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SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.

bioRxiv : the preprint server for biology

Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
PMID: 33024965
bioRxiv. 2020 Oct 26; doi: 10.1101/2020.10.02.324145.

T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class...

Cite
Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv. 2020;doi: 10.1101/2020.10.02.324145.
Weingarten-Gabbay, S., Klaeger, S., Sarkizova, S., Pearlman, L. R., Chen, D. Y., Bauer, M. R., Taylor, H. B., Conway, H. L., Tomkins-Tinch, C. H., Finkel, Y., Nachshon, A., Gentili, M., Rivera, K. D., Keskin, D. B., Rice, C. M., Clauser, K. R., Hacohen, N., Carr, S. A., Abelin, J. G., Saeed, M., & Sabeti, P. C. (2020). SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.10.02.324145
Weingarten-Gabbay, Shira, et al. "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.10.02.324145
Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv. 2020 Oct 26; doi: 10.1101/2020.10.02.324145. PMID: 33024965; PMCID: PMC7536868.
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Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cell

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H.
PMID: 34534465
Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal...

Cite
Cao L, Huang C, Cui Zhou D, et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184(19):5031-5052.e26doi: 10.1016/j.cell.2021.08.023.
Cao, L., Huang, C., Cui Zhou, D., Hu, Y., Lih, T. M., Savage, S. R., Krug, K., Clark, D. J., Schnaubelt, M., Chen, L., da Veiga Leprevost, F., Eguez, R. V., Yang, W., Pan, J., Wen, B., Dou, Y., Jiang, W., Liao, Y., Shi, Z., Terekhanova, N. V., Cao, S., Lu, R. J., Li, Y., Liu, R., Zhu, H., Ronning, P., Wu, Y., Wyczalkowski, M. A., Easwaran, H., Danilova, L., Mer, A. S., Yoo, S., Wang, J. M., Liu, W., Haibe-Kains, B., Thiagarajan, M., Jewell, S. D., Hostetter, G., Newton, C. J., Li, Q. K., Roehrl, M. H., Fenyö, D., Wang, P., Nesvizhskii, A. I., Mani, D. R., Omenn, G. S., Boja, E. S., Mesri, M., Robles, A. I., Rodriguez, H., Bathe, O. F., Chan, D. W., Hruban, R. H., Ding, L., Zhang, B., Zhang, H. (2021). Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell, 184(19), 5031-5052.e26. https://doi.org/10.1016/j.cell.2021.08.023
Cao, Liwei, et al. "Proteogenomic characterization of pancreatic ductal adenocarcinoma." Cell vol. 184,19 (2021): 5031-5052.e26. doi: https://doi.org/10.1016/j.cell.2021.08.023
Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. PMID: 34534465; PMCID: PMC8654574.
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Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment.

Molecular & cellular proteomics : MCP

Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND.
PMID: 34592423
Mol Cell Proteomics. 2021 Sep 27;20:100154. doi: 10.1016/j.mcpro.2021.100154. Epub 2021 Sep 27.

Robust methods for deep-scale enrichment and site-specific identification of ubiquitylation sites are necessary for characterizing the myriad roles of protein ubiquitylation. To this end we previously developed UbiFast, a sensitive method for highly multiplexed ubiquitylation profiling where K-ϵ-GG peptides...

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Rivera KD, Olive ME, Bergstrom EJ, et al. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics. 2021;20:100154doi: 10.1016/j.mcpro.2021.100154.
Rivera, K. D., Olive, M. E., Bergstrom, E. J., Nelson, A. J., Lee, K. A., Satpathy, S., Carr, S. A., & Udeshi, N. D. (2021). Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Molecular & cellular proteomics : MCP, 20100154. https://doi.org/10.1016/j.mcpro.2021.100154
Rivera, Keith D, et al. "Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment." Molecular & cellular proteomics : MCP vol. 20 (2021): 100154. doi: https://doi.org/10.1016/j.mcpro.2021.100154
Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics. 2021 Sep 27;20:100154. doi: 10.1016/j.mcpro.2021.100154. Epub 2021 Sep 27. PMID: 34592423.
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A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.

Molecular systems biology

Keshishian H, McDonald ER, Mundt F, Melanson R, Krug K, Porter DA, Wallace L, Forestier D, Rabasha B, Marlow SE, Jane-Valbuena J, Todres E, Specht H, Robinson ML, Jean Beltran PM, Babur O, Olive ME, Golji J, Kuhn E, Burgess M, MacMullan MA, Rejtar T, Wang K, Mani DR, Satpathy S, Gillette MA, Sellers WR, Carr SA.
PMID: 34569154
Mol Syst Biol. 2021 Sep;17(9):e10156. doi: 10.15252/msb.202010156.

