westbroek P, Westbroek JW, Bruning JW (November 1974). "Preservation of antigenic properties of macromolecules over 70 Myr". Nature. 252 (5478): 63–64. Bibcode:1974Natur.252...63D. doi:10.1038/252063a0. PMID 4139661. S2CID 4286786.
  34. ^ Ostrom PH, Macko SA, Engel MH, Silfer JA, Russell D (January 1990). "Geochemical characterization of high molecular weight material isolated from late cretaceous fossils". Organic Geochemistry. Proceedings of the 14th International Meeting on Organic Geochemistry. 16 (4): 1139–1144. doi:10.1016/0146-6380(90)90149-T. ISSN 0146-6380.
  35. ^ Ostrom PH, Gandhi H, Strahler JR, Walker AK, Andrews PC, Leykam J, et al. (2006-04-15). "Unraveling the sequence and structure of the protein osteocalcin from a 42ka fossil horse". Geochimica et Cosmochimica Acta. 70 (8): 2034–2044. Bibcode:2006GeCoA..70.2034O. doi:10.1016/j.gca.2006.01.004. ISSN 0016-7037.
  36. ^ a b c d e Kendall, Christopher; Eriksen, Anne Marie Høier; Kontopoulos, Ioannis; Collins, Matthew J.; Turner-Walker, Gordon (2018-02-01). "Diagenesis of archaeological bone and tooth". Palaeogeography, Palaeoclimatology, Palaeoecology. 491: 21–37. doi:10.1016/j.palaeo.2017.11.041. ISSN 0031-0182.
  37. ^ a b c d e f Demarchi, Beatrice; Hall, Shaun; Roncal-Herrero, Teresa; Freeman, Colin L; Woolley, Jos; Crisp, Molly K; Wilson, Julie; Fotakis, Anna; Fischer, Roman; Kessler, Benedikt M; Rakownikow Jersie-Christensen, Rosa; Olsen, Jesper V; Haile, James; Thomas, Jessica; Marean, Curtis W (2016-09-27). Krause, Johannes (ed.). "Protein sequences bound to mineral surfaces persist into deep time". eLife. 5: e17092. doi:10.7554/eLife.17092. ISSN 2050-084X.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  38. ^ Brandt, Luise Ørsted; Taurozzi, Alberto J.; Mackie, Meaghan; Sinding, Mikkel-Holger S.; Vieira, Filipe Garrett; Schmidt, Anne Lisbeth; Rimstad, Charlotte; Collins, Matthew J.; Mannering, Ulla (2022-07-27). "Palaeoproteomics identifies beaver fur in Danish high-status Viking Age burials - direct evidence of fur trade". PLOS ONE. 17 (7): e0270040. doi:10.1371/journal.pone.0270040. ISSN 1932-6203. PMC 9328512. PMID 35895633.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  39. ^ Sharma, Vaibhav; Srinivasan, Alagiri; Nikolajeff, Fredrik; Kumar, Saroj (2021-01-15). "Biomineralization process in hard tissues: The interaction complexity within protein and inorganic counterparts". Acta Biomaterialia. Biomineralization: From Cells to Biomaterials. 120: 20–37. doi:10.1016/j.actbio.2020.04.049. ISSN 1742-7061.
  40. ^ Burr, David B. (2019-01-01), Burr, David B.; Allen, Matthew R. (eds.), "Chapter 1 - Bone Morphology and Organization", Basic and Applied Bone Biology (Second Edition), Academic Press, pp. 3–26, ISBN 978-0-12-813259-3, retrieved 2023-02-20
  41. ^ Carvalho, Marta S.; Cabral, Joaquim M. S.; da Silva, Cláudia L.; Vashishth, Deepak (2021-03-30). "Bone Matrix Non-Collagenous Proteins in Tissue Engineering: Creating New Bone by Mimicking the Extracellular Matrix". Polymers. 13 (7): 1095. doi:10.3390/polym13071095. ISSN 2073-4360.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  42. ^ Warinner, Christina; Speller, Camilla; Collins, Matthew J. (2015-01-19). "A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome". Philosophical Transactions of the Royal Society B: Biological Sciences. 370 (1660): 20130376. doi:10.1098/rstb.2013.0376. ISSN 0962-8436.
  43. ^ Radini, Anita; Nikita, Efthymia; Buckley, Stephen; Copeland, Les; Hardy, Karen (2017). "Beyond food: The multiple pathways for inclusion of materials into ancient dental calculus". American Journal of Physical Anthropology. 162 Suppl 63: 71–83. doi:10.1002/ajpa.23147. ISSN 1096-8644. PMID 28105717.
