{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T03:58:55Z","timestamp":1774670335321,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T00:00:00Z","timestamp":1736640000000},"content-version":"vor","delay-in-days":11,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["23-15-00320"],"award-info":[{"award-number":["23-15-00320"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Osteogenic differentiation is crucial in normal bone formation and pathological calcification, such as calcific aortic valve disease (CAVD). Understanding the proteomic and transcriptomic landscapes underlying this differentiation can unveil potential therapeutic targets for CAVD. In this study, we employed RNA sequencing transcriptomics and proteomics on a timsTOF Pro platform to explore the multiomics profiles of valve interstitial cells (VICs) and osteoblasts during osteogenic differentiation. For proteomics, we utilized 3 data acquisition\/analysis techniques: data-dependent acquisition (DDA)\u2013parallel accumulation serial fragmentation (PASEF) and data-independent acquisition (DIA)\u2013PASEF with a classic library-based (DIA) and machine learning\u2013based library-free search (DIA-ML). Using RNA sequencing data as a biological reference, we compared these 3 analytical techniques in the context of actual biological experiments. We use this comprehensive dataset to reveal distinct proteomic and transcriptomic profiles between VICs and osteoblasts, highlighting specific biological processes in their osteogenic differentiation pathways. The study identified potential therapeutic targets specific for VICs osteogenic differentiation in CAVD, including the MAOA and ERK1\/2 pathway. From a technical perspective, we found that DIA-based methods demonstrate even higher superiority against DDA for more sophisticated human primary cell cultures than it was shown before on HeLa samples. While the classic library-based DIA approach has proved to be a gold standard for shotgun proteomics research, the DIA-ML offers significant advantages with a relatively minor compromise in data reliability, making it the method of choice for routine proteomics.<\/jats:p>","DOI":"10.1093\/gigascience\/giae110","type":"journal-article","created":{"date-parts":[[2025,1,12]],"date-time":"2025-01-12T00:27:12Z","timestamp":1736641632000},"source":"Crossref","is-referenced-by-count":6,"title":["Similar, but not the same: multiomics comparison of human valve interstitial cells and osteoblast osteogenic differentiation expanded with an estimation of data-dependent and data-independent PASEF proteomics"],"prefix":"10.1093","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0930-1171","authenticated-orcid":false,"given":"Arseniy","family":"Lobov","sequence":"first","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9415-577X","authenticated-orcid":false,"given":"Polina","family":"Kuchur","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6402-770X","authenticated-orcid":false,"given":"Nadezhda","family":"Boyarskaya","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]},{"name":"Almazov National Medical Research Centre , St. Petersburg, 197341 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5056-3368","authenticated-orcid":false,"given":"Daria","family":"Perepletchikova","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7251-1067","authenticated-orcid":false,"given":"Ivan","family":"Taraskin","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-6039-3960","authenticated-orcid":false,"given":"Andrei","family":"Ivashkin","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0641-8101","authenticated-orcid":false,"given":"Daria","family":"Kostina","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7124-9749","authenticated-orcid":false,"given":"Irina","family":"Khvorova","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7929-0594","authenticated-orcid":false,"given":"Vladimir","family":"Uspensky","sequence":"additional","affiliation":[{"name":"Almazov National Medical Research Centre , St. Petersburg, 197341 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8599-3173","authenticated-orcid":false,"given":"Egor","family":"Repkin","sequence":"additional","affiliation":[{"name":"Centre for Molecular and Cell Technologies, St. Petersburg State University , St. Petersburg, 199034 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2923-9755","authenticated-orcid":false,"given":"Evgeny","family":"Denisov","sequence":"additional","affiliation":[{"name":"Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences , Tomsk, 634050 