{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T14:52:42Z","timestamp":1787237562573,"version":"build-2736575974"},"publisher-location":"New York, NY","reference-count":15,"publisher":"Springer US","isbn-type":[{"value":"9781071645017","type":"print"},{"value":"9781071645024","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,1,1]],"date-time":"2025-01-01T00:00:00Z","timestamp":1735689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025]]},"DOI":"10.1007\/978-1-0716-4502-4_15","type":"book-chapter","created":{"date-parts":[[2025,6,14]],"date-time":"2025-06-14T02:43:44Z","timestamp":1749869024000},"page":"275-291","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["A Comprehensive Data Processing Pipeline for Phosphoproteomics in Viral Infection Studies"],"prefix":"10.1007","author":[{"given":"Sini","family":"Huuskonen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaonan","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kari","family":"Salokas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Antti","family":"Tuhkala","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Salla","family":"Keskitalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Markku","family":"Varjosalo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2025,6,15]]},"reference":[{"issue":"3","key":"15_CR1","doi-asserted-by":"publisher","first-page":"685","DOI":"10.1016\/j.cell.2020.06.034","volume":"182","author":"M Bouhaddou","year":"2020","unstructured":"Bouhaddou M, Memon D, Meyer B, White KM, Rezelj VV, Correa Marrero M, Polacco BJ, Melnyk JE, Ulferts S, Kaake RM, Batra J, Richards AL, Stevenson E, Gordon DE, Rojc A, Obernier K, Fabius JM, Soucheray M, Miorin L, Moreno E, Koh C, Tran QD, Hardy A, Robinot R, Vallet T, Nilsson-Payant BE, Hernandez-Armenta C, Dunham A, Weigang S, Knerr J, Modak M, Quintero D, Zhou Y, Dugourd A, Valdeolivas A, Patil T, Li Q, H\u00fcttenhain R, Cakir M, Muralidharan M, Kim M, Jang G, Tutuncuoglu B, Hiatt J, Guo JZ, Xu J, Bouhaddou S, Mathy CJP, Gaulton A, Manners EJ, F\u00e9lix E, Shi Y, Goff M, Lim JK, McBride T, O\u2019Neal MC, Cai Y, Chang JCJ, Broadhurst DJ, Klippsten S, De Wit E, Leach AR, Kortemme T, Shoichet B, Ott M, Saez-Rodriguez J, tenOever BR, Mullins RD, Fischer ER, Kochs G, Grosse R, Garc\u00eda-Sastre A, Vignuzzi M, Johnson JR, Shokat KM, Swaney DL, Beltrao P, Krogan NJ (2020) The global phosphorylation landscape of SARS-CoV-2 infection. Cell 182(3):685\u2013712.e19. https:\/\/doi.org\/10.1016\/j.cell.2020.06.034","journal-title":"Cell"},{"issue":"7862","key":"15_CR2","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/s41586-021-03493-4","volume":"594","author":"A Stukalov","year":"2021","unstructured":"Stukalov A, Girault V, Grass V, Karayel O, Bergant V, Urban C, Haas DA, Huang Y, Oubraham L, Wang A, Hamad MS, Piras A, Hansen FM, Tanzer MC, Paron I, Zinzula L, Engleitner T, Reinecke M, Lavacca TM, Ehmann R, W\u00f6lfel R, Jores J, Kuster B, Protzer U, Rad R, Ziebuhr J, Thiel V, Scaturro P, Mann M, Pichlmair A (2021) Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV. Nature 594(7862):246\u2013252. https:\/\/doi.org\/10.1038\/s41586-021-03493-4","journal-title":"Nature"},{"issue":"13","key":"15_CR3","doi-asserted-by":"publisher","first-page":"e00528","DOI":"10.1128\/JVI.00528-19","volume":"93","author":"A Weber","year":"2019","unstructured":"Weber A, Dam S, Saul VV, Kuznetsova I, M\u00fcller C, Fritz-Wolf K, Becker K, Linne U, Gu H, Stokes MP, Pleschka S, Kracht M, Schmitz ML (2019) Phosphoproteome analysis of cells infected with adapted and nonadapted Influenza A virus reveals novel Pro- and antiviral signaling networks. J Virol 93(13):e00528\u2013e00519. https:\/\/doi.org\/10.1128\/JVI.00528-19","journal-title":"J Virol"},{"issue":"8","key":"15_CR4","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1080\/14789450.2021.1976152","volume":"18","author":"JS Gerritsen","year":"2021","unstructured":"Gerritsen JS, White FM (2021) Phosphoproteomics: a valuable tool for uncovering molecular signaling in cancer cells. Expert Rev Proteomics 18(8):661\u2013674. https:\/\/doi.org\/10.1080\/14789450.2021.1976152","journal-title":"Expert Rev Proteomics"},{"issue":"10","key":"15_CR5","doi-asserted-by":"publisher","first-page":"5257","DOI":"10.3390\/v7102872","volume":"7","author":"F Keck","year":"2015","unstructured":"Keck F, Ataey P, Amaya M, Bailey C, Narayanan A (2015) Phosphorylation of single stranded RNA virus proteins and potential for novel therapeutic strategies. Viruses 7(10):5257\u20135273. https:\/\/doi.org\/10.3390\/v7102872","journal-title":"Viruses"},{"issue":"2","key":"15_CR6","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1038\/s41579-018-0117-x","volume":"17","author":"ZA Jaafar","year":"2019","unstructured":"Jaafar ZA, Kieft JS (2019) Viral RNA structure-based strategies to manipulate translation. Nat Rev Microbiol 17(2):110\u2013123. https:\/\/doi.org\/10.1038\/s41579-018-0117-x","journal-title":"Nat