[{"file":[{"file_size":1009723,"file_id":"21790","checksum":"1e0c66bbf4b6e0be626a8639ea664b63","content_type":"application/pdf","relation":"main_file","file_name":"2026_Proteomes_Vukajlovic.pdf","creator":"dernst","success":1,"date_updated":"2026-05-04T10:31:35Z","date_created":"2026-05-04T10:31:35Z","access_level":"open_access"}],"language":[{"iso":"eng"}],"department":[{"_id":"MassSpec"}],"volume":14,"article_type":"original","acknowledgement":"The authors thank Gábor Tóth, Uppsala University, Sweden, and Armel Nicolas, Institute for Science and Technology Austria, for their support. This research was conducted during a student residency in Vienna under the auspices of OeAD. ZI: ICM-2016-03196.","date_created":"2026-04-12T22:01:49Z","pmid":1,"ddc":["540"],"month":"03","type":"journal_article","publication_identifier":{"eissn":["2227-7382"]},"publisher":"MDPI","has_accepted_license":"1","scopus_import":"1","OA_place":"publisher","file_date_updated":"2026-05-04T10:31:35Z","title":"Comparison of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar trap columns for proteomics analyses","DOAJ_listed":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2026-05-04T10:36:21Z","day":"01","oa":1,"abstract":[{"lang":"eng","text":"Background: Low-volume trapping columns are essential for sample enrichment, desalting, and injection profile focusing on nano-LC–MS-based proteomics. They enable higher sample loading, improve chromatographic performance, and protect the analytical column by removing salts and contaminants. Recently, monolithic trap columns with micropillar architecture have emerged as alternatives to conventionally packed traps. This study compares the performance of a packed and a micropillar monolithic trap column for the analysis of tryptic peptides. Methods: A tryptic digest of HeLa cell lysate was analyzed under identical LC–MS conditions using both trap types. Peptides were detected at 214 nm and analyzed by nano-ESI on a Q Exactive Plus Orbitrap. Data were searched against the human UniProt database (February 2023) using FragPipe v20.0, and statistical evaluation of MaxLFQ intensities was performed in Perseus using Welch’s t-test and clustering analysis. Results: Over 2500 proteins were identified with both setups. The packed trap column yielded more total peptides, particularly those with post-translational modifications and higher hydrophilicity, whereas the monolithic column favored peptides of intermediate hydrophobicity. Chromatographic profiles confirmed a slight reduction in the trapping efficiency of hydrophilic peptides by the monolithic trap. Conclusions: Trap column design significantly influences peptide recovery and proteome coverage."}],"intvolume":"        14","issue":"1","author":[{"last_name":"Miletić Vukajlović","full_name":"Miletić Vukajlović, Jadranka","first_name":"Jadranka"},{"last_name":"Ilić","full_name":"Ilić, Bojana","first_name":"Bojana"},{"first_name":"Bella","id":"70abbbb3-88ea-11ec-8e0a-e8c939944834","full_name":"Bruszel, Bella","last_name":"Bruszel"},{"first_name":"Tanja","last_name":"Panić-Janković","full_name":"Panić-Janković, Tanja"},{"first_name":"Goran","full_name":"Mitulović, Goran","last_name":"Mitulović"}],"publication_status":"published","oa_version":"Published Version","fulldoi":"https://doi.org/10.3390/proteomes14010010","date_published":"2026-03-01T00:00:00Z","doi":"10.3390/proteomes14010010","quality_controlled":"1","OA_type":"gold","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"21711","year":"2026","article_number":"10","publication":"Proteomes","external_id":{"pmid":["41893725"]},"PlanS_conform":"1","article_processing_charge":"Yes","citation":{"apa":"Miletić Vukajlović, J., Ilić, B., Bruszel, B., Panić-Janković, T., &#38; Mitulović, G. (2026). Comparison of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar trap columns for proteomics analyses. <i>Proteomes</i>. MDPI. <a href=\"https://doi.org/10.3390/proteomes14010010\">https://doi.org/10.3390/proteomes14010010</a>","ista":"Miletić Vukajlović J, Ilić B, Bruszel B, Panić-Janković T, Mitulović G. 2026. Comparison of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar trap columns for proteomics analyses. Proteomes. 