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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of December 8, 2019. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM, (2014) "Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells." <i>Cell Commun Signal</i> <b>12</b>:44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25080971 25080971]; doi: [https://dx.doi.org/10.1186/s12964-014-0044-z 10.1186/s12964-014-0044-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25080971 30]. | #Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM, (2014) "Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells." <i>Cell Commun Signal</i> <b>12</b>:44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25080971 25080971]; doi: [https://dx.doi.org/10.1186/s12964-014-0044-z 10.1186/s12964-014-0044-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25080971 30]. | ||
#Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard N, Blesbois E, (2015) "Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen." <i>J Proteomics</i> <b>112</b>:313–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25086240 25086240]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.024 10.1016/j.jprot.2014.07.024]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25086240 44]. | #Labas V, Grasseau I, Cahier K, Gargaros A, Harichaux G, Teixeira-Gomes AP, Alves S, Bourin M, Gérard N, Blesbois E, (2015) "Qualitative and quantitative peptidomic and proteomic approaches to phenotyping chicken semen." <i>J Proteomics</i> <b>112</b>:313–35; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25086240 25086240]; doi: [https://dx.doi.org/10.1016/j.jprot.2014.07.024 10.1016/j.jprot.2014.07.024]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25086240 44]. | ||
- | #Berlin C, Kowalewski DJ, Schuster H, Mirza N, Walz S, Handel M, Schmid-Horch B, Salih HR, Kanz L, Rammensee HG, Stevanović S, Stickel JS, (2015) "Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy." <i>Leukemia</i> <b>29</b>(3):647–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25092142 25092142]; doi: [https://dx.doi.org/10.1038/leu.2014.233 10.1038/leu.2014.233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25092142 | + | #Berlin C, Kowalewski DJ, Schuster H, Mirza N, Walz S, Handel M, Schmid-Horch B, Salih HR, Kanz L, Rammensee HG, Stevanović S, Stickel JS, (2015) "Mapping the HLA ligandome landscape of acute myeloid leukemia: a targeted approach toward peptide-based immunotherapy." <i>Leukemia</i> <b>29</b>(3):647–59; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25092142 25092142]; doi: [https://dx.doi.org/10.1038/leu.2014.233 10.1038/leu.2014.233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25092142 146]. |
#Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA, (2014) "Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics." <i>J Gen Virol</i> <b>95</b>(Pt 11):2504–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096814 25096814]; doi: [https://dx.doi.org/10.1099/vir.0.068221-0 10.1099/vir.0.068221-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096814 22]. | #Alqahtani A, Heesom K, Bramson JL, Curiel D, Ugai H, Matthews DA, (2014) "Analysis of purified wild type and mutant adenovirus particles by SILAC based quantitative proteomics." <i>J Gen Virol</i> <b>95</b>(Pt 11):2504–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096814 25096814]; doi: [https://dx.doi.org/10.1099/vir.0.068221-0 10.1099/vir.0.068221-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096814 22]. | ||
#Jin L, Huo Y, Zheng Z, Jiang X, Deng H, Chen Y, Lian Q, Ge R, Deng H, (2014) "Down-regulation of Ras-related protein Rab 5C-dependent endocytosis and glycolysis in cisplatin-resistant ovarian cancer cell lines." <i>Mol Cell Proteomics</i> <b>13</b>(11):3138–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096996 25096996]; doi: [https://dx.doi.org/10.1074/mcp.M113.033217 10.1074/mcp.M113.033217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096996 11]. | #Jin L, Huo Y, Zheng Z, Jiang X, Deng H, Chen Y, Lian Q, Ge R, Deng H, (2014) "Down-regulation of Ras-related protein Rab 5C-dependent endocytosis and glycolysis in cisplatin-resistant ovarian cancer cell lines." <i>Mol Cell Proteomics</i> <b>13</b>(11):3138–51; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25096996 25096996]; doi: [https://dx.doi.org/10.1074/mcp.M113.033217 10.1074/mcp.M113.033217]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25096996 11]. | ||
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#Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819186 146]. | #Ayre DC, Chute IC, Joy AP, Barnett DA, Hogan AM, Grüll MP, Peña-Castillo L, Lang AS, Lewis SM, Christian SL, (2017) "CD24 induces changes to the surface receptors of B cell microvesicles with variable effects on their RNA and protein cargo." <i>Sci Rep</i> <b>7</b>(1):8642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819186 28819186]; doi: [https://dx.doi.org/10.1038/s41598-017-08094-8 10.1038/s41598-017-08094-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819186 146]. | ||
#Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R, (2017) "Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function." <i>Theranostics</i> <b>7</b>(10):2704–2717; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819457 28819457]; doi: [https://dx.doi.org/10.7150/thno.19679 10.7150/thno.19679]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819457 663]. | #Singh H, Yu Y, Suh MJ, Torralba MG, Stenzel RD, Tovchigrechko A, Thovarai V, Harkins DM, Rajagopala SV, Osborne W, Cogen FR, Kaplowitz PB, Nelson KE, Madupu R, Pieper R, (2017) "Type 1 Diabetes: Urinary Proteomics and Protein Network Analysis Support Perturbation of Lysosomal Function." <i>Theranostics</i> <b>7</b>(10):2704–2717; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28819457 28819457]; doi: [https://dx.doi.org/10.7150/thno.19679 10.7150/thno.19679]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28819457 663]. | ||
+ | #Shen H, Lim C, Schwartz AG, Andreev-Andrievskiy A, Deymier AC, Thomopoulos S, (2017) "Effects of spaceflight on the muscles of the murine shoulder." <i>FASEB J</i> <b>31</b>(12):5466–5477; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28821629 28821629]; doi: [https://dx.doi.org/10.1096/fj.201700320R 10.1096/fj.201700320R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28821629 14]. | ||
#Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28823169 14]. | #Hung CL, Pan SH, Han CL, Chang CW, Hsu YL, Su CH, Shih SC, Lai YJ, Chiang Chiau JS, Yeh HI, Liu CY, Lee HC, Lam CSP, (2017) "Membrane Proteomics of Impaired Energetics and Cytoskeletal Disorganization in Elderly Diet-Induced Diabetic Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28823169 28823169]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00148 10.1021/acs.jproteome.7b00148]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28823169 14]. | ||
#Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28827280 12]. | #Fu L, Liu KK, Sun MA, Tian CP, Sun R, Morales Betanzos C, Tallman KA, Porter NA, Yang Y, Guo DJ, Liebler DC, Yang J, (2017) "Systematic and quantitative assessment of hydrogen peroxide reactivity with cysteines across human proteomes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28827280 28827280]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000108 10.1074/mcp.RA117.000108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28827280 12]. | ||
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#Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29033902 1]. | #Grenga L, Chandra G, Saalbach G, Galmozzi CV, Kramer G, Malone JG, (2017) "Analyzing the Complex Regulatory Landscape of Hfq - an Integrative, Multi-Omics Approach." <i>Front Microbiol</i> <b>8</b>:1784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29033902 29033902]; doi: [https://dx.doi.org/10.3389/fmicb.2017.01784 10.3389/fmicb.2017.01784]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29033902 1]. | ||
#Kugeratski FG, Batista M, Lima CVP, Neilson LJ, da Cunha ES, de Godoy LMF, Zanivan S, Krieger MA, Marchini FK, (2017) "The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29043805 15]. | #Kugeratski FG, Batista M, Lima CVP, Neilson LJ, da Cunha ES, de Godoy LMF, Zanivan S, Krieger MA, Marchini FK, (2017) "The mitogen-activated protein kinase kinase 5 regulates the proliferation and biosynthetic processes in procyclic forms of Trypanosoma brucei." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29043805 29043805]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00415 10.1021/acs.jproteome.7b00415]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29043805 15]. | ||
+ | #Bartosova M, Schaefer B, Bermejo JL, Tarantino S, Lasitschka F, Macher-Goeppinger S, Sinn P, Warady BA, Zaloszyc A, Parapatics K, Májek P, Bennett KL, Oh J, Aufricht C, Schaefer F, Kratochwill K, Schmitt CP, (2018) "Complement Activation in Peritoneal Dialysis-Induced Arteriolopathy." <i>J Am Soc Nephrol</i> <b>29</b>(1):268–282; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29046343 29046343]; doi: [https://dx.doi.org/10.1681/ASN.2017040436 10.1681/ASN.2017040436]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29046343 2]. | ||
#Fabrik I, Link M, Putzova D, Plzakova L, Lubovska Z, Philimonenko V, Pavkova I, Rehulka P, Krocova Z, Hozak P, Santic M, Stulik J, (2017) "<b>The early dendritic cell signaling induced by virulent <i>Francisella</i><i>tularensis</i> strain occurs in phases and involves the activation of ERKs and p38 in the later stage.</b>" <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29046388 29046388]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000160 10.1074/mcp.RA117.000160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29046388 364]. | #Fabrik I, Link M, Putzova D, Plzakova L, Lubovska Z, Philimonenko V, Pavkova I, Rehulka P, Krocova Z, Hozak P, Santic M, Stulik J, (2017) "<b>The early dendritic cell signaling induced by virulent <i>Francisella</i><i>tularensis</i> strain occurs in phases and involves the activation of ERKs and p38 in the later stage.</b>" <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29046388 29046388]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000160 10.1074/mcp.RA117.000160]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29046388 364]. | ||
