Cleland, Timothy
Physical Scientist at the Museum Conservation Institute
Selected Publications
Article
Serafini, Ilaria, Favero, Gabriele, Curini, Roberta, Kavich, Gwénaëlle M., and Cleland, Timothy P. 2024. "Development of a Combined Protein and Dye Extraction Approach for the Analysis of Keratin-Based Textiles ." Journal of Proteome Research , 23, (9). https://doi.org/10.1021/acs.jproteome.4c00253 .
2024
Serafini, Ilaria, Favero, Gabriele, Curini, Roberta, Kavich, Gwénaëlle M., and Cleland, Timothy P. 2024. "Development of a Combined Protein and Dye Extraction Approach for the Analysis of Keratin-Based Textiles ." Journal of Proteome Research , https://doi.org/10.1021/acs.jproteome.4c00253 .
2024
Cleland, Timothy P., McGuire, Sara A., Beatrice, Jared S., Moran, Kimberlee S., and France, Christine A. M. 2024. "SPEED-E: A modified version of the sample preparation by Easy extraction and Digestion(-free) protocol for enamel-based sex estimation in archaeological remains ." Journal of Archaeological Science , 168. https://doi.org/10.1016/j.jas.2024.106006 .
2024
Newsome, G. Asher and Cleland, Timothy P. 2023. "Gas-phase dopant flow to modify nanoLC-MS and nanoESI protein charge ." International Journal of Mass Spectrometry , 487. https://doi.org/10.1016/j.ijms.2023.117026 .
2023
Corder, Molly L., Petricoin, Emanuel F., Li, Yue, Cleland, Timothy P., DeCandia, Alexandra L., Aguirre, A. A., and Pukazhenthi, Budhan S. 2023. "Metabolomic profiling implicates mitochondrial and immune dysfunction in disease syndromes of the critically endangered black rhinoceros (Diceros bicornis) ." Scientific Reports , 13, (1). https://doi.org/10.1038/s41598-023-41508-4 .
2023
Kawahara, Akito Y., Storer, Caroline G., Markee, Amanda, Heckenhauer, Jacqueline, Powell, Ashlyn, Plotkin, David, Hotaling, Scott, Cleland, Timothy P., Dikow, Rebecca B., Dikow, Torsten, Kuranishi, Ryoichi B., Messcher, Rebeccah, Pauls, Steffen U., Stewart, Russell J., Tojo, Koji, and Frandsen, Paul B. 2022. "Long-read HiFi sequencing correctly assembles repetitive heavy fibroin silk genes in new moth and caddisfly genomes ." Gigabyte , 2022 1–14. https://doi.org/10.46471/gigabyte.64 .
2022
Cleland, Timothy P. and Power, Michael L. 2022. "Variation in Milk Proteins Across Lactation in Pongo pygmaeus and Gorilla gorilla ." Journal of Proteome Research , 21 2647–2654. https://doi.org/10.1021/acs.jproteome.2c00373 .
2022
Cleland, Timothy P. and Power, Michael L. 2022. "Variation in Milk Proteins Across Lactation in Pongo pygmaeus and Gorilla gorilla." Journal of Proteome Research , 21, (11) 2647–2654. https://doi.org/10.1021/acs.jproteome.2c00373 .
2022
Solazzo, Caroline, Soulat, Jean, and Cleland, Timothy P. 2021. "Creation of a peptide database of corneous beta-proteins of marine turtles for the identification of tortoiseshell: archaeological combs as case study ." Royal Society Open Science , 8, (2) Article 201857. https://doi.org/10.1098/rsos.201857 .
2021
Schroeter, Elena R., Cleland, Timothy P., and Schweitzer, Mary H. 2021. "Deep Time Paleoproteomics: Looking Forward ." Journal of Proteome Research , https://doi.org/10.1021/acs.jproteome.1c00755 .
2021
Cleland, Timothy P., Schroeter, Elena R., and Colleary, Caitlin. 2021. "Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics ." Journal of Proteomics , 230 Article 103992. https://doi.org/10.1016/j.jprot.2020.103992 .
