Yansheng Liu, PhD

• Craig M Crews
• Don Nguyen
• Jason Sheltzer
• John Wysolmerski
• Qin Yan

Mass Spectrometry; Proteomics; Big Data

• An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cellsZhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk B, Sessa W, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nature Communications 2023, 14: 3803. PMID: 37365174, PMCID: PMC10293293, DOI: 10.1038/s41467-023-39514-1.
• Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunitiesSalovska B, Gao E, Müller‐Dott S, Li W, Cordon C, Wang S, Dugourd A, Rosenberger G, Saez‐Rodriguez J, Liu Y. Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities. Clinical And Translational Medicine 2023, 13: e1179. PMID: 36781298, PMCID: PMC9925373, DOI: 10.1002/ctm2.1179.
• Proteotype coevolution and quantitative diversity across 11 mammalian speciesBa Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.
• Global and Site-Specific Effect of Phosphorylation on Protein TurnoverWu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Developmental Cell 2020, 56: 111-124.e6. PMID: 33238149, PMCID: PMC7855865, DOI: 10.1016/j.devcel.2020.10.025.
• Oncogene-like addiction to aneuploidy in human cancersGirish V, Lakhani A, Thompson S, Scaduto C, Brown L, Hagenson R, Sausville E, Mendelson B, Kandikuppa P, Lukow D, Yuan M, Stevens E, Lee S, Schukken K, Akalu S, Vasudevan A, Zou C, Salovska B, Li W, Smith J, Taylor A, Martienssen R, Liu Y, Sun R, Sheltzer J. Oncogene-like addiction to aneuploidy in human cancers. Science 2023, 381: eadg4521. PMID: 37410869, PMCID: PMC10753973, DOI: 10.1126/science.adg4521.
• Multi-omic measurements of heterogeneity in HeLa cells across laboratoriesLiu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology 2019, 37: 314-322. PMID: 30778230, DOI: 10.1038/s41587-019-0037-y.
• Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies.Liu Q, Zhang J, Guo C, Wang M, Wang C, Yan Y, Sun L, Wang D, Zhang L, Yu H, Hou L, Wu C, Zhu Y, Jiang G, Zhu H, Zhou Y, Fang S, Zhang T, Hu L, Li J, Liu Y, Zhang H, Zhang B, Ding L, Robles AI, Rodriguez H, Gao D, Ji H, Zhou H, Zhang P. Proteogenomic characterization of small cell lung cancer identifies biological insights and subtype-specific therapeutic strategies. Cell 2024, 187: 184-203.e28. PMID: 38181741, DOI: 10.1016/j.cell.2023.12.004.
• Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis.Rosenberger G, Li W, Turunen M, He J, Subramaniam PS, Pampou S, Griffin AT, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nat Commun 2024, 15: 3909. PMID: 38724493, DOI: 10.1038/s41467-024-47957-3.
• Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury.Gui Y, Fu H, Palanza Z, Tao J, Lin YH, Min W, Qiao Y, Bonin C, Hargis G, Wang Y, Yang P, Kreutzer DL, Wang Y, Liu Y, Yu Y, Liu Y, Zhou D. Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury. J Clin Invest 2024 PMID: 38713523, DOI: 10.1172/JCI165836.
• Reciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry.Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry. Nat Commun 2024, 15: 3220. PMID: 38622115, DOI: 10.1038/s41467-024-47427-w.
• Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitisLuan Y, Hu J, Wang Q, Wang X, Li W, Qu R, Yang C, Rajendran B, Zhou H, Liu P, Zhang N, Shi Y, Liu Y, Tang W, Lu J, Wu D. Wnt5 controls splenic myelopoiesis and neutrophil functional ambivalency during DSS-induced colitis. Cell Reports 2024, 43: 113934. PMID: 38461416, DOI: 10.1016/j.celrep.2024.113934.
• Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference-Advancing Biological and Pharmaceutical Mass Spectrometry.Chen H, Fu Y, Han M, Han X, Hao L, Huan T, Huang L, Huang M, Ji Q, Jiang T, Jiang Y, Li L, Li L, Liang X, Lih M, Lin Y, Liu X, Liu T, Liu Y, Ma S, Peng J, Qi YA, Qu J, Shou W, Sun L, Wang M, Wang S, Wu R, Wu S, Yan X, Yang J, Yang W, Yang Z, Yu Y, Zhang H, Zhang H, Zhao S, Zhu J, Zhu Y, Wang Y, Weng N. Meeting Report on the 3rd Chinese American Society for Mass Spectrometry Conference-Advancing Biological and Pharmaceutical Mass Spectrometry. Biomed Chromatogr 2024, 38: e5795. PMID: 38071756, DOI: 10.1002/bmc.5795.
