Yu F - Search Results

1

Analysis and visualization of quantitative proteomics data using FragPipe-Analyst.

Hsiao Y, Zhang H, Li GX, Deng Y, Yu F, Kahrood HV, Steele JR, Schittenhelm RB, Nesvizhskii AI. Hsiao Y, et al. Among authors: yu f. bioRxiv [Preprint]. 2024 Mar 10:2024.03.05.583643. doi: 10.1101/2024.03.05.583643. bioRxiv. 2024. Update in: J Proteome Res. 2024 Oct 4;23(10):4303-4315. doi: 10.1021/acs.jproteome.4c00294. PMID: 38496650 Free PMC article. Updated. Preprint.

2

Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant.

Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Yu F, et al. Mol Cell Proteomics. 2020 Sep;19(9):1575-1585. doi: 10.1074/mcp.TIR120.002048. Epub 2020 Jul 2. Mol Cell Proteomics. 2020. PMID: 32616513 Free PMC article.

3

Identification of modified peptides using localization-aware open search.

Yu F, Teo GC, Kong AT, Haynes SE, Avtonomov DM, Geiszler DJ, Nesvizhskii AI. Yu F, et al. Nat Commun. 2020 Aug 13;11(1):4065. doi: 10.1038/s41467-020-17921-y. Nat Commun. 2020. PMID: 32792501 Free PMC article.

4

Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco.

Polasky DA, Yu F, Teo GC, Nesvizhskii AI. Polasky DA, et al. Among authors: yu f. Nat Methods. 2020 Nov;17(11):1125-1132. doi: 10.1038/s41592-020-0967-9. Epub 2020 Oct 5. Nat Methods. 2020. PMID: 33020657 Free PMC article.

5

Fast Deisotoping Algorithm and Its Implementation in the MSFragger Search Engine.

Teo GC, Polasky DA, Yu F, Nesvizhskii AI. Teo GC, et al. Among authors: yu f. J Proteome Res. 2021 Jan 1;20(1):498-505. doi: 10.1021/acs.jproteome.0c00544. Epub 2020 Dec 17. J Proteome Res. 2021. PMID: 33332123 Free PMC article.

6

PTM-Shepherd: Analysis and Summarization of Post-Translational and Chemical Modifications From Open Search Results.

Geiszler DJ, Kong AT, Avtonomov DM, Yu F, Leprevost FDV, Nesvizhskii AI. Geiszler DJ, et al. Among authors: yu f. Mol Cell Proteomics. 2021;20:100018. doi: 10.1074/mcp.TIR120.002216. Epub 2020 Dec 11. Mol Cell Proteomics. 2021. PMID: 33568339 Free PMC article.

7

IonQuant Enables Accurate and Sensitive Label-Free Quantification With FDR-Controlled Match-Between-Runs.

Yu F, Haynes SE, Nesvizhskii AI. Yu F, et al. Mol Cell Proteomics. 2021;20:100077. doi: 10.1016/j.mcpro.2021.100077. Epub 2021 Apr 2. Mol Cell Proteomics. 2021. PMID: 33813065 Free PMC article.

8

Multiattribute Glycan Identification and FDR Control for Glycoproteomics.

Polasky DA, Geiszler DJ, Yu F, Nesvizhskii AI. Polasky DA, et al. Among authors: yu f. Mol Cell Proteomics. 2022 Mar;21(3):100205. doi: 10.1016/j.mcpro.2022.100205. Epub 2022 Jan 26. Mol Cell Proteomics. 2022. PMID: 35091091 Free PMC article.

9

SP3-Enabled Rapid and High Coverage Chemoproteomic Identification of Cell-State-Dependent Redox-Sensitive Cysteines.

Desai HS, Yan T, Yu F, Sun AW, Villanueva M, Nesvizhskii AI, Backus KM. Desai HS, et al. Among authors: yu f. Mol Cell Proteomics. 2022 Apr;21(4):100218. doi: 10.1016/j.mcpro.2022.100218. Epub 2022 Feb 25. Mol Cell Proteomics. 2022. PMID: 35219905 Free PMC article.

10

dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts.

Demichev V, Szyrwiel L, Yu F, Teo GC, Rosenberger G, Niewienda A, Ludwig D, Decker J, Kaspar-Schoenefeld S, Lilley KS, Mülleder M, Nesvizhskii AI, Ralser M. Demichev V, et al. Among authors: yu f. Nat Commun. 2022 Jul 8;13(1):3944. doi: 10.1038/s41467-022-31492-0. Nat Commun. 2022. PMID: 35803928 Free PMC article.

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