14(1), 10.","ieee":"J. Miletić Vukajlović, B. Ilić, B. Bruszel, T. Panić-Janković, and G. Mitulović, “Comparison of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar trap columns for proteomics analyses,” <i>Proteomes</i>, vol. 14, no. 1. MDPI, 2026.","short":"J. Miletić Vukajlović, B. Ilić, B. Bruszel, T. Panić-Janković, G. Mitulović, Proteomes 14 (2026).","chicago":"Miletić Vukajlović, Jadranka, Bojana Ilić, Bella Bruszel, Tanja Panić-Janković, and Goran Mitulović. “Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses.” <i>Proteomes</i>. MDPI, 2026. <a href=\"https://doi.org/10.3390/proteomes14010010\">https://doi.org/10.3390/proteomes14010010</a>.","mla":"Miletić Vukajlović, Jadranka, et al. “Comparison of the Trapping Efficiency for Tryptic Peptides on Particle-Packed and Micro-Pillar Trap Columns for Proteomics Analyses.” <i>Proteomes</i>, vol. 14, no. 1, 10, MDPI, 2026, doi:<a href=\"https://doi.org/10.3390/proteomes14010010\">10.3390/proteomes14010010</a>.","ama":"Miletić Vukajlović J, Ilić B, Bruszel B, Panić-Janković T, Mitulović G. Comparison of the trapping efficiency for tryptic peptides on particle-packed and micro-pillar trap columns for proteomics analyses. <i>Proteomes</i>. 2026;14(1). doi:<a href=\"https://doi.org/10.3390/proteomes14010010\">10.3390/proteomes14010010</a>"}},{"file_date_updated":"2024-12-10T08:28:17Z","OA_place":"publisher","scopus_import":"1","has_accepted_license":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["1757-6512"]},"ddc":["570"],"type":"journal_article","supplementarymaterial":"yes","month":"12","acknowledgement":"We thank the personnel of the Lorenz-Böhler-Unfallkrankenhaus for providing the human tissue waste for primary cell isolation and the New York Stem Cell Foundation Research Institute for providing the human induced pluripotent stem cell line 1013 A and its mesenchymal progenitors. We also thank all our colleagues at the Ludwig Boltzmann Institute for Traumatology for their suggestions and ongoing support of the project. InstaText writing tool (https://instatext.io) was used to edit the English language of the final manuscript.\r\nThis work has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie actions (grant agreement No. 657716) and the Transforming European Industry call H2020-NMBP-TRIND-2020 (grant agreement No. 953134), as well as by the FFG Industrienahe Dissertation program (grant agreement No. 867803 and 853056), the FEMtech Praktika program (grant agreement No. 852154, 868917 and 877951) and the Production of the Future program (grant agreement No. 877452).","article_type":"original","volume":15,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","pmid":1,"date_created":"2024-11-24T23:01:47Z","language":[{"iso":"eng"}],"department":[{"_id":"LifeSc"}],"dataavailabilitystatement":"All data generated and analysed during this study are included in this published article and its supplementary information files. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD052766 (access details are provided in Suppl. Data File 1). The raw datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.","file":[{"relation":"main_file","content_type":"application/pdf","checksum":"91edba8edde30d781dce89fdd5cadc39","file_id":"18641","file_size":6690494,"date_created":"2024-12-10T08:28:17Z","access_level":"open_access","success":1,"date_updated":"2024-12-10T08:28:17Z","creator":"dernst","file_name":"2024_StemCellResearch_Presen.pdf"}],"oa":1,"day":"01","date_updated":"2026-10-16T08:56:29Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"DOAJ_listed":"1","title":"Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium","das_tickbox":"1","researchdata_availability":"yes","doi":"10.1186/s13287-024-03960-5","quality_controlled":"1","fulldoi":"https://doi.org/10.1186/s13287-024-03960-5","oa_version":"Published Version","isi":1,"date_published":"2024-12-01T00:00:00Z","publication_status":"published","author":[{"last_name":"Marolt Presen","full_name":"Marolt Presen, Darja","first_name":"Darja"},{"first_name":"Vanessa","full_name":"Goeschl, Vanessa","last_name":"Goeschl"},{"first_name":"Dominik","last_name":"Hanetseder","full_name":"Hanetseder, Dominik"},{"first_name":"Laura","full_name":"Ogrin, Laura","last_name":"Ogrin"},{"first_name":"Alexandra Larissa","last_name":"Stetco","full_name":"Stetco, Alexandra Larissa"},{"first_name":"Anja","last_name":"Tansek","full_name":"Tansek, Anja"},{"full_name":"Pozenel, Laura","last_name":"Pozenel","first_name":"Laura"},{"last_name":"Bruszel","full_name":"Bruszel, Bella","id":"70abbbb3-88ea-11ec-8e0a-e8c939944834","first_name":"Bella"},{"last_name":"Mitulovic","full_name":"Mitulovic, Goran","first_name":"Goran"},{"full_name":"Oesterreicher, Johannes","last_name":"Oesterreicher","first_name":"Johannes"},{"last_name":"Zipperle","full_name":"Zipperle, Johannes","first_name":"Johannes"},{"full_name":"Schaedl, Barbara","last_name":"Schaedl","first_name":"Barbara"},{"first_name":"Wolfgang","last_name":"Holnthoner","full_name":"Holnthoner, Wolfgang"},{"first_name":"Johannes","last_name":"Grillari","full_name":"Grillari, Johannes"},{"last_name":"Redl","full_name":"Redl, Heinz","first_name":"Heinz"}],"intvolume":"        15","abstract":[{"lang":"eng","text":"Background: Human induced pluripotent stem cells represent a scalable source of youthful tissue progenitors and secretomes for regenerative therapies. The aim of our study was to investigate the potential of conditioned medium (CM) from hiPSC-mesenchymal progenitors (hiPSC-MPs) to stimulate osteogenic differentiation of human bone marrow-derived mesenchymal stromal cells (MSCs). We also investigated whether prolonged cultivation or osteogenic pre-differentiation of hiPSC-MPs could enhance the stimulatory activity of CM.