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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 March 8, 2020. |
#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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#Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | #Geis-Asteggiante L, Belew AT, Clements VK, Edwards NJ, Ostrand-Rosenberg S, El-Sayed NM, Fenselau C, (2017) "Differential content of proteins, mRNAs, and miRNAs suggests that MDSC and their exosomes may mediate distinct immune suppressive functions." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29139296 29139296]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00646 10.1021/acs.jproteome.7b00646]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29139296 60]. | ||
#Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | #Worzfeld T, Finkernagel F, Reinartz S, Konzer A, Adhikary T, Nist A, Stiewe T, Wagner U, Looso M, Graumann J, Müller R, (2017) "Proteotranscriptomics Reveal Signaling Networks in the Ovarian Cancer Microenvironment." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29141914 29141914]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000400 10.1074/mcp.RA117.000400]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29141914 121]. | ||
+ | #Raffel S, Falcone M, Kneisel N, Hansson J, Wang W, Lutz C, Bullinger L, Poschet G, Nonnenmacher Y, Barnert A, Bahr C, Zeisberger P, Przybylla A, Sohn M, Tönjes M, Erez A, Adler L, Jensen P, Scholl C, Fröhling S, Cocciardi S, Wuchter P, Thiede C, Flörcken A, Westermann J, Ehninger G, Lichter P, Hiller K, Hell R, Herrmann C, Ho AD, Krijgsveld J, Radlwimmer B, Trumpp A, (2017) "BCAT1 restricts αKG levels in AML stem cells leading to IDHmut-like DNA hypermethylation." <i>Nature</i> <b>551</b>(7680):384–388; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29144447 29144447]; doi: [https://dx.doi.org/10.1038/nature24294 10.1038/nature24294]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29144447 10]. | ||
#Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | #Yilmaz O, Patinote A, Nguyen TV, Com E, Lavigne R, Pineau C, Sullivan CV, Bobe J, (2017) "Scrambled eggs: Proteomic portraits and novel biomarkers of egg quality in zebrafish (Danio rerio)." <i>PLoS One</i> <b>12</b>(11):e0188084; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145436 29145436]; doi: [https://dx.doi.org/10.1371/journal.pone.0188084 10.1371/journal.pone.0188084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145436 57]. | ||
#Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | #Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29145658 4]. | ||
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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]. | ||
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#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]. | ||
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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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#Mohanty V, Subbannayya Y, Najar MA, Pinto SM, Kasaragod S, Karuppiah H, Sreeramulu B, Singh KK, Dalal S, Manikkoth S, Arunachalam C, Prasad TSK, Murthy KR, (2019) "Proteomics and Visual Health Research: Proteome of the Human Sclera Using High-Resolution Mass Spectrometry." <i>OMICS</i> <b>23</b>(2):98–110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30767726 30767726]; doi: [https://dx.doi.org/10.1089/omi.2018.0185 10.1089/omi.2018.0185]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30767726 2]. | #Mohanty V, Subbannayya Y, Najar MA, Pinto SM, Kasaragod S, Karuppiah H, Sreeramulu B, Singh KK, Dalal S, Manikkoth S, Arunachalam C, Prasad TSK, Murthy KR, (2019) "Proteomics and Visual Health Research: Proteome of the Human Sclera Using High-Resolution Mass Spectrometry." <i>OMICS</i> <b>23</b>(2):98–110; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30767726 30767726]; doi: [https://dx.doi.org/10.1089/omi.2018.0185 10.1089/omi.2018.0185]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30767726 2]. | ||
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#Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." <i>Sci Rep</i> <b>9</b>(1):5154; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914758 30914758]; doi: [https://dx.doi.org/10.1038/s41598-019-41625-z 10.1038/s41598-019-41625-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914758 111]. | #Betancourt LH, Pawłowski K, Eriksson J, Szasz AM, Mitra S, Pla I, Welinder C, Ekedahl H, Broberg P, Appelqvist R, Yakovleva M, Sugihara Y, Miharada K, Ingvar C, Lundgren L, Baldetorp B, Olsson H, Rezeli M, Wieslander E, Horvatovich P, Malm J, Jönsson G, Marko-Varga G, (2019) "Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data." <i>Sci Rep</i> <b>9</b>(1):5154; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30914758 30914758]; doi: [https://dx.doi.org/10.1038/s41598-019-41625-z 10.1038/s41598-019-41625-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30914758 111]. | ||
