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Showing 1 to 12 of 17 entries
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Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification.

Molecular & cellular proteomics : MCP

Jiang W, Wen B, Li K, Zeng WF, da Veiga Leprevost F, Moon J, Petyuk VA, Edwards NJ, Liu T, Nesvizhskii AI, Zhang B.
PMID: 34737085
Mol Cell Proteomics. 2021 Nov 01;20:100171. doi: 10.1016/j.mcpro.2021.100171. Epub 2021 Nov 01.

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported...

Proteomic Analysis of Exosomes for Discovery of Protein Biomarkers for Prostate and Bladder Cancer.

Cancers

Wang YT, Shi T, Srivastava S, Kagan J, Liu T, Rodland KD.
PMID: 32825017
Cancers (Basel). 2020 Aug 19;12(9). doi: 10.3390/cancers12092335.

Extracellular vesicles (EVs) are released by nearly all cell types as part of normal cell physiology, transporting biological cargo, including nucleic acids and proteins, across the cell membrane. In pathological states such as cancer, EV-derived cargo may mirror the...

Author Correction: Informed-Proteomics: open-source software package for top-down proteomics.

Nature methods

Park J, Piehowski PD, Wilkins C, Zhou M, Mendoza J, Fujimoto GM, Gibbons BC, Shaw JB, Shen Y, Shukla AK, Moore RJ, Liu T, Petyuk VA, Tolić N, Paša-Tolić L, Smith RD, Payne SH, Kim S.
PMID: 29899368
Nat Methods. 2018 Jul;15(7):554. doi: 10.1038/s41592-018-0040-0.

In the version of this article initially published, the authors erroneously reported the search mode that was used for ProSightPC 3.0 in the Online Methods and in Supplementary Table 3.

Correction: Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

Cell reports. Medicine

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD.
PMID: 32954372
Cell Rep Med. 2020 Aug 25;1(5). doi: 10.1016/j.xcrm.2020.100075.

[This corrects the article PMC7289043.].

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...

leapR: An R Package for Multiomic Pathway Analysis.

Journal of proteome research

Danna V, Mitchell H, Anderson L, Godinez I, Gosline SJC, Teeguarden J, McDermott JE.
PMID: 33703901
J Proteome Res. 2021 Apr 02;20(4):2116-2121. doi: 10.1021/acs.jproteome.0c00963. Epub 2021 Mar 11.

A generalized goal of many high-throughput data studies is to identify functional mechanisms that underlie observed biological phenomena, whether they be disease outcomes or metabolic output. Increasingly, studies that rely on multiple sources of high-throughput data (genomic, transcriptomic, proteomic,...

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...

Residual tissue repositories as a resource for population-based cancer proteomic studies.

Clinical proteomics

Piehowski PD, Petyuk VA, Sontag RL, Gritsenko MA, Weitz KK, Fillmore TL, Moon J, Makhlouf H, Chuaqui RF, Boja ES, Rodriguez H, Lee JSH, Smith RD, Carrick DM, Liu T, Rodland KD.
PMID: 30087585
Clin Proteomics. 2018 Aug 03;15:26. doi: 10.1186/s12014-018-9202-4. eCollection 2018.

BACKGROUND: Mass spectrometry-based proteomics has become a powerful tool for the identification and quantification of proteins from a wide variety of biological specimens. To date, the majority of studies utilizing tissue samples have been carried out on prospectively collected...

Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells.

Communications biology

Shi T, Gaffrey MJ, Fillmore TL, Nicora CD, Yi L, Zhang P, Shukla AK, Wiley HS, Rodland KD, Liu T, Smith RD, Qian WJ.
PMID: 30271983
Commun Biol. 2018 Aug 06;1:103. doi: 10.1038/s42003-018-0107-6. eCollection 2018.

There is an unmet technical challenge for mass spectrometry (MS)-based proteomic analysis of single mammalian cells. Quantitative proteomic analysis of single cells has been previously achieved by antibody-based immunoassays but is limited by the availability of high-quality antibodies. Herein...

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...

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...

Proteogenomic Characterization of Ovarian HGSC Implicates Mitotic Kinases, Replication Stress in Observed Chromosomal Instability.

Cell reports. Medicine

McDermott JE, Arshad OA, Petyuk VA, Fu Y, Gritsenko MA, Clauss TR, Moore RJ, Schepmoes AA, Zhao R, Monroe ME, Schnaubelt M, Tsai CF, Payne SH, Huang C, Wang LB, Foltz S, Wyczalkowski M, Wu Y, Song E, Brewer MA, Thiagarajan M, Kinsinger CR, Robles AI, Boja ES, Rodriguez H, Chan DW, Zhang B, Zhang Z, Ding L, Smith RD, Liu T, Rodland KD.
PMID: 32529193
Cell Rep Med. 2020 Apr 21;1(1). doi: 10.1016/j.xcrm.2020.100004. Epub 2020 Apr 10.

In the absence of a dominant driving mutation other than uniformly present TP53 mutations, deeper understanding of the biology driving ovarian high-grade serous cancer (HGSC) requires analysis at a functional level, including post-translational modifications. Comprehensive proteogenomic and phosphoproteomic characterization...

Showing 1 to 12 of 17 entries