2021
Li, Xuankun, Ellis, Emily, Plotkin, David, Imada, Yume, Yago, Masaya, Heckenhauer, Jacqueline, Cleland, Timothy P., Dikow, Rebecca B., Dikow, Torsten, Storer, Caroline G., Kawahara, Akito Y., and Frandsen, Paul B. 2021. "First annotated genome of a mandibulate moth, Neomicropteryx cornuta , generated using PacBio HiFi sequencing ." Genome Biology and Evolution , 13, (10). https://doi.org/10.1093/gbe/evab229 .
2021
Newsome, G. Asher and Cleland, Timothy P. 2021. "In-Line Dopant Generation for Atmospheric Pressure Ionization Mass Spectrometry ." Analytical Chemistry , 93, (40) 13527–13533. https://doi.org/10.1021/acs.analchem.1c02400 .
2021
Cleland, Timothy P., Wang, Zehai, Wang, Bowen, Picu, Catalin R., and Vashishth, Deepak. 2021. "Mechano-chemical regulation of bat wing bones for flight ." Journal of the Mechanical Behavior of Biomedical Materials , 124. https://doi.org/10.1016/j.jmbbm.2021.104809 .
2021
Cleland, Timothy P., Sarancha, Julianne J., and France, Christine A. M. 2021. "Proteomic profile of bone "collagen" extracted for stable isotopes: implications for bulk and single amino acid analyses ." Rapid Communications in Mass Spectrometry , 35, (6) Article e9025. https://doi.org/10.1002/rcm.9025 .
2021
Shabestari, Maziar, Shabestari, Yashar R., Landin, Maria A., Pepaj, Milaim, Cleland, Timothy P., Reseland, Janne E., and Eriksen, Erik F. 2020. "Altered protein levels in bone marrow lesions of hip osteoarthritis: Analysis by proteomics and multiplex immunoassays ." International Journal of Rheumatic Diseases , 23, (6) 788–799. https://doi.org/10.1111/1756-185X.13843 .
2020
Early, Catherine M., Morhardt, Ashley C., Cleland, Timothy P., Milensky, Christopher M., Kavich, Gwénaëlle M., and James, Helen F. 2020. "Chemical effects of diceCT staining protocols on fluid-preserved avian specimens ." PLOS One , 15, (9) Article e0238783. https://doi.org/10.1371/journal.pone.0238783 .
2020
Colleary, Caitlin, Little, Nicole C., and Cleland, Timothy P. 2020. "Microwave‐assisted acid hydrolysis for whole-bone proteomics and paleoproteomics ." Rapid Communications in Mass Spectrometry , 34, (2) Article rcm.8568. https://doi.org/10.1002/rcm.8568 .
2020
Rowlison, Tricia, Cleland, Timothy P., Ottinger, Mary Ann, and Comizzoli, Pierre. 2020. "Novel proteomic profiling of epididymal extracellular vesicles in the domestic cat reveals proteins related to sequential sperm maturation with differences observed between normospermic and teratospermic individuals ." Molecular & Cellular Proteomics , 19, (12) 2090–2103. https://doi.org/10.1074/mcp.RA120.002251 .
2020
Schweitzer, Mary Higby, Schroeter, Elena R., Cleland, Timothy P., and Zheng, Wenxia. 2019. "Paleoproteomics of Mesozoic dinosaurs and other Mesozoic fossils ." Proteomics , 19, (16) 1800251. https://doi.org/10.1002/pmic.201800251 .
2019
Cleland, Timothy P., Newsome, G. Asher, and Hollinger, R. Eric. 2019. "Proteomic and direct analysis in real time mass spectrometry analysis of a Native American ceremonial hat." The Analyst , 144, (24) 7437–7446. https://doi.org/10.1039/c9an01557d .
2019
Alvarez-Martin, Alba, Cleland, Timothy P., Kavich, Gwénaëlle M., Janssens, Koen, and Newsome, G. Asher. 2019. "Rapid Evaluation of the Debromination Mechanism of Eosin in Oil Paint by Direct Analysis in Real Time and Direct Infusion-Electrospray Ionization Mass Spectrometry ." Analytical Chemistry , 91, (16) 10856–10863. https://doi.org/10.1021/acs.analchem.9b02568 .