#Sinclair LV, Howden AJ, Brenes A, Spinelli L, Hukelmann JL, Macintyre AN, Liu X, Thomson S, Taylor PM, Rathmell JC, Locasale JW, Lamond AI, Cantrell DA, (2019) "Antigen receptor control of methionine metabolism in T cells." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30916644 30916644]; doi: [https://dx.doi.org/10.7554/eLife.44210 10.7554/eLife.44210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30916644 7]. | #Sinclair LV, Howden AJ, Brenes A, Spinelli L, Hukelmann JL, Macintyre AN, Liu X, Thomson S, Taylor PM, Rathmell JC, Locasale JW, Lamond AI, Cantrell DA, (2019) "Antigen receptor control of methionine metabolism in T cells." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30916644 30916644]; doi: [https://dx.doi.org/10.7554/eLife.44210 10.7554/eLife.44210]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30916644 7]. | ||
+ | #Lofthouse EM, Torrens C, Manousopoulou A, Nahar M, Cleal JK, O'Kelly IM, Sengers BG, Garbis SD, Lewis RM, (2019) "Ursodeoxycholic acid inhibits uptake and vasoconstrictor effects of taurocholate in human placenta." <i>FASEB J</i> <b>33</b>(7):8211–8220; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30922127 30922127]; doi: [https://dx.doi.org/10.1096/fj.201900015RR 10.1096/fj.201900015RR]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30922127 1]. | ||
#Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G, (2019) "Hypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30926672 30926672]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001401 10.1074/mcp.RA119.001401]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30926672 69]. | #Chachami G, Stankovic-Valentin N, Karagiota A, Basagianni A, Plessmann U, Urlaub H, Melchior F, Simos G, (2019) "Hypoxia-induced changes in SUMO conjugation affect transcriptional regulation under low oxygen." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30926672 30926672]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001401 10.1074/mcp.RA119.001401]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30926672 69]. | ||
#Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T, (2019) "Proteomics profiling of arginine methylation defines PRMT5 substrate specificity." <i>Sci Signal</i> <b>12</b>(575):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30940768 30940768]; doi: [https://dx.doi.org/10.1126/scisignal.aat8388 10.1126/scisignal.aat8388]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30940768 76]. | #Musiani D, Bok J, Massignani E, Wu L, Tabaglio T, Ippolito MR, Cuomo A, Ozbek U, Zorgati H, Ghoshdastider U, Robinson RC, Guccione E, Bonaldi T, (2019) "Proteomics profiling of arginine methylation defines PRMT5 substrate specificity." <i>Sci Signal</i> <b>12</b>(575):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30940768 30940768]; doi: [https://dx.doi.org/10.1126/scisignal.aat8388 10.1126/scisignal.aat8388]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30940768 76]. | ||
#Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." <i>Nat Commun</i> <b>10</b>(1):1519; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30944321 30944321]; doi: [https://dx.doi.org/10.1038/s41467-019-09469-3 10.1038/s41467-019-09469-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30944321 3]. | #Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." <i>Nat Commun</i> <b>10</b>(1):1519; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30944321 30944321]; doi: [https://dx.doi.org/10.1038/s41467-019-09469-3 10.1038/s41467-019-09469-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30944321 3]. | ||
#Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." <i>Nat Commun</i> <b>10</b>(1):1600; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30962452 30962452]; doi: [https://dx.doi.org/10.1038/s41467-019-09018-y 10.1038/s41467-019-09018-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30962452 12]. | #Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." <i>Nat Commun</i> <b>10</b>(1):1600; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30962452 30962452]; doi: [https://dx.doi.org/10.1038/s41467-019-09018-y 10.1038/s41467-019-09018-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30962452 12]. | ||
+ | #Zecha J, Satpathy S, Kanashova T, Avanessian SC, Kane MH, Clauser KR, Mertins P, Carr SA, Kuster B, (2019) "TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach." <i>Mol Cell Proteomics</i> <b>18</b>(7):1468–1478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30967486 30967486]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001385 10.1074/mcp.TIR119.001385]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30967486 27]. | ||
#Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." <i>Cytotherapy</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30975602 30975602]; doi: [https://dx.doi.org/10.1016/j.jcyt.2019.03.002 10.1016/j.jcyt.2019.03.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30975602 8]. | #Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." <i>Cytotherapy</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30975602 30975602]; doi: [https://dx.doi.org/10.1016/j.jcyt.2019.03.002 10.1016/j.jcyt.2019.03.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30975602 8]. | ||
#Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH, (2019) "Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis." <i>J Proteomics</i> <b>201</b>:104–109; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30978464 30978464]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.04.007 10.1016/j.jprot.2019.04.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30978464 96]. | #Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH, (2019) "Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis." <i>J Proteomics</i> <b>201</b>:104–109; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30978464 30978464]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.04.007 10.1016/j.jprot.2019.04.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30978464 96]. | ||