Reliable methods to quantify dynamic signaling changes across diverse pathways are needed to better understand the effects of disease and drug treatment in cells and tissues but are presently lacking. Here, we present SigPath, a targeted mass spectrometry (MS)...

Cite
Keshishian H, McDonald ER, Mundt F, et al. A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. Mol Syst Biol. 2021;17(9):e10156doi: 10.15252/msb.202010156.
Keshishian, H., McDonald, E. R., Mundt, F., Melanson, R., Krug, K., Porter, D. A., Wallace, L., Forestier, D., Rabasha, B., Marlow, S. E., Jane-Valbuena, J., Todres, E., Specht, H., Robinson, M. L., Jean Beltran, P. M., Babur, O., Olive, M. E., Golji, J., Kuhn, E., Burgess, M., MacMullan, M. A., Rejtar, T., Wang, K., Mani, D. R., Satpathy, S., Gillette, M. A., Sellers, W. R., & Carr, S. A. (2021). A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. Molecular systems biology, 17(9), e10156. https://doi.org/10.15252/msb.202010156
Keshishian, Hasmik, et al. "A highly multiplexed quantitative phosphosite assay for biology and preclinical studies." Molecular systems biology vol. 17,9 (2021): e10156. doi: https://doi.org/10.15252/msb.202010156
Keshishian H, McDonald ER, Mundt F, Melanson R, Krug K, Porter DA, Wallace L, Forestier D, Rabasha B, Marlow SE, Jane-Valbuena J, Todres E, Specht H, Robinson ML, Jean Beltran PM, Babur O, Olive ME, Golji J, Kuhn E, Burgess M, MacMullan MA, Rejtar T, Wang K, Mani DR, Satpathy S, Gillette MA, Sellers WR, Carr SA. A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. Mol Syst Biol. 2021 Sep;17(9):e10156. doi: 10.15252/msb.202010156. PMID: 34569154; PMCID: PMC8474009.
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A proteogenomic portrait of lung squamous cell carcinoma.

Cell

Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA.
PMID: 34358469
Cell. 2021 Aug 05;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016.

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an...

Cite
Satpathy S, Krug K, Jean Beltran PM, et al. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021;184(16):4348-4371.e40doi: 10.1016/j.cell.2021.07.016.
Satpathy, S., Krug, K., Jean Beltran, P. M., Savage, S. R., Petralia, F., Kumar-Sinha, C., Dou, Y., Reva, B., Kane, M. H., Avanessian, S. C., Vasaikar, S. V., Krek, A., Lei, J. T., Jaehnig, E. J., Omelchenko, T., Geffen, Y., Bergstrom, E. J., Stathias, V., Christianson, K. E., Heiman, D. I., Cieslik, M. P., Cao, S., Song, X., Ji, J., Liu, W., Li, K., Wen, B., Li, Y., Gümüş, Z. H., Selvan, M. E., Soundararajan, R., Visal, T. H., Raso, M. G., Parra, E. R., Babur, �. �., Vats, P., Anand, S., Schraink, T., Cornwell, M., Rodrigues, F. M., Zhu, H., Mo, C. K., Zhang, Y., da Veiga Leprevost, F., Huang, C., Chinnaiyan, A. M., Wyczalkowski, M. A., Omenn, G. S., Newton, C. J., Schurer, S., Ruggles, K. V., Fenyö, D., Jewell, S. D., Thiagarajan, M., Mesri, M., Rodriguez, H., Mani, S. A., Udeshi, N. D., Getz, G., Suh, J., Li, Q. K., Hostetter, G., Paik, P. K., Dhanasekaran, S. M., Govindan, R., Ding, L., Robles, A. I., Clauser, K. R., Nesvizhskii, A. I., Wang, P., Carr, S. A., Zhang, B., Mani, D. R., Gillette, M. A. (2021). A proteogenomic portrait of lung squamous cell carcinoma. Cell, 184(16), 4348-4371.e40. https://doi.org/10.1016/j.cell.2021.07.016
Satpathy, Shankha, et al. "A proteogenomic portrait of lung squamous cell carcinoma." Cell vol. 184,16 (2021): 4348-4371.e40. doi: https://doi.org/10.1016/j.cell.2021.07.016
Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021 Aug 05;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016. PMID: 34358469; PMCID: PMC8475722.
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Methods, Tools and Current Perspectives in Proteogenomics.

Molecular & cellular proteomics : MCP

Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR.
PMID: 28456751
Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29.