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7283-0092","authenticated-orcid":false,"given":"Tatiana","family":"Gerashchenko","sequence":"additional","affiliation":[{"name":"Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences , Tomsk, 634050 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0733-2414","authenticated-orcid":false,"given":"Rashid","family":"Tikhilov","sequence":"additional","affiliation":[{"name":"Vreden National Medical Research Center of Traumatology and Orthopedics , St. Petersburg, 195427 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2083-2424","authenticated-orcid":false,"given":"Svetlana","family":"Bozhkova","sequence":"additional","affiliation":[{"name":"Vreden National Medical Research Center of Traumatology and Orthopedics , St. Petersburg, 195427 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-3020-2417","authenticated-orcid":false,"given":"Vitaly","family":"Karelkin","sequence":"additional","affiliation":[{"name":"Vreden National Medical Research Center of Traumatology and Orthopedics , St. Petersburg, 195427 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8891-1797","authenticated-orcid":false,"given":"Chunli","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hubei University of Chinese Medicine , Wuhan, 430065 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8492-2058","authenticated-orcid":false,"given":"Kang","family":"Xu","sequence":"additional","affiliation":[{"name":"School of Pharmacy, Hubei University of Chinese Medicine , Wuhan, 430065 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0820-2913","authenticated-orcid":false,"given":"Anna","family":"Malashicheva","sequence":"additional","affiliation":[{"name":"Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Science , St. Petersburg, 194064 ,","place":["Russia"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,1,11]]},"reference":[{"key":"2025022109420689200_bib1","doi-asserted-by":"publisher","first-page":"68","DOI":"10.3389\/fbioe.2017.00068","article-title":"It takes two to tango: coupling of angiogenesis and osteogenesis for bone regeneration","volume":"5","author":"Grosso","year":"2017","journal-title":"Front Bioeng Biotechnol"},{"key":"2025022109420689200_bib2","doi-asserted-by":"publisher","first-page":"185","DOI":"10.2147\/VHRM.S4822","article-title":"Vascular calcifications as a marker of increased cardiovascular risk: a meta-analysis","volume":"5","author":"Rennenberg","year":"2009","journal-title":"Vasc Health Risk Manag"},{"key":"2025022109420689200_bib3","doi-asserted-by":"publisher","first-page":"12710","DOI":"10.18632\/aging.202942","article-title":"Changing epidemiology of calcific aortic valve disease: 30-year trends of incidence, prevalence, and deaths across 204 countries and territories","volume":"13","author":"Yi","year":"2021","journal-title":"Aging"},{"key":"2025022109420689200_bib4","doi-asserted-by":"publisher","first-page":"853","DOI":"10.1038\/s41569-021-00570-z","article-title":"Global epidemiology of valvular heart disease","volume":"18","author":"Coffey","year":"2021","journal-title":"Nat Rev Cardiol"},{"key":"2025022109420689200_bib5","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-46725-8","volume-title":"Cardiovascular calcification and bone mineralization","author":"Aikawa","year":"2020."},{"key":"2025022109420689200_bib6","doi-asserted-by":"publisher","first-page":"6530","DOI":"10.1126\/science.abd0724","article-title":"Network-based screen in iPSC-derived cells reveals therapeutic candidate for heart valve disease","volume":"371","author":"Theodoris","year":"2021","journal-title":"Science"},{"key":"2025022109420689200_bib7","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1161\/JAHA.117.006339","article-title":"Valve interstitial cells: the key to understanding the pathophysiology of heart valve calcification","volume":"6","author":"Rutkovskiy","year":"2017","journal-title":"J Am Heart Assoc"},{"key":"2025022109420689200_bib8","doi-asserted-by":"publisher","first-page":"1371","DOI":"10.1161\/CIRCRESAHA.120.317979","article-title":"Multi-omics approaches to define calcific aortic valve disease pathogenesis","volume":"128","author":"Blaser","year":"21","journal-title":"Circ Res"},{"key":"2025022109420689200_bib9","doi-asserted-by":"publisher","first-page":"32","DOI":"10.21638\/spbu03.2022.104","article-title":"Osteogenic differentiation: a universal cell program of heterogeneous mesenchymal cells or a similar extracellular matrix mineralizing phenotype?","volume":"67","author":"Lobov","year":"2022","journal-title":"BioComm"},{"key":"2025022109420689200_bib10","doi-asserted-by":"publisher","first-page":"2036","DOI":"10.1021\/acs.jproteome.2c00336","article-title":"Enhancement of proteome coverage