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#Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | #Dybas JM, O'Leary CE, Ding H, Spruce LA, Seeholzer SH, Oliver PM, (2019) "Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4<sup>+</sup> T cells." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31061531 31061531]; doi: [https://dx.doi.org/10.1038/s41590-019-0381-6 10.1038/s41590-019-0381-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31061531 118]. | ||
#Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | #Papaioannou MD, Djuric U, Kao J, Karimi S, Zadeh G, Aldape K, Diamandis P, (2019) "Proteomic analysis of meningiomas reveals clinically-distinct molecular patterns." <i>Neuro Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31077268 31077268]; doi: [https://dx.doi.org/10.1093/neuonc/noz084 10.1093/neuonc/noz084]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31077268 78]. | ||
+ | #Spörrer M, Prochnicki A, Tölle RC, Nyström A, Esser PR, Homberg M, Athanasiou I, Zingkou E, Schilling A, Gerum R, Thievessen I, Winter L, Bruckner-Tuderman L, Fabry B, Magin TM, Dengjel J, Schröder R, Kiritsi D, (2019) "Treatment of keratinocytes with 4-phenylbutyrate in epidermolysis bullosa: Lessons for therapies in keratin disorders." <i>EBioMedicine</i> <b>44</b>:502–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078522 31078522]; doi: [https://dx.doi.org/10.1016/j.ebiom.2019.04.062 10.1016/j.ebiom.2019.04.062]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078522 41]. | ||
#Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | #Wang H, Sheehan RP, Palmer AC, Everley RA, Boswell SA, Ron-Harel N, Ringel AE, Holton KM, Jacobson CA, Erickson AR, Maliszewski L, Haigis MC, Sorger PK, (2019) "Adaptation of Human iPSC-Derived Cardiomyocytes to Tyrosine Kinase Inhibitors Reduces Acute Cardiotoxicity via Metabolic Reprogramming." <i>Cell Syst</i> <b>8</b>(5):412–426.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31078528 31078528]; doi: [https://dx.doi.org/10.1016/j.cels.2019.03.009 10.1016/j.cels.2019.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31078528 24]. | ||
#Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | #Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S, (2019) "Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy." <i>J Proteome Res</i> <b>18</b>(6):2666–2675; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31095916 31095916]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00173 10.1021/acs.jproteome.9b00173]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31095916 11]. | ||
#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 523]. | ||
#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]. | ||
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#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]. |
+ | #Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M, (2019) "Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis." <i>iScience</i> <b>19</b>:1114–1132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31536960 31536960]; doi: [https://dx.doi.org/10.1016/j.isci.2019.08.057 10.1016/j.isci.2019.08.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31536960 708]. | ||
#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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#Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV, (2019) "Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites." <i>Cell</i> <b>179</b>(2):543–560.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31585087 31585087]; doi: [https://dx.doi.org/10.1016/j.cell.2019.09.008 10.1016/j.cell.2019.09.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31585087 255]. | #Lundby A, Franciosa G, Emdal KB, Refsgaard JC, Gnosa SP, Bekker-Jensen DB, Secher A, Maurya SR, Paul I, Mendez BL, Kelstrup CD, Francavilla C, Kveiborg M, Montoya G, Jensen LJ, Olsen JV, (2019) "Oncogenic Mutations Rewire Signaling Pathways by Switching Protein Recruitment to Phosphotyrosine Sites." <i>Cell</i> <b>179</b>(2):543–560.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31585087 31585087]; doi: [https://dx.doi.org/10.1016/j.cell.2019.09.008 10.1016/j.cell.2019.09.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31585087 255]. | ||
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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]. | ||
#Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA, (2019) "The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep." <i>Science</i> <b>366</b>(6462):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31601739 31601739]; doi: [https://dx.doi.org/10.1126/science.aav2642 10.1126/science.aav2642]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31601739 96]. | #Noya SB, Colameo D, Brüning F, Spinnler A, Mircsof D, Opitz L, Mann M, Tyagarajan SK, Robles MS, Brown SA, (2019) "The forebrain synaptic transcriptome is organized by clocks but its proteome is driven by sleep." <i>Science</i> <b>366</b>(6462):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31601739 31601739]; doi: [https://dx.doi.org/10.1126/science.aav2642 10.1126/science.aav2642]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31601739 96]. | ||