With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics,

Cite
Ruggles KV, Krug K, Wang X, et al. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics. 2017;16(6):959-981doi: 10.1074/mcp.MR117.000024.
Ruggles, K. V., Krug, K., Wang, X., Clauser, K. R., Wang, J., Payne, S. H., Fenyö, D., Zhang, B., & Mani, D. R. (2017). Methods, Tools and Current Perspectives in Proteogenomics. Molecular & cellular proteomics : MCP, 16(6), 959-981. https://doi.org/10.1074/mcp.MR117.000024
Ruggles, Kelly V, et al. "Methods, Tools and Current Perspectives in Proteogenomics." Molecular & cellular proteomics : MCP vol. 16,6 (2017): 959-981. doi: https://doi.org/10.1074/mcp.MR117.000024
Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics. 2017 Jun;16(6):959-981. doi: 10.1074/mcp.MR117.000024. Epub 2017 Apr 29. PMID: 28456751; PMCID: PMC5461547.
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Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cell

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H.
PMID: 34534465
Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal...

Cite
Cao L, Huang C, Cui Zhou D, et al. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021;184(19):5031-5052.e26doi: 10.1016/j.cell.2021.08.023.
Cao, L., Huang, C., Cui Zhou, D., Hu, Y., Lih, T. M., Savage, S. R., Krug, K., Clark, D. J., Schnaubelt, M., Chen, L., da Veiga Leprevost, F., Eguez, R. V., Yang, W., Pan, J., Wen, B., Dou, Y., Jiang, W., Liao, Y., Shi, Z., Terekhanova, N. V., Cao, S., Lu, R. J., Li, Y., Liu, R., Zhu, H., Ronning, P., Wu, Y., Wyczalkowski, M. A., Easwaran, H., Danilova, L., Mer, A. S., Yoo, S., Wang, J. M., Liu, W., Haibe-Kains, B., Thiagarajan, M., Jewell, S. D., Hostetter, G., Newton, C. J., Li, Q. K., Roehrl, M. H., Fenyö, D., Wang, P., Nesvizhskii, A. I., Mani, D. R., Omenn, G. S., Boja, E. S., Mesri, M., Robles, A. I., Rodriguez, H., Bathe, O. F., Chan, D. W., Hruban, R. H., Ding, L., Zhang, B., Zhang, H. (2021). Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell, 184(19), 5031-5052.e26. https://doi.org/10.1016/j.cell.2021.08.023
Cao, Liwei, et al. "Proteogenomic characterization of pancreatic ductal adenocarcinoma." Cell vol. 184,19 (2021): 5031-5052.e26. doi: https://doi.org/10.1016/j.cell.2021.08.023
Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H. Proteogenomic characterization of pancreatic ductal adenocarcinoma. Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023. PMID: 34534465; PMCID: PMC8654574.
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A proteogenomic portrait of lung squamous cell carcinoma.

Cell

Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA.
PMID: 34358469
Cell. 2021 Aug 05;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016.

Lung squamous cell carcinoma (LSCC) remains a leading cause of cancer death with few therapeutic options. We characterized the proteogenomic landscape of LSCC, providing a deeper exposition of LSCC biology with potential therapeutic implications. We identify NSD3 as an...

