@article{schroeter_2024, title={Characterization of Diagenetiforms in an Expanded Proteome of the Extinct Moa (Dinornithidae): Identifying Biological, Diagenetic, Experimental Artifact, and Mislabeled Modifications in Degraded Tissues}, volume={14}, ISSN={["2075-163X"]}, DOI={10.3390/min14020137}, abstractNote={Proteomic analyses of extinct moa (Dinornithidae; ~800–1000 years) bone tissue previously revealed preserved collagens (I, II, and V), as well as several biological post-translational modifications (PTMs) and diagenetic peptide sequence alterations. The diagenetiforms detected in that study provided a baseline of PTM preservation in degraded tissues, identifying sequence alterations that could be accounted for in bioinformatic data searches (e.g., carboxymethyllysine). Subsequently, an improved extraction and sample preparation methodology, coupled with higher resolution mass spectrometry analyses, identified a wealth of previously unidentified non-collagenous proteins (NCPs) from the specimen. Here, in-depth analyses of the PTMs preserved in the expanded data set provide a detailed look at the types of PTMs (i.e., biological, diagenetic, and potential experimental artifacts) that occur in degraded tissues, the proteins they occur on, and the amino acids they modify. In total, 10 biological PTMs (e.g., ubiquitylation) and 18 diagenetic PTMs, including two advanced glycation end products (e.g., dihydroxy methylglyoxal adduction) and 12 types of oxidative damage (e.g., pyrrolidone formation from proline), were detected. In addition, peptides displaying diagenetic backbone cleavage (hydrolysis) were frequently observed to possess unidentified, variable mass shifts at their broken terminus, which search software would attempt to erroneously identify as different PTMs. The modifications characterized in the bones of this specimen, both in collagens and in NCPs, provide insight into patterns of preservation and degradation that paleoproteomic studies can utilize when searching and interpreting data sets from fossil tissue.}, number={2}, journal={MINERALS}, author={Schroeter, Elena R.}, year={2024}, month={Feb} }
 @misc{ayala_schroeter_schweitzer_2024, title={Porphyrin-Based Molecules in the Fossil Record Shed Light on the Evolution of Life}, volume={14}, ISSN={["2075-163X"]}, url={https://www.mdpi.com/2075-163X/14/2/201}, DOI={10.3390/min14020201}, abstractNote={The fossil record demonstrates the preservation of porphyrins (e.g., heme) in organic sediments and the fossilized remains of animals. These molecules are essential components in modern metabolic processes, such as electron transport (cytochromes) and oxygen transport (hemoglobin), and likely originated before the emergence of life. The integration and adaptation of porphyrins and structurally similar molecules (e.g., chlorophylls) are key aspects in the evolution of energy production (i.e., aerobic respiration and photosynthesis) and complex life (i.e., eukaryotes and multicellularity). Here, we discuss the evolution and functional diversity of heme-bound hemoglobin proteins in vertebrates, along with the preservation of these molecules in the fossil record. By elucidating the pivotal role of these molecules in the evolution of life, this review lays the groundwork necessary to explore hemoglobin as a means to investigate the paleobiology of extinct taxa, including non-avian dinosaurs.}, number={2}, journal={MINERALS}, author={Ayala, Juan D. and Schroeter, Elena R. and Schweitzer, Mary H.}, year={2024}, month={Feb} }
 @article{carter_johnson_schroeter_2022, title={Long-Term Retention of Diverse Paleontologists Requires Increasing Accessibility}, volume={10}, ISSN={["2296-701X"]}, DOI={10.3389/fevo.2022.876906}, abstractNote={Geoscience encompasses a variety of scientific subdisciplines aimed at exploring, understanding, and predicting global phenomena. Yet despite its global reach, the geosciences are the least diverse of the STEM disciplines. Paleontology, a subdiscipline which prides itself on unearthing the diversity of life, comprises no greater level of diversity among its researchers than geosciences overall. This deficiency is in direct opposition to the level of public interest generated by paleontological research. Paleontology has broad educational appeal and has been leveraged