MS-Based HLA-II Peptidomics Combined With Multiomics Will Aid the Development of Future Immunotherapies

por Taylor, Hannah B., Klaeger, Susan, Clauser, Karl R., Sarkizova, Siranush, Weingarten-Gabbay, Shira, Graham, Daniel B., Carr, Steven A., Abelin, Jennifer G.
Publicado 2021

Sensitive, High-Throughput HLA-I and HLA-II Immunopeptidomics Using Parallel Accumulation-Serial Fragmentation Mass Spectrometry

por Phulphagar, Kshiti Meera, Ctortecka, Claudia, Jacome, Alvaro Sebastian Vaca, Klaeger, Susan, Verzani, Eva K., Hernandez, Gabrielle M., Udeshi, Namrata D., Clauser, Karl R., Abelin, Jennifer G., Carr, Steven A.
Publicado 2023

HLA-I immunopeptidome profiling of human cells infected with high-containment enveloped viruses

por Weingarten-Gabbay, Shira, Pearlman, Leah R., Chen, Da-Yuan, Klaeger, Susan, Taylor, Hannah B., Welch, Nicole L., Keskin, Derin B., Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, Sabeti, Pardis C.
Publicado 2022

The OTUD6B‐LIN28B‐MYC axis determines the proliferative state in multiple myeloma

por Paulmann, Carmen, Spallek, Ria, Karpiuk, Oleksandra, Heider, Michael, Schäffer, Isabell, Zecha, Jana, Klaeger, Susan, Walzik, Michaela, Öllinger, Rupert, Engleitner, Thomas, Wirth, Matthias, Keller, Ulrich, Krönke, Jan, Rudelius, Martina, Kossatz, Susanne, Rad, Roland, Kuster, Bernhard, Bassermann, Florian
Publicado 2022

Integrated Immunopeptidomic and Proteomic Analysis of COVID-19 lung biopsies

por Yin, Shanye, Klaeger, Susan, Chea, Vipheaviny A., Carulli, Isabel P., Rachimi, Suzanna, Black, Katharine E., Filbin, Michael, Hariri, Lida P., Knipe, Rachel S., Padera, Robert F., Stevens, Jonathan D., Lane, William J., Carr, Steven A., Wu, Catherine J., Kim, Edy Yong, Keskin, Derin B.
Publicado 2023

Pharmacoproteomic characterisation of human colon and rectal cancer

por Frejno, Martin, Zenezini Chiozzi, Riccardo, Wilhelm, Mathias, Koch, Heiner, Zheng, Runsheng, Klaeger, Susan, Ruprecht, Benjamin, Meng, Chen, Kramer, Karl, Jarzab, Anna, Heinzlmeir, Stephanie, Johnstone, Elaine, Domingo, Enric, Kerr, David, Jesinghaus, Moritz, Slotta‐Huspenina, Julia, Weichert, Wilko, Knapp, Stefan, Feller, Stephan M, Kuster, Bernhard
Publicado 2017

Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples

por Klaeger, Susan, Apffel, Annie, Clauser, Karl R., Sarkizova, Siranush, Oliveira, Giacomo, Rachimi, Suzanna, Le, Phuong M., Tarren, Anna, Chea, Vipheaviny, Abelin, Jennifer G., Braun, David A., Ott, Patrick A., Keshishian, Hasmik, Hacohen, Nir, Keskin, Derin B., Wu, Catherine J., Carr, Steven A.
Publicado 2021

Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

por Wilhelm, Mathias, Zolg, Daniel P., Graber, Michael, Gessulat, Siegfried, Schmidt, Tobias, Schnatbaum, Karsten, Schwencke-Westphal, Celina, Seifert, Philipp, de Andrade Krätzig, Niklas, Zerweck, Johannes, Knaute, Tobias, Bräunlein, Eva, Samaras, Patroklos, Lautenbacher, Ludwig, Klaeger, Susan, Wenschuh, Holger, Rad, Roland, Delanghe, Bernard, Huhmer, Andreas, Carr, Steven A., Clauser, Karl R., Krackhardt, Angela M., Reimer, Ulf, Kuster, Bernhard
Publicado 2021

Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

por Wilhelm, Mathias, Zolg, Daniel P., Graber, Michael, Gessulat, Siegfried, Schmidt, Tobias, Schnatbaum, Karsten, Schwencke-Westphal, Celina, Seifert, Philipp, de Andrade Krätzig, Niklas, Zerweck, Johannes, Knaute, Tobias, Bräunlein, Eva, Samaras, Patroklos, Lautenbacher, Ludwig, Klaeger, Susan, Wenschuh, Holger, Rad, Roland, Delanghe, Bernard, Huhmer, Andreas, Carr, Steven A., Clauser, Karl R., Krackhardt, Angela M., Reimer, Ulf, Kuster, Bernhard
Publicado 2021

Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues

por Abelin, Jennifer G., Bergstrom, Erik J., Rivera, Keith D., Taylor, Hannah B., Klaeger, Susan, Xu, Charles, Verzani, Eva K., Jackson White, C., Woldemichael, Hilina B., Virshup, Maya, Olive, Meagan E., Maynard, Myranda, Vartany, Stephanie A., Allen, Joseph D., Phulphagar, Kshiti, Harry Kane, M., Rachimi, Suzanna, Mani, D. R., Gillette, Michael A., Satpathy, Shankha, Clauser, Karl R., Udeshi, Namrata D., Carr, Steven A.
Publicado 2023

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

por Sarkizova, Siranush, Klaeger, Susan, Le, Phuong M., Li, Letitia W., Oliveira, Giacomo, Keshishian, Hasmik, Hartigan, Christina R., Zhang, Wandi, Braun, David A., Ligon, Keith L., Bachireddy, Pavan, Zervantonakis, Ioannis K., Rosenbluth, Jennifer M., Ouspenskaia, Tamara, Law, Travis, Justesen, Sune, Stevens, Jonathan, Lane, William J., Eisenhaure, Thomas, Zhang, Guang Lan, Clauser, Karl R., Hacohen, Nir, Carr, Steven A., Wu, Catherine J., Keskin, Derin B.
Publicado 2019

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

por Weingarten-Gabbay, Shira, Klaeger, Susan, Sarkizova, Siranush, Pearlman, Leah R., Chen, Da-Yuan, Gallagher, Kathleen M.E., Bauer, Matthew R., Taylor, Hannah B., Dunn, W. Augustine, Tarr, Christina, Sidney, John, Rachimi, Suzanna, Conway, Hasahn L., Katsis, Katelin, Wang, Yuntong, Leistritz-Edwards, Del, Durkin, Melissa R., Tomkins-Tinch, Christopher H., Finkel, Yaara, Nachshon, Aharon, Gentili, Matteo, Rivera, Keith D., Carulli, Isabel P., Chea, Vipheaviny A., Chandrashekar, Abishek, Bozkus, Cansu Cimen, Carrington, Mary, Bhardwaj, Nina, Barouch, Dan H., Sette, Alessandro, Maus, Marcela V., Rice, Charles M., Clauser, Karl R., Keskin, Derin B., Pregibon, Daniel C., Hacohen, Nir, Carr, Steven A., Abelin, Jennifer G., Saeed, Mohsan, Sabeti, Pardis C.
Publicado 2021

Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma

por Lee, Patrick C., Klaeger, Susan, Le, Phuong M., Korthauer, Keegan, Cheng, Jingwei, Ananthapadmanabhan, Varsha, Frost, Thomas C., Stevens, Jonathan D., Wong, Alan Y.L., Iorgulescu, J. Bryan, Tarren, Anna Y., Chea, Vipheaviny A., Carulli, Isabel P., Lemvigh, Camilla K., Pedersen, Christina B., Gartin, Ashley K., Sarkizova, Siranush, Wright, Kyle T., Li, Letitia W., Nomburg, Jason, Li, Shuqiang, Huang, Teddy, Liu, Xiaoxi, Pomerance, Lucas, Doherty, Laura M., Apffel, Annie M., Wallace, Luke J., Rachimi, Suzanna, Felt, Kristen D., Wolff, Jacquelyn O., Witten, Elizabeth, Zhang, Wandi, Neuberg, Donna, Lane, William J., Zhang, Guanglan, Olsen, Lars R., Thakuria, Manisha, Rodig, Scott J., Clauser, Karl R., Starrett, Gabriel J., Doench, John G., Buhrlage, Sara J., Carr, Steven A., DeCaprio, James A., Wu, Catherine J., Keskin, Derin B.
Publicado 2022