• The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cellsLiao X, Li W, Zhou H, Rajendran B, Li A, Ren J, Luan Y, Calderwood D, Turk B, Tang W, Liu Y, Wu D. The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells. Nature Communications 2024, 15: 603. PMID: 38242867, PMCID: PMC10798966, DOI: 10.1038/s41467-024-44885-0.
• The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomicsHuang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.
• Calponin 2 regulates ketogenesis to mitigate acute kidney injuryGui Y, Palanza Z, Gupta P, Li H, Pan Y, Wang Y, Hargis G, Kreutzer D, Wang Y, Bastacky S, Liu Y, Liu S, Zhou D. Calponin 2 regulates ketogenesis to mitigate acute kidney injury. JCI Insight 2023, 8: e170521. PMID: 37751293, PMCID: PMC10721266, DOI: 10.1172/jci.insight.170521.
• A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline.Reilly L, Lara E, Ramos D, Li Z, Pantazis CB, Stadler J, Santiana M, Roberts J, Faghri F, Hao Y, Nalls MA, Narayan P, Liu Y, Singleton AB, Cookson MR, Ward ME, Qi YA. A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline. Cell Rep Methods 2023, 100593. PMID: 37729920, DOI: 10.1016/j.crmeth.2023.100593.
• 7SK methylation by METTL3 promotes transcriptional activityPerez-Pepe M, Desotell A, Li H, Li W, Han B, Lin Q, Klein D, Liu Y, Goodarzi H, Alarcón C. 7SK methylation by METTL3 promotes transcriptional activity. Science Advances 2023, 9: eade7500. PMID: 37163588, PMCID: PMC10171809, DOI: 10.1126/sciadv.ade7500.
• Meeting Report on the 2(nd) Chinese American Society for Mass Spectrometry (CASMS) Conference Advancing Biological and Pharmaceutical Mass Spectrometry.Chen Y, Ge Y, Han X, Hao L, Huan T, Li L, Li L, Li W, Liang X, Lin Y, Liu X, Liu Y, Ma S, Peng J, Shou W, Sun L, Tao WA, Tian Y, Wang YK, Wang Y, Wu R, Wu S, Xia J, Yang Z, Zhang H, Zhang H, Zhao S, Weng N, Huang L. Meeting Report on the 2(nd) Chinese American Society for Mass Spectrometry (CASMS) Conference Advancing Biological and Pharmaceutical Mass Spectrometry. Mol Cell Proteomics 2023, 100559. PMID: 37105363, DOI: 10.1016/j.mcpro.2023.100559.
• Post‐translational modification and phenotypeSalovska B, Liu Y. Post‐translational modification and phenotype. Proteomics 2023, 23: e2200535. PMID: 36799530, DOI: 10.1002/pmic.202200535.
• Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic ModalityHu Z, Chen P, Li W, Douglas T, Hines J, Liu Y, Crews C. Targeted Dephosphorylation of Tau by Phosphorylation Targeting Chimeras (PhosTACs) as a Therapeutic Modality. Journal Of The American Chemical Society 2023, 145: 4045-4055. PMID: 36753634, DOI: 10.1021/jacs.2c11706.
• A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biologyDi Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.
• Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnoverLi W, Salovska B, Fornasiero E, Liu Y. Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics 2022, 23: e2100387. PMID: 36422574, PMCID: PMC10964180, DOI: 10.1002/pmic.202100387.
• Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulationCai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. ELife 2022, 11: e78163. PMID: 36043466, PMCID: PMC9584608, DOI: 10.7554/elife.78163.
• Evolution of higher mesenchymal CD44 expression in the human lineageMa X, Dighe A, Maziarz J, Neumann E, Erkenbrack E, Hei YY, Liu Y, Suhail Y, Kshitiz, Pak I, Levchenko A, Wagner GP. Evolution of higher mesenchymal CD44 expression in the human lineage. Evolution Medicine And Public Health 2022, 10: 447-462. PMID: 36148042, PMCID: PMC9487634, DOI: 10.1093/emph/eoac036.