by ion mobility fractionation coupled to PASEF on a TIMS\u2013QTOF instrument","volume":"21","author":"Guergues","year":"2022","journal-title":"J Proteome Res"},{"key":"2025022109420689200_bib11","doi-asserted-by":"publisher","DOI":"10.1101\/2021.11.29.470373","article-title":"Comparison of TIMS-PASEF quantitative proteomics data-analysis workflows using FragPipe, DIA-NN, and Spectronaut from a user's perspective","volume-title":"Biorxiv","author":"Fern\u00e1ndez-Vega","year":"2021"},{"key":"2025022109420689200_bib12","doi-asserted-by":"publisher","first-page":"1258703","DOI":"10.3389\/fmicb.2023.1258703","article-title":"Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics","volume":"14","author":"G\u00f3mez-Varela","year":"2023","journal-title":"Front Microbiol"},{"key":"2025022109420689200_bib13","doi-asserted-by":"publisher","first-page":"107919","DOI":"10.1016\/j.dib.2022.107919","article-title":"Proteomic datasets of HeLa and SiHa cell lines acquired by DDA-PASEF and diaPASEF","volume":"41","author":"Huang","year":"2022","journal-title":"Data Brief"},{"key":"2025022109420689200_bib14","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1038\/s41597-023-02779-8","article-title":"MultiPro: DDA-PASEF and diaPASEF acquired cell line proteomic datasets with deliberate batch effects","volume-title":"Sci Data","author":"Wang","year":"2023"},{"key":"2025022109420689200_bib15","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1159\/000357096","article-title":"A single-tube real-time PCR assay for Mycoplasma detection as a routine quality control of cell therapeutics","volume":"41","author":"Janetzko","year":"2014","journal-title":"Transfus Med Hemother"},{"key":"2025022109420689200_bib16","doi-asserted-by":"publisher","first-page":"1896","DOI":"10.1038\/nprot.2007.261","article-title":"Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips","volume":"2","author":"Rappsilber","year":"2007","journal-title":"Nat Protoc"},{"key":"2025022109420689200_bib17","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2025022109420689200_bib18","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omics"},{"key":"2025022109420689200_bib19","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1039\/C5MB00663E","article-title":"ReactomePA: an R\/bioconductor package for reactome pathway analysis and visualization","volume":"12","author":"Yu","year":"2016","journal-title":"Mol BioSyst"},{"key":"2025022109420689200_bib20","article-title":"pheatmap: pretty Heatmaps","author":"Kolde","year":"2018","journal-title":"GitHub"},{"key":"2025022109420689200_bib21","doi-asserted-by":"publisher","first-page":"e43","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","author":"Gu","year":"2022","journal-title":"iMeta"},{"key":"2025022109420689200_bib22","doi-asserted-by":"publisher","DOI":"10.1007\/978-0-387-98141-3","article-title":"ggplot2","author":"Wickham","year":"2009"},{"key":"2025022109420689200_bib23","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/1471-2105-12-35","article-title":"VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R","volume":"12","author":"Chen","year":"2011","journal-title":"BMC Bioinf"},{"key":"2025022109420689200_bib24","doi-asserted-by":"publisher","first-page":"e83","DOI":"10.1093\/nar\/gkaa498","article-title":"NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses","volume":"48","author":"Wang","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025022109420689200_bib25","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.compbiolchem.2008.07.019","article-title":"Robust data imputation","volume":"33","author":"Branden","year":"2009","journal-title":"Comput Biol Chem"},{"key":"2025022109420689200_bib26","doi-asserted-by":"publisher","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2025022109420689200_bib27","doi-asserted-by":"publisher","first-page":"1043165","DOI":"10.3389\/fcvm.2022.1043165","article-title":"Multi-omics of in vitro aortic valve calcification","volume":"9","author":"Semenova","year":"2022","journal-title":"Front Cardiovasc Med"},{"key":"2025022109420689200_bib28","doi-asserted-by":"publisher","first-page":"1127879","DOI":"10.3389\/fimmu.2023.1127879","article-title":"Establishing a human bone marrow single cell reference atlas to study ageing and diseases","volume":"14","author":"Lee","year":"2023","journal-title":"Front Immunol"},{"key":"2025022109420689200_bib29","doi-asserted-by":"publisher","first-page":"3356","DOI":"10.3390\/cells11213356","article-title":"Isolation of human osteoblast cells capable for mineralization and synthetizing bone-related proteins in vitro from adult