in various ways to promote STEM learning. However, despite this widespread interest, there is an overwhelming decrease in the diversity of participants in paleontology at increasing levels of academia. At each academic career stage, from undergraduate to tenured faculty, the number of underrepresented (URP) and underserved persons (USP) dwindles. Here we highlight and discuss barriers to access experienced by URP and USP researchers that hinder their ability to progress at every level of the academic journey post-K-12, focusing on the track to a tenured professorship. Neglecting to consider the unique barriers faced by URPs and USPs when developing curricula, building programs, and evaluating productivity perpetuates the chronic lack of diversity in paleontology, regardless of individual interest in pursuing a career in the field. We also suggest actionable items for instructors, as well as members of the scientific community in positions of power and policymakers. While the lack of diversity in paleontology is dire, the field is small enough that individuals have the potential to make a meaningful difference.}, journal={FRONTIERS IN ECOLOGY AND EVOLUTION}, author={Carter, Aja Mia and Johnson, Erynn H. and Schroeter, Elena R.}, year={2022}, month={Jun} }
 @article{voegele_boles_ullmann_schroeter_zheng_lacovara_2022, title={Soft Tissue and Biomolecular Preservation in Vertebrate Fossils from Glauconitic, Shallow Marine Sediments of the Hornerstown Formation, Edelman Fossil Park, New Jersey}, volume={11}, ISSN={["2079-7737"]}, DOI={10.3390/biology11081161}, abstractNote={Endogenous biomolecules and soft tissues are known to persist in the fossil record. To date, these discoveries derive from a limited number of preservational environments, (e.g., fluvial channels and floodplains), and fossils from less common depositional environments have been largely unexplored. We conducted paleomolecular analyses of shallow marine vertebrate fossils from the Cretaceous–Paleogene Hornerstown Formation, an 80–90% glauconitic greensand from Jean and Ric Edelman Fossil Park in Mantua Township, NJ. Twelve samples were demineralized and found to yield products morphologically consistent with vertebrate osteocytes, blood vessels, and bone matrix. Specimens from these deposits that are dark in color exhibit excellent histological preservation and yielded a greater recovery of cells and soft tissues, whereas lighter-colored specimens exhibit poor histology and few to no cells/soft tissues. Additionally, a well-preserved femur of the marine crocodilian Thoracosaurus was found to have retained endogenous collagen I by immunofluorescence and enzyme-linked immunosorbent assays. Our results thus not only corroborate previous findings that soft tissue and biomolecular recovery from fossils preserved in marine environments are possible but also expand the range of depositional environments documented to preserve endogenous biomolecules, thus broadening the suite of geologic strata that may be fruitful to examine in future paleomolecular studies.}, number={8}, journal={BIOLOGY-BASEL}, author={Voegele, Kristyn K. and Boles, Zachary M. and Ullmann, Paul V and Schroeter, Elena R. and Zheng, Wenxia and Lacovara, Kenneth J.}, year={2022}, month={Aug} }
 @article{schroeter_ullmann_macauley_ash_zheng_schweitzer_lacovara_2022, title={Soft-Tissue, Rare Earth Element, and Molecular Analyses of Dreadnoughtus schrani, an Exceptionally Complete Titanosaur from Argentina}, volume={11}, ISSN={["2079-7737"]}, DOI={10.3390/biology11081158}, abstractNote={Evidence that organic material preserves in deep time (>1 Ma) has been reported using a wide variety of analytical techniques. However, the comprehensive geochemical data that could aid in building robust hypotheses for how soft-tissues persist over millions of years are lacking from most paleomolecular reports. Here, we analyze the molecular preservation and taphonomic history of the Dreadnougtus schrani holotype (MPM-PV 1156) at both macroscopic and microscopic levels. We review the stratigraphy, depositional setting, and physical taphonomy of the D. schrani skeletal assemblage, and extensively characterize the preservation and taphonomic history of the humerus at a micro-scale via: (1) histological analysis (structural integrity) and