  44. ^ Lin, Lu; Jiang, Wenbin; Xu, Xuesong; Xu, Pei (2020-06-01). "A critical review of the application of electromagnetic fields for scaling control in water systems: mechanisms, characterization, and operation". npj Clean Water. 3 (1): 1–19. doi:10.1038/s41545-020-0071-9. ISSN 2059-7037.
  45. ^ Brown, Terry; Brown, Keri (2011-02-04). Biomolecular Archaeology: An Introduction (1 ed.). Wiley. doi:10.1002/9781444392449. ISBN 978-1-4051-7960-7.
  46. ^ Saitta, Evan T.; Rogers, Chris; Brooker, Richard A.; Abbott, Geoffrey D.; Kumar, Sumit; O'Reilly, Shane S.; Donohoe, Paul; Dutta, Suryendu; Summons, Roger E.; Vinther, Jakob (2017). Smith, Andrew (ed.). "Low fossilization potential of keratin protein revealed by experimental taphonomy". Palaeontology. 60 (4): 547–556. doi:10.1111/pala.12299.
  47. ^ Solazzo, Caroline; Dyer, Jolon M.; Clerens, Stefan; Plowman, Jeff; Peacock, Elizabeth E.; Collins, Matthew J. (2013-05-01). "Proteomic evaluation of the biodegradation of wool fabrics in experimental burials". International Biodeterioration & Biodegradation. 80: 48–59. doi:10.1016/j.ibiod.2012.11.013. ISSN 0964-8305.
  48. ^ Yang, Yimin; Shevchenko, Anna; Knaust, Andrea; Abuduresule, Idelisi; Li, Wenying; Hu, Xingjun; Wang, Changsui; Shevchenko, Andrej (2014-05-01). "Proteomics evidence for kefir dairy in Early Bronze Age China". Journal of Archaeological Science. 45: 178–186. doi:10.1016/j.jas.2014.02.005. ISSN 0305-4403.
  49. ^ Hollemeyer K, Altmeyer W, Heinzle E, Pitra C (September 2008). "Species identification of Oetzi's clothing with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry based on peptide pattern similarities of hair digests". Rapid Communications in Mass Spectrometry. 22 (18): 2751–2767. Bibcode:2008RCMS...22.2751H. doi:10.1002/rcm.3679. PMID 18720427.
  50. ^ Amirrah, Ibrahim N.; Lokanathan, Yogeswaran; Zulkiflee, Izzat; Wee, M. F. Mohd Razip; Motta, Antonella; Fauzi, Mh Busra (2022). "A Comprehensive Review on Collagen Type I Development of Biomaterials for Tissue Engineering: From Biosynthesis to Bioscaffold". Biomedicines. 10 (9): 2307. doi:10.3390/biomedicines10092307. ISSN 2227-9059.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  51. ^ BONE CELL BIOMECHANICS, MECHANOBIOLOGY AND BONE DISEASES. [S.l.]: ELSEVIER ACADEMIC PRESS. 2023. ISBN 0-323-96123-1. OCLC 1336986913.
  52. ^ Martínez Cortizas, Antonio; López-Costas, Olalla (2020-10-21). "Linking structural and compositional changes in archaeological human bone collagen: an FTIR-ATR approach". Scientific Reports. 10 (1): 17888. doi:10.1038/s41598-020-74993-y. ISSN 2045-2322.
  53. ^ Hendy, Jessica; Warinner, Christina; Bouwman, Abigail; Collins, Matthew J.; Fiddyment, Sarah; Fischer, Roman; Hagan, Richard; Hofman, Courtney A.; Holst, Malin; Chaves, Eros; Klaus, Lauren; Larson, Greger; Mackie, Meaghan; McGrath, Krista; Mundorff, Amy Z. (2018-07-25). "Proteomic evidence of dietary sources in ancient dental calculus". Proceedings of the Royal Society B: Biological Sciences. 285 (1883): 20180977. doi:10.1098/rspb.2018.0977. ISSN 0962-8452. PMC 6083251. PMID 30051838.
  54. ^ Liu, H.C.; Chen, W.L.; Mao, S.J.T. (2007). "Antioxidant Nature of Bovine Milk β-Lactoglobulin". Journal of Dairy Science. 90 (2): 547–555. doi:10.3168/jds.s0022-0302(07)71538-2. ISSN 0022-0302.
  55. ^ Brownlow, Sharon; Cabral, João H. Morais; Cooper, Ron; Flower, Darren R.; Yewdall, Stephen J.; Polikarpov, Igor; North, Anthony CT; Sawyer, Lindsay (1997-04-15). "Bovine β-lactoglobulin at 1.8 Å resolution — still an enigmatic lipocalin". Structure. 5 (4): 481–495. doi:10.1016/S0969-2126(97)00205-0. ISSN 0969-2126. PMID 9115437.