#Raschdorf O, Bonn F, Zeytuni N, Zarivach R, Becher D, Schüler D, (2017) "A quantitative assessment of the membrane-integral sub-proteome of a bacterial magnetic organelle." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29054541 29054541]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.007 10.1016/j.jprot.2017.10.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29054541 127]. | #Raschdorf O, Bonn F, Zeytuni N, Zarivach R, Becher D, Schüler D, (2017) "A quantitative assessment of the membrane-integral sub-proteome of a bacterial magnetic organelle." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29054541 29054541]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.10.007 10.1016/j.jprot.2017.10.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29054541 127]. | ||
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#Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T, (2018) "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons." <i>Cell</i> <b>172</b>(1-2):262–274.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29328915 29328915]; doi: [https://dx.doi.org/10.1016/j.cell.2017.12.022 10.1016/j.cell.2017.12.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29328915 6]. | #Ashley J, Cordy B, Lucia D, Fradkin LG, Budnik V, Thomson T, (2018) "Retrovirus-like Gag Protein Arc1 Binds RNA and Traffics across Synaptic Boutons." <i>Cell</i> <b>172</b>(1-2):262–274.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29328915 29328915]; doi: [https://dx.doi.org/10.1016/j.cell.2017.12.022 10.1016/j.cell.2017.12.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29328915 6]. | ||
#Khan SY, Ali M, Kabir F, Renuse S, Na CH, Talbot CC Jr, Hackett SF, Riazuddin SA, (2018) "Proteome Profiling of Developing Murine Lens Through Mass Spectrometry." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):100–107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29332127 29332127]; doi: [https://dx.doi.org/10.1167/iovs.17-21601 10.1167/iovs.17-21601]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29332127 3]. | #Khan SY, Ali M, Kabir F, Renuse S, Na CH, Talbot CC Jr, Hackett SF, Riazuddin SA, (2018) "Proteome Profiling of Developing Murine Lens Through Mass Spectrometry." <i>Invest Ophthalmol Vis Sci</i> <b>59</b>(1):100–107; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29332127 29332127]; doi: [https://dx.doi.org/10.1167/iovs.17-21601 10.1167/iovs.17-21601]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29332127 3]. | ||
+ | #Meng H, Fitzgerald MC, (2018) "Proteome-Wide Characterization of Phosphorylation-Induced Conformational Changes in Breast Cancer." <i>J Proteome Res</i> <b>17</b>(3):1129–1137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29332387 29332387]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00795 10.1021/acs.jproteome.7b00795]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29332387 36]. | ||
#Kim DK, Park J, Han D, Yang J, Kim A, Woo J, Kim Y, Mook-Jung I, (2018) "Molecular and functional signatures in a novel Alzheimer's disease mouse model assessed by quantitative proteomics." <i>Mol Neurodegener</i> <b>13</b>(1):2; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29338754 29338754]; doi: [https://dx.doi.org/10.1186/s13024-017-0234-4 10.1186/s13024-017-0234-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29338754 8]. | #Kim DK, Park J, Han D, Yang J, Kim A, Woo J, Kim Y, Mook-Jung I, (2018) "Molecular and functional signatures in a novel Alzheimer's disease mouse model assessed by quantitative proteomics." <i>Mol Neurodegener</i> <b>13</b>(1):2; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29338754 29338754]; doi: [https://dx.doi.org/10.1186/s13024-017-0234-4 10.1186/s13024-017-0234-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29338754 8]. | ||
#Sousa DZ, Visser M, van Gelder AH, Boeren S, Pieterse MM, Pinkse MWH, Verhaert PDEM, Vogt C, Franke S, Kümmel S, Stams AJM, (2018) "The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways." <i>Nat Commun</i> <b>9</b>(1):239; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29339722 29339722]; doi: [https://dx.doi.org/10.1038/s41467-017-02518-9 10.1038/s41467-017-02518-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29339722 84]. | #Sousa DZ, Visser M, van Gelder AH, Boeren S, Pieterse MM, Pinkse MWH, Verhaert PDEM, Vogt C, Franke S, Kümmel S, Stams AJM, (2018) "The deep-subsurface sulfate reducer Desulfotomaculum kuznetsovii employs two methanol-degrading pathways." <i>Nat Commun</i> <b>9</b>(1):239; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29339722 29339722]; doi: [https://dx.doi.org/10.1038/s41467-017-02518-9 10.1038/s41467-017-02518-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29339722 84]. | ||