bone","volume":"11","author":"Kostina","year":"2022","journal-title":"Cells"},{"key":"2025022109420689200_bib30","doi-asserted-by":"publisher","first-page":"673","DOI":"10.3390\/biomedicines9060673","article-title":"Context-specific osteogenic potential of mesenchymal stem cells","volume":"9","author":"Kostina","year":"2021","journal-title":"Biomedicines"},{"key":"2025022109420689200_bib31","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1161\/CIRCULATIONAHA.105.001115","article-title":"Role of human valve interstitial cells in valve calcification and their response to atorvastatin","volume":"114","author":"Osman","year":"2006","journal-title":"Circulation"},{"key":"2025022109420689200_bib32","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1134\/S1990519X22060025","article-title":"Osteogenic differentiation in vitro of human osteoblasts is associated with only slight shift in their proteomics profile","volume":"16","author":"Khvorova","year":"2022","journal-title":"Cell Tiss Biol"},{"key":"2025022109420689200_bib33","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1093\/stmcls\/sxad081","article-title":"Mesenchymal cells retain the specificity of embryonal origin during osteogenic differentiation","volume":"42","author":"Lobov","year":"2024","journal-title":"Stem Cells"},{"key":"2025022109420689200_bib34","doi-asserted-by":"publisher","first-page":"1575","DOI":"10.1074\/mcp.TIR120.002048","article-title":"Fast quantitative analysis of timsTOF PASEF data with MSFragger and IonQuant","volume":"19","author":"Yu","year":"2020","journal-title":"Mol Cell Proteomics"},{"key":"2025022109420689200_bib35","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","article-title":"DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput","volume":"17","author":"Demichev","year":"2020","journal-title":"Nat Methods"},{"key":"2025022109420689200_bib36","doi-asserted-by":"publisher","first-page":"689","DOI":"10.1038\/msb.2013.47","article-title":"Protein synthesis rate is the predominant regulator of protein expression during differentiation","volume":"9","author":"Kristensen","year":"2013","journal-title":"Mol Syst Biol"},{"key":"2025022109420689200_bib37","doi-asserted-by":"publisher","first-page":"e1005901","DOI":"10.1371\/journal.pgen.1005901","article-title":"Genome-wide and experimental resolution of relative translation elongation speed at individual gene level in human cells","volume":"12","author":"Lian","year":"2016","journal-title":"PLoS Genet"},{"key":"2025022109420689200_bib38","doi-asserted-by":"publisher","first-page":"1720","DOI":"10.1128\/mcb.19.3.1720","article-title":"Correlation between protein and mRNA abundance in yeast","volume":"19","author":"Gygi","year":"1999","journal-title":"Mol Cell Biol"},{"key":"2025022109420689200_bib39","doi-asserted-by":"publisher","first-page":"e8503","DOI":"10.15252\/msb.20188503","article-title":"A deep proteome and transcriptome abundance atlas of 29 healthy human tissues","volume":"15","author":"Wang","year":"2019","journal-title":"Mol Syst Biol"},{"key":"2025022109420689200_bib40","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1111\/jnc.14664","article-title":"Poor transcript-protein correlation in the brain: negatively correlating gene products reveal neuronal polarity as a potential cause","volume":"149","author":"Moritz","year":"2019","journal-title":"J Neurochem"},{"key":"2025022109420689200_bib41","doi-asserted-by":"publisher","first-page":"3153","DOI":"10.1021\/acs.jproteome.0c00153","article-title":"Impact of the identification strategy on the reproducibility of the DDA and DIA results","volume":"19","author":"Fern\u00e1ndez-Costa","year":"2020","journal-title":"J Proteome Res"},{"key":"2025022109420689200_bib42","doi-asserted-by":"publisher","first-page":"101984","DOI":"10.1016\/j.gde.2022.101984","article-title":"Correlation between protein abundance and sequence conservation: what do recent experiments say?","volume":"77","author":"B\u00e9dard","year":"2022","journal-title":"Curr Opin Genet Dev"},{"key":"2025022109420689200_bib43","doi-asserted-by":"publisher","first-page":"e5815","DOI":"10.1371\/journal.pone.0005815","article-title":"Influence of protein abundance on high-throughput protein-protein interaction detection","volume":"4","author":"Ivanic","year":"2009","journal-title":"PLoS One"},{"key":"2025022109420689200_bib44","doi-asserted-by":"publisher","first-page":"1522","DOI":"10.1161\/01.CIR.103.11.1522","article-title":"Bone formation and inflammation in cardiac valves","volume":"103","author":"Mohler","year":"2001","journal-title":"Circulation"},{"key":"2025022109420689200_bib45","doi-asserted-by":"publisher","first-page":"20703","DOI":"10.1038\/s41598-020-77656-0","article-title":"Systems