  56. ^ Le Maux, Solène; Bouhallab, Saïd; Giblin, Linda; Brodkorb, André; Croguennec, Thomas (2014). "Bovine β-lactoglobulin/fatty acid complexes: binding, structural, and biological properties". Dairy Science & Technology. 94 (5): 409–426. doi:10.1007/s13594-014-0160-y. ISSN 1958-5586. PMC 4121524. PMID 25110551.
  57. ^ Organic chemistry. Jonathan Clayden. Oxford: Oxford University Press. 2001. ISBN 0-19-850347-4. OCLC 43338068.{{cite book}}: CS1 maint: others (link)
  58. ^ Pavelka, Jaroslav; Smejda, Ladislav; Hynek, Radovan; Hrdlickova Kuckova, Stepanka (2016-09-01). "Immunological detection of denatured proteins as a method for rapid identification of food residues on archaeological pottery". Journal of Archaeological Science. 73: 25–35. doi:10.1016/j.jas.2016.07.004. ISSN 0305-4403.
  59. ^ Fonseca, Beatriz; Freeman, Colin L.; Collins, Matthew J. (2022-09-01). "Conformational analysis and water dynamics: a molecular dynamics study on the survival of a β-lactoglobulin peptide in the archaeological record". Chemical Physics. 561: 111602. doi:10.1016/j.chemphys.2022.111602. ISSN 0301-0104.
  60. ^ Müller, Manuel M. (2018-01-16). "Post-Translational Modifications of Protein Backbones: Unique Functions, Mechanisms, and Challenges". Biochemistry. 57 (2): 177–185. doi:10.1021/acs.biochem.7b00861. ISSN 0006-2960. PMC 5770884. PMID 29064683.
  61. ^ Boudier-Lemosquet, Axel; Mahler, Adrien; Bobo, Claude; Dufossée, Mélody; Priault, Muriel (2022-04-01). "Introducing protein deamidation: Landmark discoveries, societal outreach, and tentative priming workflow to address deamidation". Methods. Intrinsic protein instability : deamidation. 200: 3–14. doi:10.1016/j.ymeth.2021.11.012. ISSN 1046-2023.
  62. ^ Riggs, Dylan L.; Silzel, Jacob W.; Lyon, Yana A.; Kang, Amrik S.; Julian, Ryan R. (2019-10-15). "Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics". Analytical Chemistry. 91 (20): 13032–13038. doi:10.1021/acs.analchem.9b03127. ISSN 0003-2700. PMC 8805438. PMID 31498611.
  63. ^ Robinson, Noah E.; Robinson, Arthur B. (2001-01-30). "Molecular clocks". Proceedings of the National Academy of Sciences. 98 (3): 944–949. doi:10.1073/pnas.98.3.944. ISSN 0027-8424. PMC 14689. PMID 11158575.
  64. ^ Ramsøe, Abigail; Crispin, Mia; Mackie, Meaghan; McGrath, Krista; Fischer, Roman; Demarchi, Beatrice; Collins, Matthew J.; Hendy, Jessica; Speller, Camilla (2021-04-08). "Assessing the degradation of ancient milk proteins through site-specific deamidation patterns". Scientific Reports. 11 (1): 7795. doi:10.1038/s41598-021-87125-x. ISSN 2045-2322.
  65. ^ a b Orlando, Ludovic; Allaby, Robin; Skoglund, Pontus; Der Sarkissian, Clio; Stockhammer, Philipp W.; Ávila-Arcos, María C.; Fu, Qiaomei; Krause, Johannes; Willerslev, Eske; Stone, Anne C.; Warinner, Christina (2021-02-11). "Ancient DNA analysis". Nature Reviews Methods Primers. 1 (1): 1–26. doi:10.1038/s43586-020-00011-0. ISSN 2662-8449.
  66. ^ Allentoft, Morten E.; Collins, Matthew; Harker, David; Haile, James; Oskam, Charlotte L.; Hale, Marie L.; Campos, Paula F.; Samaniego, Jose A.; Gilbert, M. Thomas P.; Willerslev, Eske; Zhang, Guojie; Scofield, R. Paul; Holdaway, Richard N.; Bunce, Michael (2012-12-07). "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils". Proceedings. Biological Sciences. 279 (1748): 4724–4733. doi:10.1098/rspb.2012.1745. ISSN 1471-2954. PMC 3497090. PMID 23055061.