X-ray diffraction (exogenous mineral content); (2) laser ablation-inductively coupled plasma mass spectrometry (analyses of rare earth element content throughout cortex); (3) demineralization and optical microscopy (soft-tissue microstructures); (4) in situ and in-solution immunological assays (presence of endogenous protein). Our data show the D. schrani holotype preserves soft-tissue microstructures and remnants of endogenous bone protein. Further, it was exposed to LREE-enriched groundwaters and weakly-oxidizing conditions after burial, but experienced negligible further chemical alteration after early-diagenetic fossilization. These findings support previous hypotheses that fossils that display low trace element uptake are favorable targets for paleomolecular analyses.}, number={8}, journal={BIOLOGY-BASEL}, author={Schroeter, Elena R. and Ullmann, Paul V and Macauley, Kyle and Ash, Richard D. and Zheng, Wenxia and Schweitzer, Mary H. and Lacovara, Kenneth J.}, year={2022}, month={Aug} }
 @article{schroeter_cleland_schweitzer_2021, title={Deep Time Paleoproteomics: Looking Forward}, volume={12}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.1c00755}, abstractNote={The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schroeter, Elena R. and Cleland, Timothy P. and Schweitzer, Mary H.}, year={2021}, month={Dec} }
 @article{cleland_schroeter_colleary_2021, title={Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics}, volume={230}, ISSN={["1876-7737"]}, DOI={10.1016/j.jprot.2020.103992}, abstractNote={The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.e., physical and chemical change imparted by burial), a novel term is needed that both addresses issues of combinatorics and distinguishes diagenetic-specific alteration. The term diagenetiform provides the opportunity to communicate clearly the sets of diagenetic changes found on preserved proteins. The diagenetiform nomenclature will allow for top-down paleoproteomic studies to accurately describe the total changes detected on ancient proteins.}, journal={JOURNAL OF PROTEOMICS}, author={Cleland, Timothy P. and Schroeter, Elena R. and Colleary, Caitlin}, year={2021}, month={Jan} }
 @article{ullmann_voegele_grandstaff_ash_zheng_schroeter_schweitzer_lacovara_2020, title={Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation}, volume={10}, ISSN={["2045-2322"]}, DOI={10.1038/s41598-020-72648-6}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, author={Ullmann, Paul V. and Voegele, Kristyn K. and Grandstaff, David E. and Ash, Richard D. and Zheng, Wenxia and Schroeter, Elena R. and Schweitzer, Mary H. and Lacovara, Kenneth J.}, year={2020}, month={Sep} }
 @article{schweitzer_schroeter_cleland_zheng_2019, title={Paleoproteomics of Mesozoic Dinosaurs and Other Mesozoic Fossils}, volume={19}, ISSN={1615-9853 1615-9861}, url={http://dx.doi.org/10.1002/pmic.201800251}, DOI={10.1002/pmic.201800251}, abstractNote={Abstract}, number={16}, journal={PROTEOMICS}, publisher={Wiley}, author={Schweitzer, Mary Higby and Schroeter, Elena R. and Cleland, Timothy P. and Zheng, Wenxia}, year={2019}, month={Jul}, pages={1800251} }
 @article{schroeter_blackburn_goshe_schweitzer_2019, title={Proteomic method to extract, concentrate, digest and enrich peptides from fossils with coloured (humic) substances for mass spectrometry analyses}, volume={6}, ISSN={["2054-5703"]}, DOI={10.1098/rsos.181433}, abstractNote={Humic substances are breakdown products of decaying organic matter that co-extract with proteins from fossils. These substances are difficult to separate from proteins in solution and interfere with analyses of fossil proteomes. We introduce a method combining multiple recent advances in extraction protocols to both concentrate proteins from fossil specimens with high humic content and remove humics, producing clean samples easily analysed by mass spectrometry (MS). This method includes: (i) a non-demineralizing extraction buffer that eliminates protein loss during the demineralization step in routine methods; (ii) filter-aided sample preparation (FASP) of peptides, which concentrates and digests extracts in one filter, allowing the separation of large humics after digestion; (iii) centrifugal stage tipping, which further clarifies and concentrates samples in a uniform process performed simultaneously on multiple samples. We apply this method to a moa fossil (approx. 800–1000 years) dark with humic content, generating colourless samples and enabling the detection of more proteins with greater sequence coverage than previous MS analyses on this same specimen. This workflow allows analyses of low-abundance proteins in fossils containing humics and thus may widen the range of extinct organisms and regions of their proteomes we can explore with MS.}, number={8}, journal={ROYAL SOCIETY OPEN SCIENCE}, author={Schroeter, Elena R. and Blackburn, Kevin and Goshe, Michael B. and Schweitzer, Mary H.}, year={2019}, month={Aug} }
