Genentech: Susan Klaeger | Principal Scientist Discovery Proteomics, Proteomic and Genomic Technologies, Joint Appointment with Discovery Oncology, Research Biology

Scientists / Our Scientists

"Genentech’s research environment empowers experts from diverse fields to collaborate effectively, translating their work into scientific innovations and discoveries that benefit patients."

Years at Genentech

Awards & Honors

I joined Genentech in early 2022 as a Principal Scientist in the Proteomic and Genomics Technologies department. My group studies proteins and peptides on the surface of cells using innovative proteomics methodologies. We collaborate across departments in research biology, drug discovery and computational sciences.

Prior to joining Genentech, I trained in Molecular Biotechnology and Proteomics. During my PhD at the Technical University of Munich and the German Cancer Consortium, I applied chemoproteomics approaches to study selectivity of clinical kinase inhibitors. Motivated by the possible translational impact of my research, I joined the Proteomics Platform at the Broad Institute, where I used mass spectrometry-based proteomics to understand antigen processing and presentation on MHC molecules in tumor samples. This research contributed to better MHC binding predictors, discovery of novel peptides from non canonical open reading frames and improvement of technology to detect low abundant, clinically relevant peptides presented on MHC.

Featured Publication

diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens.

Mol Cell Proteomics . 2025

Oliinyk D, Gurung HR, Zhou Z, Leskoske K, Rose CM, Klaeger S.

View Abstract

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer .

Nat Biotechnol . 2022

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A.

View Abstract

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

Cell. 2021

Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Gallagher KME, Bauer MR, Taylor HB, Dunn WA, Tarr C, Sidney J, Rachimi S, Conway HL, Katsis K, Wang Y, Leistritz-Edwards D, Durkin MR, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Carulli IP, Chea VA, Chandrashekar A, Bozkus CC, Carrington M; MGH COVID-19 Collection & Processing Team; Bhardwaj N, Barouch DH, Sette A, Maus MV, Rice CM, Clauser KR, Keskin DB, Pregibon DC, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC

View Abstract

A large peptidome dataset improves HLA class I epitope prediction across most of the human population .

Nat Biotechnol . 2020

Sarkizova S, Klaeger S, Le PM, Li LW, Oliveira G, Keshishian H, Hartigan CR, Zhang W, Braun DA, Ligon KL, Bachireddy P, Zervantonakis IK, Rosenbluth JM, Ouspenskaia T, Law T, Justesen S, Stevens J, Lane WJ, Eisenhaure T, Lan Zhang G, Clauser KR, Hacohen N, Carr SA, Wu CJ, Keskin DB.

View Abstract

The target landscape of clinical kinase drugs .

Science . 2017

Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B.

View Abstract

My group focuses on identifying and quantifying proteins and peptides on the surface of cells. We develop and use innovative proteomics methods to understand the immunopeptidome and its changes in disease with a focus on oncology. Furthermore, we employ innovative discovery proteomics methods to study protein expression in cancer. We collaborate with Research Biology, Drug Discovery and Computational Sciences groups to discover and characterize possible targets.

Technical University of Munich, PhD. Molecular Biotechnology – 2017
Technical University of Munich, M.Sc. Molecular Biotechnology – 2012
Technical University of Munich, B.Sc. Molecular Biotechnology – 2010

GWP Emerging Leader – 2025
MCP contributions to proteomics – 2022
Broad Ignite Award – 2019
CRI Irvington Postdoctoral Fellowship – 2018
Walter and Christine Richtzenhain Foundation prize – 2017

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Susan Klaeger

Principal Scientist Discovery Proteomics, Proteomic and Genomic Technologies, Joint Appointment with Discovery Oncology, Research Biology

Featured Publication

diaPASEF Analysis for HLA-I Peptides Enables Quantification of Common Cancer Neoantigens.

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer .

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

A large peptidome dataset improves HLA class I epitope prediction across most of the human population .

The target landscape of clinical kinase drugs .