\r\nMethods: MSCs were isolated from 13 donors (age 20–90 years). CM derived from hiPSC-MPs was added to the MSC cultures and the effects on proliferation and osteogenic differentiation were examined after 14 days and 6 weeks. The stimulatory activity of hiPSC-MP-CM was compared with the activity of MSC-derived CM and with the activity of CM prepared from hiPSC-MPs pre-cultured in growth or osteogenic medium for 14 days. Comparative proteomic analysis of CM was performed to gain insight into the molecular components responsible for the stimulatory activity.\r\nResults: Primary bone marrow-derived MSC exhibited variability, with a tendency towards lower proliferation and tri-lineage differentiation in older donors. hiPSC-MP-CM increased the proliferation and alkaline phosphatase activity of MSC from several adult/aged donors after 14 days of continuous supplementation under osteogenic conditions. However, CM supplementation failed to improve the mineralization of MSC pellets after 6 weeks under osteogenic conditions. hiPSC-MP-CM showed greater enhancement of proliferation and ALP activity than CM derived from bone marrow-derived MSCs. Moreover, 14-day cultivation but not osteogenic pre-differentiation of hiPSC-MPs strongly enhanced CM stimulatory activity. Quantitative proteomic analysis of d14-CM revealed a distinct profile of components that formed a highly interconnected associations network with two clusters, one functionally associated with binding and organization of actin/cytoskeletal components and the other with structural constituents of the extracellular matrix, collagen, and growth factor binding. Several hub proteins were identified that were reported to have functions in cell-extracellular matrix interaction, osteogenic differentiation and development.\r\nConclusions: Our data show that hiPSC-MP-CM enhances early osteogenic differentiation of human bone marrow-derived MSCs and that prolonged cultivation of hiPSC-MPs enhances CM-stimulatory activity. Proteomic analysis of the upregulated protein components provides the basis for further optimization of hiPSC-MP-CM for bone regenerative therapies."}],"citation":{"ama":"Marolt Presen D, Goeschl V, Hanetseder D, et al. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. 2024;15. doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>","ista":"Marolt Presen D, Goeschl V, Hanetseder D, Ogrin L, Stetco AL, Tansek A, Pozenel L, Bruszel B, Mitulovic G, Oesterreicher J, Zipperle J, Schaedl B, Holnthoner W, Grillari J, Redl H. 2024. Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. Stem Cell Research and Therapy. 15, 434.","ieee":"D. Marolt Presen <i>et al.</i>, “Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium,” <i>Stem Cell Research and Therapy</i>, vol. 15. Springer Nature, 2024.","apa":"Marolt Presen, D., Goeschl, V., Hanetseder, D., Ogrin, L., Stetco, A. L., Tansek, A., … Redl, H. (2024). Prolonged cultivation enhances the stimulatory activity of hiPSC mesenchymal progenitor-derived conditioned medium. <i>Stem Cell Research and Therapy</i>. Springer Nature. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>","chicago":"Marolt Presen, Darja, Vanessa Goeschl, Dominik Hanetseder, Laura Ogrin, Alexandra Larissa Stetco, Anja Tansek, Laura Pozenel, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>. Springer Nature, 2024. <a href=\"https://doi.org/10.1186/s13287-024-03960-5\">https://doi.org/10.1186/s13287-024-03960-5</a>.","mla":"Marolt Presen, Darja, et al. “Prolonged Cultivation Enhances the Stimulatory Activity of HiPSC Mesenchymal Progenitor-Derived Conditioned Medium.” <i>Stem Cell Research and Therapy</i>, vol. 15, 434, Springer Nature, 2024, doi:<a href=\"https://doi.org/10.1186/s13287-024-03960-5\">10.1186/s13287-024-03960-5</a>.","short":"D. Marolt Presen, V. Goeschl, D. Hanetseder, L. Ogrin, A.L. Stetco, A. Tansek, L. Pozenel, B. Bruszel, G. Mitulovic, J. Oesterreicher, J. Zipperle, B. Schaedl, W. Holnthoner, J. Grillari, H. Redl, Stem Cell Research and Therapy 15 (2024)."},"external_id":{"isi":["001356479400001"],"pmid":["39551765"]},"article_processing_charge":"Yes","publication":"Stem Cell Research and Therapy","article_number":"434","year":"2024","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"18581","OA_type":"gold"}]