  67. ^ Craig, Oliver E.; Saul, Hayley; Spiteri, Cynthianne (2020), Britton, Kate; Richards, Michael P. (eds.), "Residue Analysis", Archaeological Science: An Introduction, Cambridge: Cambridge University Press, pp. 70–98, ISBN 978-0-521-19522-5, retrieved 2023-02-21
  68. ^ Welker, Frido; Ramos-Madrigal, Jazmín; Gutenbrunner, Petra; Mackie, Meaghan; Tiwary, Shivani; Rakownikow Jersie-Christensen, Rosa; Chiva, Cristina; Dickinson, Marc R.; Kuhlwilm, Martin; de Manuel, Marc; Gelabert, Pere; Martinón-Torres, María; Margvelashvili, Ann; Arsuaga, Juan Luis; Carbonell, Eudald (2020). "The dental proteome of Homo antecessor". Nature. 580 (7802): 235–238. doi:10.1038/s41586-020-2153-8. ISSN 1476-4687.
  69. ^ Chen, Fahu; Welker, Frido; Shen, Chuan-Chou; Bailey, Shara E.; Bergmann, Inga; Davis, Simon; Xia, Huan; Wang, Hui; Fischer, Roman; Freidline, Sarah E.; Yu, Tsai-Luen; Skinner, Matthew M.; Stelzer, Stefanie; Dong, Guangrong; Fu, Qiaomei (2019). "A late Middle Pleistocene Denisovan mandible from the Tibetan Plateau". Nature. 569 (7756): 409–412. doi:10.1038/s41586-019-1139-x. ISSN 1476-4687.
  70. ^ Cleland, Timothy P.; Schroeter, Elena R.; Colleary, Caitlin (2021-01-06). "Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics". Journal of Proteomics. 230: 103992. doi:10.1016/j.jprot.2020.103992. ISSN 1874-3919.
  71. ^ Palmer, Karren S.; Makarewicz, Cheryl A.; Tishkin, Alexey A.; Tur, Svetlana S.; Chunag, Amartuvshin; Diimajav, Erdenebaatar; Jamsranjav, Bayarsaikhan; Buckley, Michael (2021-03-05). "Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics". Journal of Proteome Research. 20 (3): 1689–1704. doi:10.1021/acs.jproteome.0c00862. ISSN 1535-3893.
  72. ^ Sechi, Salvatore; Chait, Brian T. (1998-12-01). "Modification of Cysteine Residues by Alkylation. A Tool in Peptide Mapping and Protein Identification". Analytical Chemistry. 70 (24): 5150–5158. doi:10.1021/ac9806005. ISSN 0003-2700.
  73. ^ Fischer, Roman; Kessler, Benedikt M. (2015). "Gel‐aided sample preparation (GASP)—A simplified method for gel‐assisted proteomic sample generation from protein extracts and intact cells". PROTEOMICS. 15 (7): 1224–1229. doi:10.1002/pmic.201400436. ISSN 1615-9853. PMC 4409837. PMID 25515006.{{cite journal}}: CS1 maint: PMC format (link)
  74. ^ Wiśniewski, Jacek R. (2018), Becher, Dörte (ed.), "Filter-Aided Sample Preparation for Proteome Analysis", Microbial Proteomics, vol. 1841, New York, NY: Springer New York, pp. 3–10, doi:10.1007/978-1-4939-8695-8_1, ISBN 978-1-4939-8693-4, retrieved 2023-02-21
  75. ^ Hughes, Christopher S.; Moggridge, Sophie; Müller, Torsten; Sorensen, Poul H.; Morin, Gregg B.; Krijgsveld, Jeroen (2019). "Single-pot, solid-phase-enhanced sample preparation for proteomics experiments". Nature Protocols. 14 (1): 68–85. doi:10.1038/s41596-018-0082-x. ISSN 1750-2799.
  76. ^ a b Richter, Kristine Korzow; Codlin, Maria C.; Seabrook, Melina; Warinner, Christina (2022-05-17). "A primer for ZooMS applications in archaeology". Proceedings of the National Academy of Sciences. 119 (20): e2109323119. doi:10.1073/pnas.2109323119. ISSN 0027-8424. PMC 9171758. PMID 35537051.{{cite journal}}: CS1 maint: PMC format (link)
  77. ^ Hosseini, Samira; Martinez-Chapa, Sergio O. (2017), Hosseini, Samira; Martinez-Chapa, Sergio O. (eds.), "Principles and Mechanism of MALDI-ToF-MS Analysis", Fundamentals of MALDI-ToF-MS Analysis: Applications in Bio-diagnosis, Tissue Engineering and Drug Delivery, Singapore: Springer, pp. 1–19, doi:10.1007/978-981-10-2356-9_1, ISBN 978-981-10-2356-9, retrieved 2023-02-21
  78. ^ Patterson, Scott D.; Aebersold, Ruedi H. (2003). "Proteomics: the first decade and beyond". Nature Genetics. 33 (3): 311–323. doi:10.1038/ng1106. ISSN 1546-1718.