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#Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R, (2018) "Cleavable crosslinkers as tissue fixation reagents for proteomic analysis." <i>Chembiochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29356267 29356267]; doi: [https://dx.doi.org/10.1002/cbic.201700625 10.1002/cbic.201700625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29356267 15]. | #Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R, (2018) "Cleavable crosslinkers as tissue fixation reagents for proteomic analysis." <i>Chembiochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29356267 29356267]; doi: [https://dx.doi.org/10.1002/cbic.201700625 10.1002/cbic.201700625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29356267 15]. | ||
#Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29358734 96]. | #Topf U, Suppanz I, Samluk L, Wrobel L, Böser A, Sakowska P, Knapp B, Pietrzyk MK, Chacinska A, Warscheid B, (2018) "Quantitative proteomics identifies redox switches for global translation modulation by mitochondrially produced reactive oxygen species." <i>Nat Commun</i> <b>9</b>(1):324; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29358734 29358734]; doi: [https://dx.doi.org/10.1038/s41467-017-02694-8 10.1038/s41467-017-02694-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29358734 96]. | ||
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#Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | #Adav SS, Wei J, Terence Y, Ang BC, Yip LW, Sze SK, (2018) "Proteomic Analysis of Aqueous Humor from Primary Open Angle Glaucoma Patients on Drug Treatment Revealed Altered Complement Activation Cascade." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29901396 29901396]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00244 10.1021/acs.jproteome.8b00244]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29901396 80]. | ||
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#Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | #Ott E, Kawaguchi Y, Özgen N, Yamagishi A, Rabbow E, Rettberg P, Weckwerth W, Milojevic T, (2019) "Proteomic and Metabolomic Profiling of <i>Deinococcus radiodurans</i> Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions." <i>Front Microbiol</i> <b>10</b>:909; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31110498 31110498]; doi: [https://dx.doi.org/10.3389/fmicb.2019.00909 10.3389/fmicb.2019.00909]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31110498 17]. | ||
#Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | #Chu F, Mason KE, Anex DS, Jones AD, Hart BR, (2019) "Hair Proteome Variation at Different Body Locations on Genetically Variant Peptide Detection for Protein-Based Human Identification." <i>Sci Rep</i> <b>9</b>(1):7641; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31113963 31113963]; doi: [https://dx.doi.org/10.1038/s41598-019-44007-7 10.1038/s41598-019-44007-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31113963 36]. | ||
+ | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 47]. | ||
#Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | #Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | ||
#Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | #Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | ||
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#Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS, (2019) "Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality." <i>Cell Rep</i> <b>28</b>(6):1635–1647.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31390575 31390575]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.07.019 10.1016/j.celrep.2019.07.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31390575 723]. | #Hillier C, Pardo M, Yu L, Bushell E, Sanderson T, Metcalf T, Herd C, Anar B, Rayner JC, Billker O, Choudhary JS, (2019) "Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality." <i>Cell Rep</i> <b>28</b>(6):1635–1647.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31390575 31390575]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.07.019 10.1016/j.celrep.2019.07.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31390575 723]. | ||
#Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB, (2019) "Proteogenomic landscape of squamous cell lung cancer." <i>Nat Commun</i> <b>10</b>(1):3578; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31395880 31395880]; doi: [https://dx.doi.org/10.1038/s41467-019-11452-x 10.1038/s41467-019-11452-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31395880 58]. | #Stewart PA, Welsh EA, Slebos RJC, Fang B, Izumi V, Chambers M, Zhang G, Cen L, Pettersson F, Zhang Y, Chen Z, Cheng CH, Thapa R, Thompson Z, Fellows KM, Francis JM, Saller JJ, Mesa T, Zhang C, Yoder S, DeNicola GM, Beg AA, Boyle TA, Teer JK, Ann Chen Y, Koomen JM, Eschrich SA, Haura EB, (2019) "Proteogenomic landscape of squamous cell lung cancer." <i>Nat Commun</i> <b>10</b>(1):3578; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31395880 31395880]; doi: [https://dx.doi.org/10.1038/s41467-019-11452-x 10.1038/s41467-019-11452-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31395880 58]. | ||
- | #Olson MG, Widner RE, Jorgenson LM, Lawrence A, Lagundzin D, Woods NT, Ouellette SP, Rucks EA, (2019) "Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells." <i>Infect Immun</i> <b>87</b>(11):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31405957 31405957]; doi: [https://dx.doi.org/10.1128/IAI.00537-19 10.1128/IAI.00537-19]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31405957 | + | #Olson MG, Widner RE, Jorgenson LM, Lawrence A, Lagundzin D, Woods NT, Ouellette SP, Rucks EA, (2019) "Proximity Labeling To Map Host-Pathogen Interactions at the Membrane of a Bacterium-Containing Vacuole in Chlamydia trachomatis-Infected Human Cells." <i>Infect Immun</i> <b>87</b>(11):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31405957 31405957]; doi: [https://dx.doi.org/10.1128/IAI.00537-19 10.1128/IAI.00537-19]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31405957 314]. |
#Brophy RH, Cai L, Duan X, Zhang Q, Townsend RR, Nunley RM, Guilak F, Rai MF, (2019) "Proteomic analysis of synovial fluid identifies periostin as a biomarker for anterior cruciate ligament injury." <i>Osteoarthritis Cartilage</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31430535 31430535]; doi: [https://dx.doi.org/10.1016/j.joca.2019.08.002 10.1016/j.joca.2019.08.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31430535 11]. | #Brophy RH, Cai L, Duan X, Zhang Q, Townsend RR, Nunley RM, Guilak F, Rai MF, (2019) "Proteomic analysis of synovial fluid identifies periostin as a biomarker for anterior cruciate ligament injury." <i>Osteoarthritis Cartilage</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31430535 31430535]; doi: [https://dx.doi.org/10.1016/j.joca.2019.08.002 10.1016/j.joca.2019.08.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31430535 11]. | ||
#Ong JWJ, Tan KS, Ler SG, Gunaratne J, Choi H, Seet JE, Chow VT, (2019) "Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics." <i>Cells</i> <b>8</b>(9):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31455003 31455003]; doi: [https://dx.doi.org/10.3390/cells8090975 10.3390/cells8090975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31455003 1]. | #Ong JWJ, Tan KS, Ler SG, Gunaratne J, Choi H, Seet JE, Chow VT, (2019) "Insights into Early Recovery from Influenza Pneumonia by Spatial and Temporal Quantification of Putative Lung Regenerating Cells and by Lung Proteomics." <i>Cells</i> <b>8</b>(9):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31455003 31455003]; doi: [https://dx.doi.org/10.3390/cells8090975 10.3390/cells8090975]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31455003 1]. | ||
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#Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM, (2019) "Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft." <i>Immunogenetics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31520135 31520135]; doi: [https://dx.doi.org/10.1007/s00251-019-01129-6 10.1007/s00251-019-01129-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31520135 77]. | #Kampstra ASB, van Heemst J, Janssen GM, de Ru AH, van Lummel M, van Veelen PA, Toes REM, (2019) "Ligandomes obtained from different HLA-class II-molecules are homologous for N- and C-terminal residues outside the peptide-binding cleft." <i>Immunogenetics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31520135 31520135]; doi: [https://dx.doi.org/10.1007/s00251-019-01129-6 10.1007/s00251-019-01129-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31520135 77]. | ||
#Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A, (2019) "Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease." <i>Alzheimers Res Ther</i> <b>11</b>(1):82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31521194 31521194]; doi: [https://dx.doi.org/10.1186/s13195-019-0533-9 10.1186/s13195-019-0533-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31521194 27]. | #Sjödin S, Brinkmalm G, Öhrfelt A, Parnetti L, Paciotti S, Hansson O, Hardy J, Blennow K, Zetterberg H, Brinkmalm A, (2019) "Endo-lysosomal proteins and ubiquitin CSF concentrations in Alzheimer's and Parkinson's disease." <i>Alzheimers Res Ther</i> <b>11</b>(1):82; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31521194 31521194]; doi: [https://dx.doi.org/10.1186/s13195-019-0533-9 10.1186/s13195-019-0533-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31521194 27]. | ||