2019
Cleland, Timothy P. and Schroeter, Elena R. 2018. "A Comparison of Common Mass Spectrometry Approaches for Paleoproteomics ." Journal of Proteome Research , 17, (3) 936–945. https://doi.org/10.1021/acs.jproteome.7b00703 .
2018
Thomas, Corinne J., Cleland, Timothy P., Sroga, Grazyna E., and Vashishth, Deepak. 2018. "Accumulation of carboxymethyl-lysine (CML) in human cortical bone ." Bone , 110 128–133. https://doi.org/10.1016/j.bone.2018.01.028 .
2018
Popowich, Aleksandra K., Cleland, Timothy P., and Solazzo, Caroline. 2018. "Characterization of membrane metal threads by proteomics and analysis of a 14th c. thread from an Italian textile ." Journal of Cultural Heritage , 33 10–07. https://doi.org/10.1016/j.culher.2018.03.007 .
2018
Cleland, Timothy P. 2018. "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. https://doi.org/10.1021/acs.jproteome.8b00637 .
2018
Cleland, Timothy P. 2018. "Solid Digestion of Demineralized Bone as a Method To Access Potentially Insoluble Proteins and Post-Translational Modifications ." Journal of Proteome Research , 17, (1) 536–542. https://doi.org/10.1021/acs.jproteome.7b00670 .
2018
Schroeter, Elena R., DeHart, Caroline, Cleland, Timothy P., Zheng, Wenxia, Thomas, Paul M., Kelleher, Neil L., Bern, Marshall, and Schweitzer, Mary H. 2017. "Expansion for the Brachylophosaurus canadensis collagen I sequence and additional evidence of the preservation of Cretaceous protein ." Journal of Proteome Research , 16, (2) 920–932. https://doi.org/10.1021/acs.jproteome.6b00873 .
2017
Cleland, Timothy P., DeHart, Caroline J., Fellers, Ryan T., VanNispen, Alexandra J., Greer, Joseph B., LeDuc, Richard D., Parker, W. R., Thomas, Paul M., Kelleher, Neil L., and Brodbelt, Jennifer S. 2017. "High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer ." Journal of Proteome Research , 16, (5) 2072–2079. https://doi.org/10.1021/acs.jproteome.7b00043 .
2017
Thomas, Corinne J., Cleland, Timothy P., Zhang, Sheng, Gundberg, Caren M., and Vashishth, Deepak. 2017. "Identification and characterization of glycation adducts on osteocalcin ." Analytical Biochemistry , 525 46–53. https://doi.org/10.1016/j.ab.2017.02.011 .
2017
Schroeter, Elena R. and Cleland, Timothy P. 2016. "Glutamine deamidation: an indicator of antiquity, or preservational quality? " Rapid Communications in Mass Spectrometry , 30, (2) 251–255. https://doi.org/10.1002/rcm.7445 .
2016
Cleland, Timothy P., Thomas, Corinne J., Gundberg, Caren M., and Vashishth, Deepak. 2016. "Influence of carboxylation on osteocalcin detection by mass spectrometry ." Rapid Communications in Mass Spectrometry , 30, (19) 2109–2115. https://doi.org/10.1002/rcm.7692 .
2016
Cleland, Timothy P., Schroeter, Elena R., Feranec, Robert S., and Vashishth, Deepak. 2016. "Peptide sequences from the first Castoroides ohioensis skull and the utility of old museum collections for palaeoproteomics ." Proceedings of the Royal Society B: Biological Sciences , 283, (1832). https://doi.org/10.1098/rspb.2016.0593 .
2016
Cleland, Timothy P., Schroeter, Elena R., and Schweitzer, Mary H. 2015. "Biologically and diagenetically derived peptide modifications in moa collagens ." Proceedings of the Royal Society B: Biological Sciences , 282. https://doi.org/10.1098/rspb.2015.0015 .
2015
Cleland, Timothy P. and Vashishth, Deepak. 2015. "Bone protein extraction without demineralization using principles from hydroxyapatite chromatography ." Analytical Biochemistry , 472 62–66. https://doi.org/10.1016/j.ab.2014.12.006 .