 @article{pan_zheng_sawyer_pennington_zheng_wang_wang_hu_o’connor_zhao_et al._2019, title={The molecular evolution of feathers with direct evidence from fossils}, volume={116}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1815703116}, DOI={10.1073/pnas.1815703116}, abstractNote={Significance}, number={8}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Pan, Yanhong and Zheng, Wenxia and Sawyer, Roger H. and Pennington, Michael W. and Zheng, Xiaoting and Wang, Xiaoli and Wang, Min and Hu, Liang and O’Connor, Jingmai and Zhao, Tao and et al.}, year={2019}, month={Jan}, pages={3018–3023} }
 @misc{cleland_schroeter_2018, title={A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics}, volume={17}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.7b00703}, abstractNote={The last two decades have seen a broad diversity of methods used to identify and/or characterize proteins in the archeological and paleontological record. Of these, mass spectrometry has opened an unprecedented window into the proteomes of the past, providing protein sequence data from long extinct animals as well as historical and prehistorical artifacts. Thus, application of mass spectrometry to fossil remains has become an attractive source for ancient molecular sequences with which to conduct evolutionary studies, particularly in specimens older than the proposed limit of amplifiable DNA detection. However, "mass spectrometry" covers a range of mass-based proteomic approaches, each of which utilize different technology and physical principles to generate unique types of data, with their own strengths and challenges. Here, we discuss a variety of mass spectrometry techniques that have or may be used to detect and characterize archeological and paleontological proteins, with a particular focus on MALDI-MS, LC-MS/MS, TOF-SIMS, and MSi. The main differences in their functionality, the types of data they produce, and the potential effects of diagenesis on their results are considered.}, number={3}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Cleland, Timothy P. and Schroeter, Elena R.}, year={2018}, month={Mar}, pages={936–945} }
 @article{schroeter_dehart_cleland_zheng_thomas_kelleher_bern_schweitzer_2017, title={Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein}, volume={16}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.6b00873}, abstractNote={Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the previous study with substantially less sample material. Data are available via ProteomeXchange with identifier PXD005087.}, number={2}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Schroeter, Elena R. and DeHart, Caroline J. and Cleland, Timothy P. and Zheng, Wenxia and Thomas, Paul M. and Kelleher, Neil L. and Bern, Marshall and Schweitzer, Mary H.}, year={2017}, month={Feb}, pages={920–932} }
 @article{schroeter_dehart_schweitzer_thomas_kelleher_2016, title={Bone protein "extractomics": comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics}, volume={4}, journal={PeerJ}, author={Schroeter, E. R. and DeHart, C. J. and Schweitzer, M. H. and Thomas, P. M. and Kelleher, N. L.}, year={2016} }
 @article{schroeter_cleland_2016, title={Glutamine deamidation: an indicator of antiquity, or preservational quality?}, volume={30}, ISSN={["1097-0231"]}, DOI={10.1002/rcm.7445}, abstractNote={RationaleMuch credence has been given in the paleoproteomic community to glutamine deamidation as a proxy for the age of proteins derived from fossil and subfossil material, and this modification has been invoked as a means for determining the endogeneity of molecules recovered from very old fossil specimens.}, number={2}, journal={RAPID COMMUNICATIONS IN MASS SPECTROMETRY}, author={Schroeter, Elena R. and Cleland, Timothy P.}, year={2016}, month={Jan}, pages={251–255} }