• A peptidoform based proteomic strategy for studying functions of post‐translational modificationsLiu Y. A peptidoform based proteomic strategy for studying functions of post‐translational modifications. Proteomics 2021, 22: e2100316. PMID: 34878717, PMCID: PMC8959388, DOI: 10.1002/pmic.202100316.
• MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cellsJeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.
• Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic AnalysisYu C, Wang X, Li W, Liu Y, Huang L. Developing a Bimolecular Affinity Purification Strategy to Isolate 26S Proteasome Holocomplexes for Complex-Centric Proteomic Analysis. Analytical Chemistry 2021, 93: 13407-13413. PMID: 34550675, PMCID: PMC8999942, DOI: 10.1021/acs.analchem.1c03551.
• Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypesGao E, Li W, Wu C, Shao W, Di Y, Liu Y. Data-independent acquisition-based proteome and phosphoproteome profiling across six melanoma cell lines reveals determinants of proteotypes. Molecular Omics 2021, 17: 413-425. PMID: 33728422, PMCID: PMC8205956, DOI: 10.1039/d0mo00188k.
• Identification and Characterization of Epigenetic Regulators of Breast Cancer Metastasis to the BrainChen J, Cai W, Chen H, Wingrove E, Li W, Liu Y, Westbrook T, Nguyen D, Yan Q. Identification and Characterization of Epigenetic Regulators of Breast Cancer Metastasis to the Brain. The FASEB Journal 2021, 35 DOI: 10.1096/fasebj.2021.35.s1.03094.
• A PKD-MFF signaling axis couples mitochondrial fission to mitotic progressionPangou E, Bielska O, Guerber L, Schmucker S, Agote-Arán A, Ye T, Liao Y, Puig-Gamez M, Grandgirard E, Kleiss C, Liu Y, Compe E, Zhang Z, Aebersold R, Ricci R, Sumara I. A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression. Cell Reports 2021, 35: 109129. PMID: 34010649, DOI: 10.1016/j.celrep.2021.109129.
• BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex SamplesSalovska B, Li W, Di Y, Liu Y. BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. Analytical Chemistry 2021, 93: 3103-3111. PMID: 33533601, PMCID: PMC8959401, DOI: 10.1021/acs.analchem.0c04293.
• Cross-compartment signal propagation in the mitotic exit networkZhou X, Li W, Liu Y, Amon A. Cross-compartment signal propagation in the mitotic exit network. ELife 2021, 10: e63645. PMID: 33481703, PMCID: PMC7822594, DOI: 10.7554/elife.63645.
• SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS ProfilesRosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Systems 2020, 11: 589-607.e8. PMID: 33333029, PMCID: PMC8034988, DOI: 10.1016/j.cels.2020.11.006.
• FGF23 contains two distinct high-affinity binding sites enabling bivalent interactions with α-KlothoSuzuki Y, Kuzina E, An SJ, Tome F, Mohanty J, Li W, Lee S, Liu Y, Lax I, Schlessinger J. FGF23 contains two distinct high-affinity binding sites enabling bivalent interactions with α-Klotho. Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 31800-31807. PMID: 33257569, PMCID: PMC7749347, DOI: 10.1073/pnas.2018554117.
• Strategies to enable large-scale proteomics for reproducible research.Poulos RC, Hains PG, Shah R, Lucas N, Xavier D, Manda SS, Anees A, Koh JMS, Mahboob S, Wittman M, Williams SG, Sykes EK, Hecker M, Dausmann M, Wouters MA, Ashman K, Yang J, Wild PJ, deFazio A, Balleine RL, Tully B, Aebersold R, Speed TP, Liu Y, Reddel RR, Robinson PJ, Zhong Q. Strategies to enable large-scale proteomics for reproducible research. Nature Communications 2020, 11: 3793. PMID: 32732981, PMCID: PMC7393074, DOI: 10.1038/s41467-020-17641-3.
• NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analysesWang S, Li W, Hu L, Cheng J, Yang H, Liu Y. NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses. Nucleic Acids Research 2020, 48: gkaa498-. PMID: 32526036, PMCID: PMC7641313, DOI: 10.1093/nar/gkaa498.
• Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic InvestigationGao X, Li Q, Liu Y, Zeng R. Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation. Analytical Chemistry 2020, 92: 8943-8951. PMID: 32479063, DOI: 10.1021/acs.analchem.0c00906.
• Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments*Tsai TH, Choi M, Banfai B, Liu Y, MacLean B, Dunkley T, Vitek O. Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments*. Molecular & Cellular Proteomics 2020, 19: 944-959. PMID: 32234965, PMCID: PMC7261813, DOI: 10.1074/mcp.ra119.001792.
• Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradationSalovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: e9170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.
• Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypesHausmann A, Russo G, Grossmann J, Zünd M, Schwank G, Aebersold R, Liu Y, Sellin ME, Hardt W. Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes. Cellular Microbiology 2020, 22: e13191. PMID: 32068945, PMCID: PMC7317401, DOI: 10.1111/cmi.13191.
• A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MSHeusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R. A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Systems 2020, 10: 133-155.e6. PMID: 32027860, PMCID: PMC7042714, DOI: 10.1016/j.cels.2020.01.001.
• motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification MotifsWang S, Cai Y, Cheng J, Li W, Liu Y, Yang H. motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. Proteomics 2019, 19: e1900245. PMID: 31622013, DOI: 10.1002/pmic.201900245.
• Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass SpectrometryBouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Reports 2019, 28: 832-843.e7. PMID: 31315058, PMCID: PMC6656695, DOI: 10.1016/j.celrep.2019.06.046.
• Capillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top–down proteomicsMcCool EN, Chen D, Li W, Liu Y, Sun L. Capillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top–down proteomics. Analytical Methods 2019, 11: 2855-2861. PMID: 31608127, PMCID: PMC6788745, DOI: 10.1039/c9ay00585d.
• Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019, 19: e1800438. PMID: 30901150, DOI: 10.1002/pmic.201800438.
• Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins.Shao W, Guo T, Toussaint NC, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser CD, Poyet C, Ljubicic J, Rupp N, Rüschoff JH, Zhong Q, Beyer A, Ji J, Collins BC, Liu Y, Rätsch G, Wild PJ, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 2019, 10: 2524. PMID: 31175306, PMCID: PMC6555818, DOI: 10.1038/s41467-019-10513-5.
• Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent AcquisitionLi W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y. Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. Journal Of The American Society For Mass Spectrometry 2019, 30: 1396-1405. PMID: 31147889, DOI: 10.1007/s13361-019-02243-1.
• Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry.Yang B, Wu H, Schnier PD, Liu Y, Liu J, Wang N, DeGrado WF, Wang L. Proximity-enhanced SuFEx chemical cross-linker for specific and multitargeting cross-linking mass spectrometry. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: 11162-11167. PMID: 30322930, PMCID: PMC6217395, DOI: 10.1073/pnas.1813574115.
• Separation of blood microsamples by exploiting sedimentation at the microscaleForchelet D, Béguin S, Sajic T, Bararpour N, Pataky Z, Frias M, Grabherr S, Augsburger M, Liu Y, Charnley M, Déglon J, Aebersold R, Thomas A, Renaud P. Separation of blood microsamples by exploiting sedimentation at the microscale. Scientific Reports 2018, 8: 14101. PMID: 30237536, PMCID: PMC6147834, DOI: 10.1038/s41598-018-32314-4.
• Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancerEbhardt HA, Root A, Liu Y, Gauthier NP, Sander C, Aebersold R. Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. Npj Systems Biology And Applications 2018, 4: 26. PMID: 29977602, PMCID: PMC6026592, DOI: 10.1038/s41540-018-0064-1.
• Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MSSajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, Omlin A, Gillessen S, Claassen M, Aebersold R. Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell Reports 2018, 23: 2819-2831.e5. PMID: 29847809, DOI: 10.1016/j.celrep.2018.04.114.
• Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cellsLiu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications 2017, 8: 1212. PMID: 29089484, PMCID: PMC5663699, DOI: 10.1038/s41467-017-01422-6.
• Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analysesRosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods 2017, 14: 921-927. PMID: 28825704, PMCID: PMC5581544, DOI: 10.1038/nmeth.4398.
• Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometryCollins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications 2017, 8: 291. PMID: 28827567, PMCID: PMC5566333, DOI: 10.1038/s41467-017-00249-5.
• Impact of Alternative Splicing on the Human ProteomeLiu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports 2017, 20: 1229-1241. PMID: 28768205, PMCID: PMC5554779, DOI: 10.1016/j.celrep.2017.07.025.
• Protein kinase D at the Golgi controls NLRP3 inflammasome activationZhang Z, Meszaros G, He WT, Xu Y, de Fatima Magliarelli H, Mailly L, Mihlan M, Liu Y, Gámez M, Goginashvili A, Pasquier A, Bielska O, Neven B, Quartier P, Aebersold R, Baumert TF, Georgel P, Han J, Ricci R. Protein kinase D at the Golgi controls NLRP3 inflammasome activation. Journal Of Experimental Medicine 2017, 214: 2671-2693. PMID: 28716882, PMCID: PMC5584123, DOI: 10.1084/jem.20162040.