  79. ^ Akash, Muhammad Sajid Hamid; Rehman, Kanwal (2020), Akash, Muhammad Sajid Hamid; Rehman, Kanwal (eds.), "High Performance Liquid Chromatography", Essentials of Pharmaceutical Analysis, Singapore: Springer Nature, pp. 175–184, doi:10.1007/978-981-15-1547-7_14, ISBN 978-981-15-1547-7, retrieved 2023-02-21
  80. ^ Niessen, W. M. A. (2006). Liquid chromatography--mass spectrometry (3rd ed.). Boca Raton. ISBN 0-429-11680-2. OCLC 1329091536.{{cite book}}: CS1 maint: location missing publisher (link)
  81. ^ Seger, Christoph; Salzmann, Linda (2020-08-01). "After another decade: LC–MS/MS became routine in clinical diagnostics". Clinical Biochemistry. Advancement and Applications of Mass Spectrometry in Laboratory Medicine. 82: 2–11. doi:10.1016/j.clinbiochem.2020.03.004. ISSN 0009-9120.
  82. ^ Encyclopedia of spectroscopy and spectrometry. John C. Lindon, George E. Tranter, David W. Koppenaal (3rd ed.). Kidlington, Oxford, United Kingdom. 2016. ISBN 978-0-12-803225-1. OCLC 960910529.{{cite book}}: CS1 maint: location missing publisher (link) CS1 maint: others (link)
  83. ^ Tyanova, Stefka; Temu, Tikira; Cox, Juergen (2016). "The MaxQuant computational platform for mass spectrometry-based shotgun proteomics". Nature Protocols. 11 (12): 2301–2319. doi:10.1038/nprot.2016.136. ISSN 1750-2799.
  84. ^ Hirosawa, Makoto; Hoshida, Masaki; Ishikawa, Masato; Toya, Tomoyuki (1993). "MASCOT: multiple alignment system for protein sequences based on three-way dynamic programming". Bioinformatics. 9 (2): 161–167. doi:10.1093/bioinformatics/9.2.161. ISSN 1367-4803.
  85. ^ Ma, Bin; Zhang, Kaizhong; Hendrie, Christopher; Liang, Chengzhi; Li, Ming; Doherty-Kirby, Amanda; Lajoie, Gilles (2003-10-30). "PEAKS: powerful software for peptidede novo sequencing by tandem mass spectrometry". Rapid Communications in Mass Spectrometry. 17 (20): 2337–2342. doi:10.1002/rcm.1196. ISSN 0951-4198.
  86. ^ Solntsev, Stefan K.; Shortreed, Michael R.; Frey, Brian L.; Smith, Lloyd M. (2018-05-04). "Enhanced Global Post-translational Modification Discovery with MetaMorpheus". Journal of Proteome Research. 17 (5): 1844–1851. doi:10.1021/acs.jproteome.7b00873. ISSN 1535-3893.
  87. ^ Sun, Jinshuai; Shi, Jiahui; Wang, Yihao; Wu, Shujia; Zhao, Liping; Li, Yanchang; Wang, Hong; Chang, Lei; Lyu, Zhitang; Wu, Junzhu; Liu, Fengsong; Li, Wenjun; He, Fuchu; Zhang, Yao; Xu, Ping (2019-12-06). "Open-pFind Enhances the Identification of Missing Proteins from Human Testis Tissue". Journal of Proteome Research. 18 (12): 4189–4196. doi:10.1021/acs.jproteome.9b00376. ISSN 1535-3893.
  88. ^ Geiszler, Daniel J.; Kong, Andy T.; Avtonomov, Dmitry M.; Yu, Fengchao; Leprevost, Felipe da Veiga; Nesvizhskii, Alexey I. (2021-01-01). "PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results". Molecular & Cellular Proteomics. 20. doi:10.1074/mcp.TIR120.002216. ISSN 1535-9476. PMID 33568339.{{cite journal}}: CS1 maint: unflagged free DOI (link)
  89. ^ Tran, Ngoc Hieu; Zhang, Xianglilan; Xin, Lei; Shan, Baozhen; Li, Ming (2017). "De novo peptide sequencing by deep learning". Proceedings of the National Academy of Sciences. 114 (31): 8247–8252. doi:10.1073/pnas.1705691114. ISSN 0027-8424. PMC 5547637. PMID 28720701.{{cite journal}}: CS1 maint: PMC format (link)
  90. ^ Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G.; Martens, Lennart; Vaudel, Marc; Barsnes, Harald (2014-02-07). "DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra". Journal of Proteome Research. 13 (2): 1143–1146. doi:10.1021/pr4008078. ISSN 1535-3893. PMC 3923451. PMID 24295440.{{cite journal}}: CS1 maint: PMC format (link)
  91. ^ Qiao, Rui; Tran, Ngoc Hieu; Xin, Lei; Chen, Xin; Li, Ming; Shan, Baozhen; Ghodsi, Ali (2021). "Computationally instrument-resolution-independent de novo peptide sequencing for high-resolution devices". Nature Machine Intelligence. 3 (5): 420–425. doi:10.1038/s42256-021-00304-3. ISSN 2522-5839.
