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For: Li K, Vaudel M, Zhang B, Ren Y, Wen B. PDV: an integrative proteomics data viewer. Bioinformatics 2020;35:1249-1251. [PMID: 30169737 DOI: 10.1093/bioinformatics/bty770] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 08/22/2018] [Accepted: 08/29/2018] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
51
Impact of DJ-1 and Helix 8 on the Proteome and Degradome of Neuron-Like Cells. Cells 2021;10:cells10020404. [PMID: 33669258 PMCID: PMC7920061 DOI: 10.3390/cells10020404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/04/2022]  Open
52
Hotta T, Haynes SE, Blasius TL, Gebbie M, Eberhardt EL, Sept D, Cianfrocco M, Verhey KJ, Nesvizhskii AI, Ohi R. Parthenolide Destabilizes Microtubules by Covalently Modifying Tubulin. Curr Biol 2021;31:900-907.e6. [PMID: 33482110 DOI: 10.1016/j.cub.2020.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022]
53
Philosopher: a versatile toolkit for shotgun proteomics data analysis. Nat Methods 2020;17:869-870. [PMID: 32669682 DOI: 10.1038/s41592-020-0912-y] [Citation(s) in RCA: 251] [Impact Index Per Article: 62.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
54
Polasky DA, Yu F, Teo GC, Nesvizhskii AI. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 2020;17:1125-1132. [PMID: 33020657 PMCID: PMC7606558 DOI: 10.1038/s41592-020-0967-9] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/31/2020] [Indexed: 12/15/2022]
55
Polasky DA, Yu F, Teo GC, Nesvizhskii AI. Fast and comprehensive N- and O-glycoproteomics analysis with MSFragger-Glyco. Nat Methods 2020. [PMID: 33020657 DOI: 10.1101/2020.05.18.102665] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
56
Li K, Jain A, Malovannaya A, Wen B, Zhang B. DeepRescore: Leveraging Deep Learning to Improve Peptide Identification in Immunopeptidomics. Proteomics 2020;20:e1900334. [PMID: 32864883 PMCID: PMC7718998 DOI: 10.1002/pmic.201900334] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 08/27/2020] [Indexed: 12/23/2022]
57
Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B. Data, Reagents, Assays and Merits of Proteomics for SARS-CoV-2 Research and Testing. Mol Cell Proteomics 2020;19:1503-1522. [PMID: 32591346 PMCID: PMC7780043 DOI: 10.1074/mcp.ra120.002164] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Indexed: 12/14/2022]  Open
58
Yu F, Haynes SE, Teo GC, Avtonomov DM, Polasky DA, Nesvizhskii AI. Fast Quantitative Analysis of timsTOF PASEF Data with MSFragger and IonQuant. Mol Cell Proteomics 2020;19:1575-1585. [PMID: 32616513 PMCID: PMC7996969 DOI: 10.1074/mcp.tir120.002048] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/21/2020] [Indexed: 01/01/2023]  Open
59
Ming L, Zou Y, Zhao Y, Zhang L, He N, Chen Z, Li SSC, Li L. MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non-Modified Peptides. Proteomics 2020;20:e2000061. [PMID: 32643287 DOI: 10.1002/pmic.202000061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/06/2020] [Indexed: 11/11/2022]
60
Gillette MA, Satpathy S, Cao S, Dhanasekaran SM, Vasaikar SV, Krug K, Petralia F, Li Y, Liang WW, Reva B, Krek A, Ji J, Song X, Liu W, Hong R, Yao L, Blumenberg L, Savage SR, Wendl MC, Wen B, Li K, Tang LC, MacMullan MA, Avanessian SC, Kane MH, Newton CJ, Cornwell M, Kothadia RB, Ma W, Yoo S, Mannan R, Vats P, Kumar-Sinha C, Kawaler EA, Omelchenko T, Colaprico A, Geffen Y, Maruvka YE, da Veiga Leprevost F, Wiznerowicz M, Gümüş ZH, Veluswamy RR, Hostetter G, Heiman DI, Wyczalkowski MA, Hiltke T, Mesri M, Kinsinger CR, Boja ES, Omenn GS, Chinnaiyan AM, Rodriguez H, Li QK, Jewell SD, Thiagarajan M, Getz G, Zhang B, Fenyö D, Ruggles KV, Cieslik MP, Robles AI, Clauser KR, Govindan R, Wang P, Nesvizhskii AI, Ding L, Mani DR, Carr SA. Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. Cell 2020;182:200-225.e35. [PMID: 32649874 PMCID: PMC7373300 DOI: 10.1016/j.cell.2020.06.013] [Citation(s) in RCA: 392] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/06/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