Rev Microbiol"},{"issue":"11","key":"15_CR7","doi-asserted-by":"publisher","first-page":"2197","DOI":"10.3390\/v13112197","volume":"13","author":"C Chamontin","year":"2021","unstructured":"Chamontin C, Bossis G, Nisole S, Arhel NJ, Maarifi G (2021) Regulation of viral restriction by post-translational modifications. Viruses 13(11):2197. https:\/\/doi.org\/10.3390\/v13112197","journal-title":"Viruses"},{"key":"15_CR8","doi-asserted-by":"publisher","DOI":"10.3389\/fcell.2021.622610","volume":"9","author":"LA Tavares","year":"2021","unstructured":"Tavares LA, Janu\u00e1rio YC, daSilva LLP (2021) HIV-1 hijacking of host ATPases and GTPases that control protein trafficking. Front Cell Dev Biol 9:622610. https:\/\/doi.org\/10.3389\/fcell.2021.622610","journal-title":"Front Cell Dev Biol"},{"issue":"6","key":"15_CR9","doi-asserted-by":"publisher","first-page":"452","DOI":"10.1080\/10409238.2016.1226250","volume":"51","author":"MS Crow","year":"2016","unstructured":"Crow MS, Lum KK, Sheng X, Song B, Cristea IM (2016) Diverse mechanisms evolved by DNA viruses to inhibit early host defenses. Crit Rev Biochem Mol Biol 51(6):452\u2013481. https:\/\/doi.org\/10.1080\/10409238.2016.1226250","journal-title":"Crit Rev Biochem Mol Biol"},{"issue":"10","key":"15_CR10","doi-asserted-by":"publisher","first-page":"3182","DOI":"10.1038\/s41596-020-0365-x","volume":"15","author":"X Liu","year":"2020","unstructured":"Liu X, Salokas K, Weldatsadik RG, Gawriyski L, Varjosalo M (2020) Combined proximity labeling and affinity purification\u2212mass spectrometry workflow for mapping and visualizing protein interaction networks. Nat Protoc 15(10):3182\u20133211. https:\/\/doi.org\/10.1038\/s41596-020-0365-x","journal-title":"Nat Protoc"},{"issue":"1","key":"15_CR11","doi-asserted-by":"publisher","first-page":"15782","DOI":"10.1038\/s41598-019-51995-z","volume":"9","author":"AL Capriotti","year":"2019","unstructured":"Capriotti AL, Antonelli M, Antonioli D, Cavaliere C, Chiarcos R, Gianotti V, Piovesana S, Sparnacci K, Laus M, Lagan\u00e0 A (2019) Effect of shell structure of Ti-immobilized metal ion affinity chromatography core-shell magnetic particles for phosphopeptide enrichment. Sci Rep 9(1):15782. https:\/\/doi.org\/10.1038\/s41598-019-51995-z","journal-title":"Sci Rep"},{"issue":"12","key":"15_CR12","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1038\/s41592-020-00998-0","volume":"17","author":"F Meier","year":"2020","unstructured":"Meier F, Brunner A-D, Frank M, Ha A, Bludau I, Voytik E, Kaspar-Schoenefeld S, Lubeck M, Raether O, Bache N, Aebersold R, Collins BC, R\u00f6st HL, Mann M (2020) diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition. Nat Methods 17(12):1229\u20131236. https:\/\/doi.org\/10.1038\/s41592-020-00998-0","journal-title":"Nat Methods"},{"issue":"1","key":"15_CR13","doi-asserted-by":"publisher","first-page":"3944","DOI":"10.1038\/s41467-022-31492-0","volume":"13","author":"V Demichev","year":"2022","unstructured":"Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, M\u00fclleder M, Nesvizhskii AI, Ralser M (2022) Dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts. Nat Commun 13(1):3944. https:\/\/doi.org\/10.1038\/s41467-022-31492-0","journal-title":"Nat Commun"},{"key":"15_CR14","doi-asserted-by":"publisher","unstructured":"Huuskonen S, Liu X, Redchuk T, Salokas K, Lundberg R, Maljanen S, Belik M, Reinholm A, Kolehmainen P, Tripathi G, Laine P, Belanov S, Auvinen P, Vartiainen M, Laine L, \u00d6sterlund P, Julkkunen I, Kakkola L, Varjosalo M (2024) The comprehensive SARS-CoV-2 \u2018Hijackome\u2019 knowledge base\u2014reveals significant changes in host cell protein expression and activation by multiple SARS-CoV-2 variants. Res Square. https:\/\/doi.org\/10.21203\/rs.3.rs-4322477\/v1","DOI":"10.21203\/rs.3.rs-4322477\/v1"},{"issue":"1","key":"15_CR15","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-019-0638-x","volume":"17","author":"V Demichev","year":"2020","unstructured":"Demichev V, Messner CB, Vernardis SI, Lilley KS, Ralser M (2020) DIA-NN: neural networks and interference correction enable deep proteome coverage in high throughput. Nat Methods 17(1):41\u201344. https:\/\/doi.org\/10.1038\/s41592-019-0638-x","journal-title":"Nat Methods"}],"container-title":["Methods in Molecular Biology","Activity-Based Proteomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-0716-4502-4_15","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,14]],"date-time":"2025-06-14T02:43:44Z","timestamp":1749869024000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-1-0716-4502-4_15"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025]]},"ISBN":["9781071645017","9781071645024"],"references-count":15,"URL":"https:\/\/doi.org\/10.1007\/978-1-0716-4502-4_15","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025]]},"assertion":[{"value":"15 June 2025","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}