  92. ^ Yilmaz, Melih; Fondrie, William; Bittremieux, Wout; Oh, Sewoong; Noble, William S. (2022-06-28). "De novo mass spectrometry peptide sequencing with a transformer model". Proceedings of the 39th International Conference on Machine Learning. PMLR: 25514–25522.
  93. ^ Bona, Agnes; Papai, Zoltan; Maasz, Gabor; Toth, Gabor A.; Jambor, Eva; Schmidt, Janos; Toth, Csaba; Farkas, Csilla; Mark, Laszlo (2014-01-27). "Mass Spectrometric Identification of Ancient Proteins as Potential Molecular Biomarkers for a 2000-Year-Old Osteogenic Sarcoma". PLOS ONE. 9 (1): e87215. doi:10.1371/journal.pone.0087215. ISSN 1932-6203. PMC 3903643. PMID 24475253.{{cite journal}}: CS1 maint: PMC format (link) CS1 maint: unflagged free DOI (link)
  94. ^ Cappellini, Enrico; Jensen, Lars J.; Szklarczyk, Damian; Ginolhac, Aurélien; da Fonseca, Rute A. R.; Stafford, Thomas W.; Holen, Steven R.; Collins, Matthew J.; Orlando, Ludovic; Willerslev, Eske; Gilbert, M. Thomas P.; Olsen, Jesper V. (2012-02-03). "Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins". Journal of Proteome Research. 11 (2): 917–926. doi:10.1021/pr200721u. ISSN 1535-3893.
  95. ^ Cappellini, Enrico; Welker, Frido; Pandolfi, Luca; Ramos-Madrigal, Jazmín; Samodova, Diana; Rüther, Patrick L.; Fotakis, Anna K.; Lyon, David; Moreno-Mayar, J. Víctor; Bukhsianidze, Maia; Rakownikow Jersie-Christensen, Rosa; Mackie, Meaghan; Ginolhac, Aurélien; Ferring, Reid; Tappen, Martha (2019). "Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny". Nature. 574 (7776): 103–107. doi:10.1038/s41586-019-1555-y. ISSN 1476-4687.
  96. ^ Cleland, Timothy P.; Schroeter, Elena R.; Schweitzer, Mary H. (2015-06-07). "Biologically and diagenetically derived peptide modifications in moa collagens". Proceedings of the Royal Society B: Biological Sciences. 282 (1808): 20150015. doi:10.1098/rspb.2015.0015. ISSN 0962-8452. PMC 4455796. PMID 25972464.{{cite journal}}: CS1 maint: PMC format (link)
  97. ^ a b Welker, Frido; Hajdinjak, Mateja; Talamo, Sahra; Jaouen, Klervia; Dannemann, Michael; David, Francine; Julien, Michèle; Meyer, Matthias; Kelso, Janet; Barnes, Ian; Brace, Selina; Kamminga, Pepijn; Fischer, Roman; Kessler, Benedikt M.; Stewart, John R. (2016-10-04). "Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne". Proceedings of the National Academy of Sciences. 113 (40): 11162–11167. doi:10.1073/pnas.1605834113. ISSN 0027-8424. PMC 5056053. PMID 27638212.{{cite journal}}: CS1 maint: PMC format (link)
  98. ^ Hajdinjak, Mateja; Mafessoni, Fabrizio; Skov, Laurits; Vernot, Benjamin; Hübner, Alexander; Fu, Qiaomei; Essel, Elena; Nagel, Sarah; Nickel, Birgit; Richter, Julia; Moldovan, Oana Teodora; Constantin, Silviu; Endarova, Elena; Zahariev, Nikolay; Spasov, Rosen (2021). "Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry". Nature. 592 (7853): 253–257. doi:10.1038/s41586-021-03335-3. ISSN 1476-4687.
  99. ^ Hublin, Jean-Jacques; Sirakov, Nikolay; Aldeias, Vera; Bailey, Shara; Bard, Edouard; Delvigne, Vincent; Endarova, Elena; Fagault, Yoann; Fewlass, Helen; Hajdinjak, Mateja; Kromer, Bernd; Krumov, Ivaylo; Marreiros, João; Martisius, Naomi L.; Paskulin, Lindsey (2020). "Initial Upper Palaeolithic Homo sapiens from Bacho Kiro Cave, Bulgaria". Nature. 581 (7808): 299–302. doi:10.1038/s41586-020-2259-z. ISSN 1476-4687.