• Inference and quantification of peptidoforms in large sample cohorts by SWATH-MSRosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology 2017, 35: 781-788. PMID: 28604659, PMCID: PMC5593115, DOI: 10.1038/nbt.3908.
• A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome InstabilityTan SLW, Chadha S, Liu Y, Gabasova E, Perera D, Ahmed K, Constantinou S, Renaudin X, Lee M, Aebersold R, Venkitaraman AR. A Class of Environmental and Endogenous Toxins Induces BRCA2 Haploinsufficiency and Genome Instability. Cell 2017, 169: 1105-1118.e15. PMID: 28575672, PMCID: PMC5457488, DOI: 10.1016/j.cell.2017.05.010.
• Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissuesFaktor J, Sucha R, Paralova V, Liu Y, Bouchal P. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics 2017, 17 PMID: 27966270, DOI: 10.1002/pmic.201600323.
• Shotgun and Targeted Plasma Proteomics to Predict Prognosis of Non-Small Cell Lung Cancer.Li QR, Liu YS, Zeng R. Shotgun and Targeted Plasma Proteomics to Predict Prognosis of Non-Small Cell Lung Cancer. Methods In Molecular Biology (Clifton, N.J.) 2017, 1619: 385-394. PMID: 28674898, DOI: 10.1007/978-1-4939-7057-5_26.
• Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal CellsYu C, Gao J, Zhou Y, Chen X, Xiao R, Zheng J, Liu Y, Zhou H. Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells. Frontiers In Physiology 2016, 7: 635. PMID: 28066266, PMCID: PMC5179568, DOI: 10.3389/fphys.2016.00635.
• TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomicsRöst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods 2016, 13: 777-783. PMID: 27479329, PMCID: PMC5008461, DOI: 10.1038/nmeth.3954.
• Image-based computational quantification and visualization of genetic alterations and tumour heterogeneityZhong Q, Rüschoff JH, Guo T, Gabrani M, Schüffler PJ, Rechsteiner M, Liu Y, Fuchs TJ, Rupp NJ, Fankhauser C, Buhmann JM, Perner S, Poyet C, Blattner M, Soldini D, Moch H, Rubin MA, Noske A, Rüschoff J, Haffner MC, Jochum W, Wild PJ. Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity. Scientific Reports 2016, 6: 24146. PMID: 27052161, PMCID: PMC4823793, DOI: 10.1038/srep24146.
• On the Dependency of Cellular Protein Levels on mRNA AbundanceLiu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016, 165: 535-550. PMID: 27104977, DOI: 10.1016/j.cell.2016.03.014.
• The interdependence of transcript and protein abundance: new data–new complexitiesLiu Y, Aebersold R. The interdependence of transcript and protein abundance: new data–new complexities. Molecular Systems Biology 2016, 12: 856. PMID: 26792872, PMCID: PMC4731012, DOI: 10.15252/msb.20156720.
• Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N‑Linked Glycosite-Containing Peptides in SerumThomas SN, Harlan R, Chen J, Aiyetan P, Liu Y, Sokoll LJ, Aebersold R, Chan DW, Zhang H. Multiplexed Targeted Mass Spectrometry-Based Assays for the Quantification of N‑Linked Glycosite-Containing Peptides in Serum. Analytical Chemistry 2015, 87: 10830-10838. PMID: 26451657, PMCID: PMC4708883, DOI: 10.1021/acs.analchem.5b02063.
• Prediction of colorectal cancer diagnosis based on circulating plasma proteinsSurinova S, Choi M, Tao S, Schüffler PJ, Chang CY, Clough T, Vysloužil K, Khoylou M, Srovnal J, Liu Y, Matondo M, Hüttenhain R, Weisser H, Buhmann JM, Hajdúch M, Brenner H, Vitek O, Aebersold R. Prediction of colorectal cancer diagnosis based on circulating plasma proteins. EMBO Molecular Medicine 2015, 7: 1166-1178. PMID: 26253081, PMCID: PMC4568950, DOI: 10.15252/emmm.201404873.
• Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applicationsSajic T, Liu Y, Aebersold R. Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications. Proteomics Clinical Applications 2015, 9: 307-321. PMID: 25504613, DOI: 10.1002/prca.201400117.