61
Li H, Zhou R, Xu S, Chen X, Hong Y, Lu Q, Liu H, Zhou B, Liang X. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow. J Proteome Res 2020;19:2226-2235. [DOI: 10.1021/acs.jproteome.9b00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
62
Wen B, Li K, Zhang Y, Zhang B. Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis. Nat Commun 2020;11:1759. [PMID: 32273506 PMCID: PMC7145864 DOI: 10.1038/s41467-020-15456-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 03/10/2020] [Indexed: 01/01/2023]  Open
63
Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun 2020;11:1723. [PMID: 32265444 PMCID: PMC7138853 DOI: 10.1038/s41467-020-15283-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022]  Open
64
McGowan T, Johnson JE, Kumar P, Sajulga R, Mehta S, Jagtap PD, Griffin TJ. Multi-omics Visualization Platform: An extensible Galaxy plug-in for multi-omics data visualization and exploration. Gigascience 2020;9:giaa025. [PMID: 32236523 PMCID: PMC7102281 DOI: 10.1093/gigascience/giaa025] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/13/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022]  Open
65
Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D. Proteogenomic Characterization of Endometrial Carcinoma. Cell 2020;180:729-748.e26. [PMID: 32059776 PMCID: PMC7233456 DOI: 10.1016/j.cell.2020.01.026] [Citation(s) in RCA: 273] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/11/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
66
Karunratanakul K, Tang HY, Speicher DW, Chuangsuwanich E, Sriswasdi S. Uncovering Thousands of New Peptides with Sequence-Mask-Search Hybrid De Novo Peptide Sequencing Framework. Mol Cell Proteomics 2019;18:2478-2491. [PMID: 31591261 PMCID: PMC6885704 DOI: 10.1074/mcp.tir119.001656] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/09/2019] [Indexed: 01/03/2023]  Open
67
Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B, Lih TSM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L, Krek A, Li Y, Rykunov D, Li QK, Chen LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W, Ruggles K, Calinawan A, Gümüş ZH, Geiszler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR, Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B, Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang P, Zhang H. Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell 2019;179:964-983.e31. [PMID: 31675502 PMCID: PMC7331093 DOI: 10.1016/j.cell.2019.10.007] [Citation(s) in RCA: 394] [Impact Index Per Article: 78.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 07/15/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023]
68
Wen B, Wang X, Zhang B. PepQuery enables fast, accurate, and convenient proteomic validation of novel genomic alterations. Genome Res 2019;29:485-493. [PMID: 30610011 PMCID: PMC6396417 DOI: 10.1101/gr.235028.118] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 12/28/2018] [Indexed: 12/20/2022]
69
Rong M, Zhou B, Zhou R, Liao Q, Zeng Y, Xu S, Liu Z. PPIP: Automated Software for Identification of Bioactive Endogenous Peptides. J Proteome Res 2019;18:721-727. [PMID: 30540478 DOI: 10.1021/acs.jproteome.8b00718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
70
Ren Z, Qi D, Pugh N, Li K, Wen B, Zhou R, Xu S, Liu S, Jones AR. Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets. Mol Cell Proteomics 2019;18:86-98. [PMID: 30293062 PMCID: PMC6317475 DOI: 10.1074/mcp.ra118.000832] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/31/2018] [Indexed: 01/22/2023]  Open
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