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First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. Iacobucci C, et al. Among authors: yilmaz s. Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22. Anal Chem. 2019. PMID: 31045356 Free PMC article.
MaxDIA enables library-based and library-free data-independent acquisition proteomics.
Sinitcyn P, Hamzeiy H, Salinas Soto F, Itzhak D, McCarthy F, Wichmann C, Steger M, Ohmayer U, Distler U, Kaspar-Schoenefeld S, Prianichnikov N, Yılmaz Ş, Rudolph JD, Tenzer S, Perez-Riverol Y, Nagaraj N, Humphrey SJ, Cox J. Sinitcyn P, et al. Among authors: yilmaz s. Nat Biotechnol. 2021 Dec;39(12):1563-1573. doi: 10.1038/s41587-021-00968-7. Epub 2021 Jul 8. Nat Biotechnol. 2021. PMID: 34239088 Free PMC article.
MaxQuant goes Linux.
Sinitcyn P, Tiwary S, Rudolph J, Gutenbrunner P, Wichmann C, Yılmaz Ş, Hamzeiy H, Salinas F, Cox J. Sinitcyn P, et al. Among authors: yilmaz s. Nat Methods. 2018 Jun;15(6):401. doi: 10.1038/s41592-018-0018-y. Nat Methods. 2018. PMID: 29855570 No abstract available.
The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Perez-Riverol Y, Csordas A, Bai J, Bernal-Llinares M, Hewapathirana S, Kundu DJ, Inuganti A, Griss J, Mayer G, Eisenacher M, Pérez E, Uszkoreit J, Pfeuffer J, Sachsenberg T, Yilmaz S, Tiwary S, Cox J, Audain E, Walzer M, Jarnuczak AF, Ternent T, Brazma A, Vizcaíno JA. Perez-Riverol Y, et al. Among authors: yilmaz s. Nucleic Acids Res. 2019 Jan 8;47(D1):D442-D450. doi: 10.1093/nar/gky1106. Nucleic Acids Res. 2019. PMID: 30395289 Free PMC article.
Methods to Calculate Spectrum Similarity.
Yilmaz Ş, Vandermarliere E, Martens L. Yilmaz Ş, et al. Methods Mol Biol. 2017;1549:75-100. doi: 10.1007/978-1-4939-6740-7_7. Methods Mol Biol. 2017. PMID: 27975285
A Pipeline for Differential Proteomics in Unsequenced Species.
Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L. Yılmaz Ş, et al. J Proteome Res. 2016 Jun 3;15(6):1963-70. doi: 10.1021/acs.jproteome.6b00140. Epub 2016 May 2. J Proteome Res. 2016. PMID: 27089233
2,604 results