  100. ^ Rüther, Patrick Leopold; Husic, Immanuel Mirnes; Bangsgaard, Pernille; Gregersen, Kristian Murphy; Pantmann, Pernille; Carvalho, Milena; Godinho, Ricardo Miguel; Friedl, Lukas; Cascalheira, João; Taurozzi, Alberto John; Jørkov, Marie Louise Schjellerup; Benedetti, Michael M.; Haws, Jonathan; Bicho, Nuno; Welker, Frido (2022-05-05). "SPIN enables high throughput species identification of archaeological bone by proteomics". Nature Communications. 13 (1): 2458. doi:10.1038/s41467-022-30097-x. ISSN 2041-1723.
  101. ^ Bai, Yushi; Yu, Zanlin; Ackerman, Larry; Zhang, Yan; Bonde, Johan; Li, Wu; Cheng, Yifan; Habelitz, Stefan (2020-08-11). "Protein nanoribbons template enamel mineralization". Proceedings of the National Academy of Sciences. 117 (32): 19201–19208. doi:10.1073/pnas.2007838117. ISSN 0027-8424. PMC 7431033. PMID 32737162.{{cite journal}}: CS1 maint: PMC format (link)
  102. ^ Welker, Frido; Ramos-Madrigal, Jazmín; Kuhlwilm, Martin; Liao, Wei; Gutenbrunner, Petra; de Manuel, Marc; Samodova, Diana; Mackie, Meaghan; Allentoft, Morten E.; Bacon, Anne-Marie; Collins, Matthew J.; Cox, Jürgen; Lalueza-Fox, Carles; Olsen, Jesper V.; Demeter, Fabrice (2019). "Enamel proteome shows that Gigantopithecus was an early diverging pongine". Nature. 576 (7786): 262–265. doi:10.1038/s41586-019-1728-8. ISSN 1476-4687.
  103. ^ Nogueira, Fabio C. S.; Neves, Leandro Xavier; Pessoa-Lima, Caroline; Langer, Max Cardoso; Domont, Gilberto B.; Line, Sergio Roberto Peres; Paes Leme, Adriana Franco; Gerlach, Raquel Fernanda (2021-05-30). "Ancient enamel peptides recovered from the South American Pleistocene species Notiomastodon platensis and Myocastor cf. coypus". Journal of Proteomics. 240: 104187. doi:10.1016/j.jprot.2021.104187. ISSN 1874-3919.
  104. ^ Sakalauskaite, Jorune; Marin, Frédéric; Pergolizzi, Barbara; Demarchi, Beatrice (2020-09-15). "Shell palaeoproteomics: First application of peptide mass fingerprinting for the rapid identification of mollusc shells in archaeology". Journal of Proteomics. 227: 103920. doi:10.1016/j.jprot.2020.103920. ISSN 1874-3919.
  105. ^ McGrath, Krista; Rowsell, Keri; Gates St-Pierre, Christian; Tedder, Andrew; Foody, George; Roberts, Carolynne; Speller, Camilla; Collins, Matthew (2019-07-30). "Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points". Scientific Reports. 9 (1): 11027. doi:10.1038/s41598-019-47299-x. ISSN 2045-2322.
  106. ^ Demarchi, Beatrice; Boano, Rosa; Ceron, Arianna; Bello, Federica Dal; Favero-Longo, Sergio E.; Fiddyment, Sarah; Marochetti, Elisa Fiore; Mangiapane, Gianluigi; Mattonai, Marco; Pennacini, Cecilia; Ribechini, Erika; Woolley, Jos; Zilberstein, Gleb; Righetti, Pier Giorgio (2020-07-01). "Never boring: Non-invasive palaeoproteomics of mummified human skin". Journal of Archaeological Science. 119: 105145. doi:10.1016/j.jas.2020.105145. ISSN 0305-4403.
  107. ^ Martisius, Naomi L.; Welker, Frido; Dogandžić, Tamara; Grote, Mark N.; Rendu, William; Sinet-Mathiot, Virginie; Wilcke, Arndt; McPherron, Shannon J. P.; Soressi, Marie; Steele, Teresa E. (2020-05-08). "Non-destructive ZooMS identification reveals strategic bone tool raw material selection by Neandertals". Scientific Reports. 10 (1): 7746. doi:10.1038/s41598-020-64358-w. ISSN 2045-2322. PMC 7210944. PMID 32385291.{{cite journal}}: CS1 maint: PMC format (link)
  108. ^ Craig, Oliver E; Collins, Matthew J (2000-03-06). "An improved method for the immunological detection of mineral bound protein using hydrofluoric acid and direct capture". Journal of Immunological Methods. 236 (1): 89–97. doi:10.1016/S0022-1759(99)00242-2. ISSN 0022-1759.