2015
Cleland, Timothy P., Schroeter, Elena R., Zamdborg, Leonid, Zheng, Wenxia, Lee, Ji Eun, Tran, John C., Bern, Marshall, Duncan, Michael B., Lebleu, Valerie S., Ahlf, Dorothy R., Thomas, Paul M., Kalluri, Raghu, Kelleher, Neil L., and Schweitzer, Mary H. 2015. "Mass spectrometry and antibody-based characterization of blood vessels from Brachylophosaurus canadensis ." Journal of Proteome Research , 14, (12) 5252–5262. https://doi.org/10.1021/acs.jproteome.5b00675 .
2015
Schweitzer, Mary H., Zheng, Wenxia, Cleland, Timothy P., Goodwin, Mark B., Boatman, Elizabeth, Theil, Elizabeth, Marcus, Matthew A., and Fakra, Sirine C. 2014. "A role for iron and oxygen chemistry in preserving soft tissues, cells and molecules from deep time ." Proceedings of the Royal Society B: Biological Sciences , 281, (1775). https://doi.org/10.1098/rspb.2013.2741 .
2014
Schweitzer, Mary Higby, Zheng, Wenxia, Cleland, Timothy P., and Bern, Marshall. 2013. "Molecular analyses of dinosaur osteocytes supports the presence of endogenous molecules." Bone , 52, (1) 414–423. https://doi.org/10.1016/j.bone.2012.10.010 .
2013
Cleland, Timothy P., Voegele, Kristyn, and Schweitzer, Mary H. 2012. "Empirical evaluation of bone extraction protocols ." PLoS One , 7, (2). https://doi.org/10.1371/journal.pone.0031443 .
2012
Boyd, Clint A., Cleland, Timothy P., Marrero, Nico L., and Clarke, Julia A. 2011. "Exploring the effects of phylogenetic uncertainty and consensus trees on stratigraphic consistency scores: a new program and a standardized method ." Cladistics , 27, (1) 52–60. https://doi.org/10.1111/j.1096-0031.2010.00320.x .
2011
Cleland, Timothy P., Stoskopf, Michael K., and Schweitzer, Mary H. 2011. "Histological, chemical, and morphological reexamination of the "heart" of a small Late Cretaceous Thescelosaurus ." Naturwissenschaften , 98, (3) 203–211. https://doi.org/10.1007/s00114-010-0760-1 .
2011
Boyd, Clint A., Cleland, Timothy P., and Novas, Fernando. 2011. "Osteogenesis, homology, and function of the intercostal plates in ornithischian dinosaurs (Tetrapoda, Sauropsida) ." Zoomorphology , 130, (4) 305–313. https://doi.org/10.1007/s00435-011-0136-x .
2011
Conference Paper
Green, Daniel, Uno, Kevin, Miller, Ellen, Feibel, Craig, Aoron, Eipa, Beck, Catherine, Grossman, Aryeh, Kirera, Francis, Kirinya, Martin, Leakey, Louise, Liutkus-Pierce, Cynthia, Manthi, Fredrick, Ndiema, Emmanuel, Nyete, Cyprian, Rowan, John, Russo, Gabrielle, Sanders, William, Smiley, Tara, Princehouse, Patricia, Vitek, Natasha, and Cleland, Timothy P. 2024. "29 million years of diverse mammalian enamel proteomes from Turkana in the East African Rift System ." from EGU General Assembly 2024 . https://doi.org/10.5194/egusphere-egu24-21192 .
2024
Patent
Cleland, Timothy P. and Vashishth, Deepak. 2017. "Bone Protein Extraction Without Demineralization, United States Patent Application 20170369526."
2017
Presentations
Presentation
Newsome, G. Asher and Cleland, Timothy P. 2018. Multimodal Mass Spectrometric Analysis of an 18th-19th Century Cultural Heritage Object [presentation] . 39th East Coast Ion Chemistry Conference, October 1, 2018. Newark, Delaware.
Cleland, Timothy P. 2024. Proteins at the Museum: An exploration of Proteomics and Paleoproteomics projects at the Smithsonian [presentation] . Biology Department Seminar, Holland, Michigan: Hope College.
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