- | #Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 | + | #Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 21]. |
#Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | #Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | ||
#Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | #Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | ||
+ | #Baers LL, Breckels LM, Mills LA, Gatto L, Deery M, Stevens TJ, Howe CJ, Lilley KS, Lea-Smith DJ, (2019) "Proteome mapping of a cyanobacterium reveals distinct compartment organisation and cell-dispersed metabolism." <i>Plant Physiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31578229 31578229]; doi: [https://dx.doi.org/10.1104/pp.19.00897 10.1104/pp.19.00897]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31578229 39]. | ||
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#Lin Z, Zhang Y, Pan H, Hao P, Li S, He Y, Yang H, Liu S, Ren Y, (2019) "An alternative strategy to explore missing proteins with low molecular weight." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31592669 31592669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00353 10.1021/acs.jproteome.9b00353]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31592669 3]. | #Lin Z, Zhang Y, Pan H, Hao P, Li S, He Y, Yang H, Liu S, Ren Y, (2019) "An alternative strategy to explore missing proteins with low molecular weight." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31592669 31592669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00353 10.1021/acs.jproteome.9b00353]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31592669 3]. | ||
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+ | #Radzisheuskaya A, Shliaha PV, Grinev V, Lorenzini E, Kovalchuk S, Shlyueva D, Gorshkov V, Hendrickson RC, Jensen ON, Helin K, (2019) "PRMT5 methylome profiling uncovers a direct link to splicing regulation in acute myeloid leukemia." <i>Nat Struct Mol Biol</i> <b>26</b>(11):999–1012; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31611688 31611688]; doi: [https://dx.doi.org/10.1038/s41594-019-0313-z 10.1038/s41594-019-0313-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31611688 148]. | ||
#Racle J, Michaux J, Rockinger GA, Arnaud M, Bobisse S, Chong C, Guillaume P, Coukos G, Harari A, Jandus C, Bassani-Sternberg M, Gfeller D, (2019) "Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31611696 31611696]; doi: [https://dx.doi.org/10.1038/s41587-019-0289-6 10.1038/s41587-019-0289-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31611696 131]. | #Racle J, Michaux J, Rockinger GA, Arnaud M, Bobisse S, Chong C, Guillaume P, Coukos G, Harari A, Jandus C, Bassani-Sternberg M, Gfeller D, (2019) "Robust prediction of HLA class II epitopes by deep motif deconvolution of immunopeptidomes." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31611696 31611696]; doi: [https://dx.doi.org/10.1038/s41587-019-0289-6 10.1038/s41587-019-0289-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31611696 131]. | ||
#Stadlmann J, Hudecz O, Krššáková G, Ctortecka C, Van Raemdonck G, Op De Beeck J, Desmet G, Penninger JM, Jacobs P, Mechtler K, (2019) "Improved Sensitivity in Low-Input Proteomics using Micro-Pillar Array-based Chromatography." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31612716 31612716]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b02899 10.1021/acs.analchem.9b02899]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31612716 68]. | #Stadlmann J, Hudecz O, Krššáková G, Ctortecka C, Van Raemdonck G, Op De Beeck J, Desmet G, Penninger JM, Jacobs P, Mechtler K, (2019) "Improved Sensitivity in Low-Input Proteomics using Micro-Pillar Array-based Chromatography." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31612716 31612716]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b02899 10.1021/acs.analchem.9b02899]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31612716 68]. | ||
+ | #McRae EKS, Dupas SJ, Booy EP, Piragasam RS, Fahlman RP, McKenna SA, (2019) "An RNA guanine quadruplex regulated pathway to TRAIL-sensitization by DDX21." <i>RNA</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31653714 31653714]; doi: [https://dx.doi.org/10.1261/rna.072199.119 10.1261/rna.072199.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31653714 108]. | ||
+ | #Kenny A, Jiménez-Mateos EM, Zea-Sevilla MA, Rábano A, Gili-Manzanaro P, Prehn JHM, Henshall DC, Ávila J, Engel T, Hernández F, (2019) "Proteins and microRNAs are differentially expressed in tear fluid from patients with Alzheimer's disease." <i>Sci Rep</i> <b>9</b>(1):15437; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31659197 31659197]; doi: [https://dx.doi.org/10.1038/s41598-019-51837-y 10.1038/s41598-019-51837-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31659197 32]. | ||
+ | #Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | ||
+ | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 158]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of December 8, 2019.