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Proteomics Platform

Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples.

Klaeger S, Apffel A, Clauser KR, et al. Optimized liquid and gas phase fractionation increases HLA-peptidome coverage for primary cell and tissue samples. Mol Cell Proteomics. 2021:100133. doi:10.1016/j.mcpro.2021.100133

Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma.

Oliveira G, Stromhaug K, Klaeger S, et al. Phenotype, specificity and avidity of antitumour CD8 T cells in melanoma. Nature. 2021;596(7870):119-125. doi:10.1038/s41586-021-03704-y

Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling.

Whiteaker JR, Sharma K, Hoffman MA, et al. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods. 2021;1(3). doi:10.1016/j.crmeth.2021.100015

Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs.

Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. Profiling SARS-CoV-2 HLA-I peptidome reveals T cell epitopes from out-of-frame ORFs. Cell. 2021;184(15):3962-3980.e17. doi:10.1016/j.cell.2021.05.046

Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase.

Garvie CW, Wu X, Papanastasiou M, et al. Structure of PDE3A-SLFN12 complex reveals requirements for activation of SLFN12 RNase. Nat Commun. 2021;12(1):4375. doi:10.1038/s41467-021-24495-w

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma.

Adane B, Alexe G, Seong BKA, et al. STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma. Cancer Cell. 2021;39(6):827-844.e10. doi:10.1016/j.ccell.2021.05.007

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics.

Wilhelm M, Zolg DP, Graber M, et al. Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics. Nat Commun. 2021;12(1):3346. doi:10.1038/s41467-021-23713-9

Identification of a Novel Regulator of Clostridioides difficile Cortex Formation.

Touchette MH, de la Puebla HB, Feliciano CA, et al. Identification of a Novel Regulator of Clostridioides difficile Cortex Formation. mSphere. 2021:e0021121. doi:10.1128/mSphere.00211-21

Human plasma proteomic profiles indicative of cardiorespiratory fitness.

Robbins JM, Peterson B, Schranner D, et al. Human plasma proteomic profiles indicative of cardiorespiratory fitness. Nat Metab. 2021. doi:10.1038/s42255-021-00400-z

PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis.

Mani DR, Maynard M, Kothadia R, et al. PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis. Nat Methods. 2021. doi:10.1038/s41592-021-01176-6