Cite
Satpathy S, Krug K, Jean Beltran PM, et al. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021;184(16):4348-4371.e40doi: 10.1016/j.cell.2021.07.016.
Satpathy, S., Krug, K., Jean Beltran, P. M., Savage, S. R., Petralia, F., Kumar-Sinha, C., Dou, Y., Reva, B., Kane, M. H., Avanessian, S. C., Vasaikar, S. V., Krek, A., Lei, J. T., Jaehnig, E. J., Omelchenko, T., Geffen, Y., Bergstrom, E. J., Stathias, V., Christianson, K. E., Heiman, D. I., Cieslik, M. P., Cao, S., Song, X., Ji, J., Liu, W., Li, K., Wen, B., Li, Y., Gümüş, Z. H., Selvan, M. E., Soundararajan, R., Visal, T. H., Raso, M. G., Parra, E. R., Babur, �. �., Vats, P., Anand, S., Schraink, T., Cornwell, M., Rodrigues, F. M., Zhu, H., Mo, C. K., Zhang, Y., da Veiga Leprevost, F., Huang, C., Chinnaiyan, A. M., Wyczalkowski, M. A., Omenn, G. S., Newton, C. J., Schurer, S., Ruggles, K. V., Fenyö, D., Jewell, S. D., Thiagarajan, M., Mesri, M., Rodriguez, H., Mani, S. A., Udeshi, N. D., Getz, G., Suh, J., Li, Q. K., Hostetter, G., Paik, P. K., Dhanasekaran, S. M., Govindan, R., Ding, L., Robles, A. I., Clauser, K. R., Nesvizhskii, A. I., Wang, P., Carr, S. A., Zhang, B., Mani, D. R., Gillette, M. A. (2021). A proteogenomic portrait of lung squamous cell carcinoma. Cell, 184(16), 4348-4371.e40. https://doi.org/10.1016/j.cell.2021.07.016
Satpathy, Shankha, et al. "A proteogenomic portrait of lung squamous cell carcinoma." Cell vol. 184,16 (2021): 4348-4371.e40. doi: https://doi.org/10.1016/j.cell.2021.07.016
Satpathy S, Krug K, Jean Beltran PM, Savage SR, Petralia F, Kumar-Sinha C, Dou Y, Reva B, Kane MH, Avanessian SC, Vasaikar SV, Krek A, Lei JT, Jaehnig EJ, Omelchenko T, Geffen Y, Bergstrom EJ, Stathias V, Christianson KE, Heiman DI, Cieslik MP, Cao S, Song X, Ji J, Liu W, Li K, Wen B, Li Y, Gümüş ZH, Selvan ME, Soundararajan R, Visal TH, Raso MG, Parra ER, Babur Ö, Vats P, Anand S, Schraink T, Cornwell M, Rodrigues FM, Zhu H, Mo CK, Zhang Y, da Veiga Leprevost F, Huang C, Chinnaiyan AM, Wyczalkowski MA, Omenn GS, Newton CJ, Schurer S, Ruggles KV, Fenyö D, Jewell SD, Thiagarajan M, Mesri M, Rodriguez H, Mani SA, Udeshi ND, Getz G, Suh J, Li QK, Hostetter G, Paik PK, Dhanasekaran SM, Govindan R, Ding L, Robles AI, Clauser KR, Nesvizhskii AI, Wang P, Carr SA, Zhang B, Mani DR, Gillette MA. A proteogenomic portrait of lung squamous cell carcinoma. Cell. 2021 Aug 05;184(16):4348-4371.e40. doi: 10.1016/j.cell.2021.07.016. PMID: 34358469; PMCID: PMC8475722.
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SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.

bioRxiv : the preprint server for biology

Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
PMID: 33024965
bioRxiv. 2020 Oct 26; doi: 10.1101/2020.10.02.324145.

T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class...

Cite
Weingarten-Gabbay S, Klaeger S, Sarkizova S, et al. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv. 2020;doi: 10.1101/2020.10.02.324145.
Weingarten-Gabbay, S., Klaeger, S., Sarkizova, S., Pearlman, L. R., Chen, D. Y., Bauer, M. R., Taylor, H. B., Conway, H. L., Tomkins-Tinch, C. H., Finkel, Y., Nachshon, A., Gentili, M., Rivera, K. D., Keskin, D. B., Rice, C. M., Clauser, K. R., Hacohen, N., Carr, S. A., Abelin, J. G., Saeed, M., & Sabeti, P. C. (2020). SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.10.02.324145
Weingarten-Gabbay, Shira, et al. "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.10.02.324145
Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC. SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs. bioRxiv. 2020 Oct 26; doi: 10.1101/2020.10.02.324145. PMID: 33024965; PMCID: PMC7536868.
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Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment.

Molecular & cellular proteomics : MCP

Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND.
PMID: 34592423
Mol Cell Proteomics. 2021;20:100154. doi: 10.1016/j.mcpro.2021.100154. Epub 2021 Sep 27.

Robust methods for deep-scale enrichment and site-specific identification of ubiquitylation sites are necessary for characterizing the myriad roles of protein ubiquitylation. To this end we previously developed UbiFast, a sensitive method for highly multiplexed ubiquitylation profiling where K-ϵ-GG peptides...

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Rivera KD, Olive ME, Bergstrom EJ, et al. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics. 2021;20:100154doi: 10.1016/j.mcpro.2021.100154.
Rivera, K. D., Olive, M. E., Bergstrom, E. J., Nelson, A. J., Lee, K. A., Satpathy, S., Carr, S. A., & Udeshi, N. D. (2021). Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Molecular & cellular proteomics : MCP, 20100154. https://doi.org/10.1016/j.mcpro.2021.100154
Rivera, Keith D, et al. "Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment." Molecular & cellular proteomics : MCP vol. 20 (2021): 100154. doi: https://doi.org/10.1016/j.mcpro.2021.100154
Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics. 2021;20:100154. doi: 10.1016/j.mcpro.2021.100154. Epub 2021 Sep 27. PMID: 34592423.
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