  109. ^ Procopio, Noemi; Buckley, Michael (2017-02-03). "Minimizing Laboratory-Induced Decay in Bone Proteomics". Journal of Proteome Research. 16 (2): 447–458. doi:10.1021/acs.jproteome.6b00564. ISSN 1535-3893.
  110. ^ Cleland, Timothy P. (2018-11-02). "Human Bone Paleoproteomics Utilizing the Single-Pot, Solid-Phase-Enhanced Sample Preparation Method to Maximize Detected Proteins and Reduce Humics". Journal of Proteome Research. 17 (11): 3976–3983. doi:10.1021/acs.jproteome.8b00637. ISSN 1535-3893.
  111. ^ Perdigão, Nelson; Heinrich, Julian; Stolte, Christian; Sabir, Kenneth S.; Buckley, Michael J.; Tabor, Bruce; Signal, Beth; Gloss, Brian S.; Hammang, Christopher J.; Rost, Burkhard; Schafferhans, Andrea; O’Donoghue, Seán I. (2015-12-29). "Unexpected features of the dark proteome". Proceedings of the National Academy of Sciences. 112 (52): 15898–15903. doi:10.1073/pnas.1508380112. ISSN 0027-8424. PMC 4702990. PMID 26578815.{{cite journal}}: CS1 maint: PMC format (link)
  112. ^ Ankeny, Rachel A.; Leonelli, Sabina (2020). "Model Organisms". Elements in the Philosophy of Biology. doi:10.1017/9781108593014.
  113. ^ Schroeter, Elena R.; Cleland, Timothy P. (2016-01-30). "Glutamine deamidation: an indicator of antiquity, or preservational quality?: Glutamine deamidation: indicator of antiquity?". Rapid Communications in Mass Spectrometry. 30 (2): 251–255. doi:10.1002/rcm.7445.
  114. ^ Brown, Samantha; Kozlikin, Maxim; Shunkov, Michael; Derevianko, Anatoly; Higham, Thomas; Douka, Katerina; Richter, Kristine Korzow (2021-09-01). "Examining collagen preservation through glutamine deamidation at Denisova Cave". Journal of Archaeological Science. 133: 105454. doi:10.1016/j.jas.2021.105454. ISSN 0305-4403.
  115. ^ Asara, John M.; Schweitzer, Mary H.; Freimark, Lisa M.; Phillips, Matthew; Cantley, Lewis C. (2007-04-13). "Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry". Science. 316 (5822): 280–285. doi:10.1126/science.1137614. ISSN 0036-8075.
  116. ^ Schweitzer, Mary H.; Zheng, Wenxia; Organ, Chris L.; Avci, Recep; Suo, Zhiyong; Freimark, Lisa M.; Lebleu, Valerie S.; Duncan, Michael B.; Vander Heiden, Matthew G.; Neveu, John M.; Lane, William S.; Cottrell, John S.; Horner, John R.; Cantley, Lewis C.; Kalluri, Raghu (2009). "Biomolecular Characterization and Protein Sequences of the Campanian Hadrosaur B. canadensis". Science. 324 (5927): 626–631. doi:10.1126/science.1165069. ISSN 0036-8075.
  117. ^ Buckley, Michael; Warwood, Stacey; van Dongen, Bart; Kitchener, Andrew C.; Manning, Phillip L. (2017-05-31). "A fossil protein chimera; difficulties in discriminating dinosaur peptide sequences from modern cross-contamination". Proceedings of the Royal Society B: Biological Sciences. 284 (1855): 20170544. doi:10.1098/rspb.2017.0544. ISSN 0962-8452. PMC 5454271. PMID 28566488.{{cite journal}}: CS1 maint: PMC format (link)
  118. ^ Pal Chowdhury, Manasij; Makarewicz, Cheryl; Piezonka, Henny; Buckley, Michael (2022-11-04). "Novel Deep Eutectic Solvent-Based Protein Extraction Method for Pottery Residues and Archeological Implications". Journal of Proteome Research. 21 (11): 2619–2634. doi:10.1021/acs.jproteome.2c00340. ISSN 1535-3893. PMC 9639204. PMID 36268809.{{cite journal}}: CS1 maint: PMC format (link)
  119. ^ Beslic, Denis; Tscheuschner, Georg; Renard, Bernhard Y; Weller, Michael G; Muth, Thilo (2022-12-21). "Comprehensive evaluation of peptide de novo sequencing tools for monoclonal antibody assembly". Briefings in Bioinformatics. 24 (1). doi:10.1093/bib/bbac542. ISSN 1467-5463.
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