 @article{pan_zheng_moyer_jingmai k. o'connor_wang_zheng_wang_schroeter_zhou_schweitzer_2016, title={Molecular evidence of keratin and melanosomes in feathers of the Early Cretaceous bird Eoconfuciusornis}, volume={113}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1617168113}, abstractNote={Significance}, number={49}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Pan, Yanhong and Zheng, Wenxia and Moyer, Alison E. and Jingmai K. O'Connor and Wang, Min and Zheng, Xiaoting and Wang, Xiaoli and Schroeter, Elena R. and Zhou, Zhonghe and Schweitzer, Mary H.}, year={2016}, month={Dec}, pages={E7900–E7907} }
 @article{cleland_schroeter_feranec_vashishth_2016, title={Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics}, volume={283}, ISSN={["1471-2954"]}, DOI={10.1098/rspb.2016.0593}, abstractNote={
            Vertebrate fossils have been collected for hundreds of years and are stored in museum collections around the world. These remains provide a readily available resource to search for preserved proteins; however, the vast majority of palaeoproteomic studies have focused on relatively recently collected bones with a well-known handling history. Here, we characterize proteins from the nasal turbinates of the first
            Castoroides ohioensis
            skull ever discovered. Collected in 1845, this is the oldest museum-curated specimen characterized using palaeoproteomic tools. Our mass spectrometry analysis detected many collagen I peptides, a peptide from haemoglobin beta, and
            in vivo
            and diagenetic post-translational modifications. Additionally, the identified collagen I sequences provide enough resolution to place
            C. ohioensis
            within Rodentia. This study illustrates the utility of archived museum specimens for both the recovery of preserved proteins and phylogenetic analyses.
          }, number={1832}, journal={PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Cleland, Timothy P. and Schroeter, Elena R. and Feranec, Robert S. and Vashishth, Deepak}, year={2016}, month={Jun} }
 @article{cleland_schroeter_schweitzer_2015, title={Biologically and diagenetically derived peptide modifications in moa collagens}, volume={282}, number={1808}, journal={Proceedings of the Royal Society of London. Series B}, author={Cleland, T. P. and Schroeter, E. R. and Schweitzer, M. H.}, year={2015} }
 @article{cleland_schroeter_zamdborg_zheng_lee_tran_bern_duncan_lebleu_ahlf_et al._2015, title={Mass Spectrometry and Antibody-Based Characterization of Blood Vessels from Brachylophosaurus canadensis}, volume={14}, ISSN={["1535-3907"]}, DOI={10.1021/acs.jproteome.5b00675}, abstractNote={Structures similar to blood vessels in location, morphology, flexibility, and transparency have been recovered after demineralization of multiple dinosaur cortical bone fragments from multiple specimens, some of which are as old as 80 Ma. These structures were hypothesized to be either endogenous to the bone (i.e., of vascular origin) or the result of biofilm colonizing the empty osteonal network after degradation of original organic components. Here, we test the hypothesis that these structures are endogenous and thus retain proteins in common with extant archosaur blood vessels that can be detected with high-resolution mass spectrometry and confirmed by immunofluorescence. Two lines of evidence support this hypothesis. First, peptide sequencing of Brachylophosaurus canadensis blood vessel extracts is consistent with peptides comprising extant archosaurian blood vessels and is not consistent with a bacterial, cellular slime mold, or fungal origin. Second, proteins identified by mass spectrometry can be localized to the tissues using antibodies specific to these proteins, validating their identity. Data are available via ProteomeXchange with identifier PXD001738.}, number={12}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Cleland, Timothy P. and Schroeter, Elena R. and Zamdborg, Leonid and Zheng, Wenxia and Lee, Ji Eun and Tran, John C. and Bern, Marshall and Duncan, Michael B. and Lebleu, Valerie S. and Ahlf, Dorothy R. and et al.}, year={2015}, month={Dec}, pages={5252–5262} }