biology analysis of osteogenic differentiation behavior by canine mesenchymal stem cells derived from bone marrow and dental pulp","volume":"10","author":"Nantavisai","year":"2020","journal-title":"Sci Rep"},{"key":"2025022109420689200_bib46","doi-asserted-by":"publisher","first-page":"11814","DOI":"10.1111\/jcmm.15797","article-title":"Comparative proteomic analysis of osteogenic differentiated human adipose tissue and bone marrow-derived stromal cells","volume":"24","author":"Dadras","year":"2020","journal-title":"J Cell Mol Med"},{"key":"2025022109420689200_bib47","doi-asserted-by":"publisher","first-page":"1606","DOI":"10.3390\/biomedicines9111606","article-title":"Comparative analysis of dental pulp and periodontal stem cells: differences in morphology, functionality, osteogenic differentiation and proteome","volume":"9","author":"Kotova","year":"2021","journal-title":"Biomedicines"},{"key":"2025022109420689200_bib48","doi-asserted-by":"publisher","first-page":"110685","DOI":"10.1016\/j.celrep.2022.110685","article-title":"A disease-driver population within interstitial cells of human calcific aortic valves identified via single-cell and proteomic profiling","volume":"39","author":"Decano","year":"2022","journal-title":"Cell Rep"},{"key":"2025022109420689200_bib49","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1136\/jmedgenet-2015-103684","article-title":"AKAP2 identified as a novel gene mutated in a Chinese family with adolescent idiopathic scoliosis","volume":"53","author":"Li","year":"2016","journal-title":"J Med Genet"},{"key":"2025022109420689200_bib50","doi-asserted-by":"publisher","first-page":"115875","DOI":"10.1016\/j.bone.2021.115875","article-title":"AKAP2 overexpression modulates growth plate chondrocyte functions through ERK1\/2 signaling","volume":"146","author":"Wang","year":"2021","journal-title":"Bone"},{"key":"2025022109420689200_bib51","doi-asserted-by":"publisher","first-page":"e58574","DOI":"10.1371\/journal.pone.0058574","article-title":"GLIPR-2 overexpression in HK-2 cells promotes cell EMT and migration through ERK1\/2 activation","volume":"8","author":"Huang","year":"2013","journal-title":"PLoS One"},{"key":"2025022109420689200_bib52","doi-asserted-by":"publisher","first-page":"3761","DOI":"10.3390\/ijms19123761","article-title":"Role of p38 MAPK in atherosclerosis and aortic valve sclerosis","volume":"19","author":"Reustle","year":"2018","journal-title":"Int J Mol Sci"},{"key":"2025022109420689200_bib53","doi-asserted-by":"publisher","first-page":"109985","DOI":"10.1016\/j.biopha.2020.109985","article-title":"The natural compound andrographolide inhibits human aortic valve interstitial cell calcification via the NF-kappa B\/Akt\/ERK pathway","volume":"125","author":"Huang","year":"2020","journal-title":"Biomed Pharmacother"},{"key":"2025022109420689200_bib54","doi-asserted-by":"publisher","first-page":"2397","DOI":"10.1021\/acs.jproteome.2c00265","article-title":"In search of a universal method: a comparative survey of bottom-up proteomics sample preparation methods","volume":"21","author":"Varnavides","year":"2022","journal-title":"J Proteome Res"},{"key":"2025022109420689200_bib55","doi-asserted-by":"publisher","first-page":"761","DOI":"10.1021\/pr9006365","article-title":"Repeatability and reproducibility in proteomic identifications by liquid chromatography\u2212 tandem mass spectrometry","volume":"9","author":"Tabb","year":"2010","journal-title":"J Proteome Res"},{"key":"2025022109420689200_bib56","doi-asserted-by":"publisher","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025022109420689200_bib57","doi-asserted-by":"crossref","unstructured":"Lobov A, Kuchur P, Boyarskaya N, et al. \u00a0Supporting data for \u201cSimilar, but Not the Same: Multiomics Comparison of Human Valve Interstitial Cells and Osteoblast Osteogenic Differentiation Expanded with an Estimation of Data-Dependent and Data-Independent PASEF Proteomic.\u201d \u00a0GigaScience Database. 2024. 10.5524\/102619.","DOI":"10.1093\/gigascience\/giae110"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giae110\/61415424\/giae110.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/doi\/10.1093\/gigascience\/giae110\/61415424\/giae110.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T09:51:34Z","timestamp":1740131494000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giae110\/7951946"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"references-count":57,"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giae110","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025]]},"published":{"date-parts":[[2025]]},"article-number":"giae110"}}