• Quantitative variability of 342 plasma proteins in a human twin populationLiu Y, Buil A, Collins BC, Gillet L, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology 2015, 11: 786. PMID: 25652787, PMCID: PMC4358658, DOI: 10.15252/msb.20145728.
• Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisitionCheng L, Liu Y, Chang C, Röst H, Aebersold R, Vitek O. Statistical elimination of spectral features with large between-run variation enhances quantitative protein-level conclusions in experiments with data-independent spectral acquisition. BMC Bioinformatics 2015, 16: a4. PMCID: PMC4331794, DOI: 10.1186/1471-2105-16-s2-a4.
• A repository of assays to quantify 10,000 human proteins by SWATH-MSRosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 2014, 1: 140031. PMID: 25977788, PMCID: PMC4322573, DOI: 10.1038/sdata.2014.31.
• Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*Liu Y, Chen J, Sethi A, Li QK, Chen L, Collins B, Gillet LC, Wollscheid B, Zhang H, Aebersold R. Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness*. Molecular & Cellular Proteomics 2014, 13: 1753-1768. PMID: 24741114, PMCID: PMC4083113, DOI: 10.1074/mcp.m114.038273.
• Mass spectrometric protein maps for biomarker discovery and clinical researchLiu Y, Hüttenhain R, Collins B, Aebersold R. Mass spectrometric protein maps for biomarker discovery and clinical research. Expert Review Of Molecular Diagnostics 2013, 13: 811-825. PMID: 24138574, PMCID: PMC3833812, DOI: 10.1586/14737159.2013.845089.
• Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MSLiu Y, Hüttenhain R, Surinova S, Gillet L, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS. Proteomics 2013, 13: 1247-1256. PMID: 23322582, DOI: 10.1002/pmic.201200417.
• Integrative Proteomics and Tissue Microarray Profiling Indicate the Association between Overexpressed Serum Proteins and Non-Small Cell Lung CancerLiu Y, Luo X, Hu H, Wang R, Sun Y, Zeng R, Chen H. Integrative Proteomics and Tissue Microarray Profiling Indicate the Association between Overexpressed Serum Proteins and Non-Small Cell Lung Cancer. PLOS ONE 2012, 7: e51748. PMID: 23284758, PMCID: PMC3526638, DOI: 10.1371/journal.pone.0051748.
• Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer.Liu YS, Luo XY, Li QR, Li H, Li C, Ni H, Li RX, Wang R, Hu HC, Pan YJ, Chen HQ, Zeng R. Shotgun and targeted proteomics reveal that pre-surgery serum levels of LRG1, SAA, and C4BP may refine prognosis of resected squamous cell lung cancer. Journal Of Molecular Cell Biology 2012, 4: 344-7. PMID: 23042802, DOI: 10.1093/jmcb/mjs050.
• Quantitative proteomics reveal up-regulated protein expression of the SET complex associated with hepatocellular carcinoma.Li C, Ruan HQ, Liu YS, Xu MJ, Dai J, Sheng QH, Tan YX, Yao ZZ, Wang HY, Wu JR, Zeng R. Quantitative proteomics reveal up-regulated protein expression of the SET complex associated with hepatocellular carcinoma. Journal Of Proteome Research 2012, 11: 871-85. PMID: 22082227, DOI: 10.1021/pr2006999.
• A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancerLuo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. Journal Of Proteomics 2011, 74: 528-538. PMID: 21262398, DOI: 10.1016/j.jprot.2011.01.011.
• Proteomic mining in the dysplastic liver of WHV/c‐myc mice – insights and indicators for early hepatocarcinogenesisLiu Y, Li C, Xing Z, Yuan X, Wu Y, Xu M, Tu K, Li Q, Wu C, Zhao M, Zeng R. Proteomic mining in the dysplastic liver of WHV/c‐myc mice – insights and indicators for early hepatocarcinogenesis. The FEBS Journal 2010, 277: 4039-4053. PMID: 20807235, DOI: 10.1111/j.1742-4658.2010.07795.x.
• Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing.Li Y, Chi H, Wang LH, Wang HP, Fu Y, Yuan ZF, Li SJ, Liu YS, Sun RX, Zeng R, He SM. Speeding up tandem mass spectrometry based database searching by peptide and spectrum indexing. Rapid Communications In Mass Spectrometry : RCM 2010, 24: 807-14. PMID: 20187083, DOI: 10.1002/rcm.4448.