+ | #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]. | ||
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+ | #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]. | ||
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+ | #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 193]. | ||
+ | #Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | ||
+ | #Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, (2019) "Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity." <i>Genes Dev</i> <b>33</b>(23-24):1751–1774; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31753913 31753913]; doi: [https://dx.doi.org/10.1101/gad.331231.119 10.1101/gad.331231.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31753913 66]. | ||
+ | #Fang EF, Hou Y, Lautrup S, Jensen MB, Yang B, SenGupta T, Caponio D, Khezri R, Demarest TG, Aman Y, Figueroa D, Morevati M, Lee HJ, Kato H, Kassahun H, Lee JH, Filippelli D, Okur MN, Mangerich A, Croteau DL, Maezawa Y, Lyssiotis CA, Tao J, Yokote K, Rusten TE, Mattson MP, Jasper H, Nilsen H, Bohr VA, (2019) "NAD<sup>+</sup> augmentation restores mitophagy and limits accelerated aging in Werner syndrome." <i>Nat Commun</i> <b>10</b>(1):5284; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31754102 31754102]; doi: [https://dx.doi.org/10.1038/s41467-019-13172-8 10.1038/s41467-019-13172-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31754102 32]. | ||
+ | #Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | ||
+ | #Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | ||
+ | #Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | ||
+ | #Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | ||
+ | #Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | ||
+ | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | ||
+ | #Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | ||
+ | #Mugahid DA, Sengul TG, You X, Wang Y, Steil L, Bergmann N, Radke MH, Ofenbauer A, Gesell-Salazar M, Balogh A, Kempa S, Tursun B, Robbins CT, Völker U, Chen W, Nelson L, Gotthardt M, (2019) "Proteomic and Transcriptomic Changes in Hibernating Grizzly Bears Reveal Metabolic and Signaling Pathways that Protect against Muscle Atrophy." <i>Sci Rep</i> <b>9</b>(1):19976; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31882638 31882638]; doi: [https://dx.doi.org/10.1038/s41598-019-56007-8 10.1038/s41598-019-56007-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31882638 16]. | ||
+ | #Rispoli LA, Edwards JL, Pohler KG, Russell S, Somiari RI, Payton RR, Schrick FN, (2019) "Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows." <i>PLoS One</i> <b>14</b>(12):e0227095; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31887207 31887207]; doi: [https://dx.doi.org/10.1371/journal.pone.0227095 10.1371/journal.pone.0227095]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31887207 5]. | ||
+ | #Róka B, Tod P, Kaucsár T, Vizovišek M, Vidmar R, Turk B, Fonović M, Szénási G, Hamar P, (2019) "The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice." <i>Int J Mol Sci</i> <b>21</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31892161 31892161]; doi: [https://dx.doi.org/10.3390/ijms21010200 10.3390/ijms21010200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31892161 120]. | ||
+ | #Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | ||
+ | #Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | ||
+ | #Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR, (2020) "Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31959955 31959955]; doi: [https://dx.doi.org/10.1038/s41587-019-0391-9 10.1038/s41587-019-0391-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31959955 874]. | ||
+ | #Xu K, Yang L, Zhang L, Qi H, (2020) "Lack of AKAP3 disrupts integrity of the subcellular structure and proteome of mouse sperm and causes male sterility." <i>Development</i> <b>147</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31969357 31969357]; doi: [https://dx.doi.org/10.1242/dev.181057 10.1242/dev.181057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31969357 3]. | ||
+ | #Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31975592 31975592]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00800 10.1021/acs.jproteome.9b00800]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31975592 3]. | ||
+ | #Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." <i>J Proteomics</i> <b>216</b>:103670; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31991189 31991189]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103670 10.1016/j.jprot.2020.103670]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31991189 48]. | ||
+ | #Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH, Krawczyk B, Rist W, Simon E, (2020) "Biomarker discovery for chronic liver diseases by multi-omics - a preclinical case study." <i>Sci Rep</i> <b>10</b>(1):1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31992752 31992752]; doi: [https://dx.doi.org/10.1038/s41598-020-58030-6 10.1038/s41598-020-58030-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31992752 4]. | ||
+ | #Yasuda S, Tsuchiya H, Kaiho A, Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernández-Busnadiego R, Tanaka K, Saeki Y, (2020) "Stress- and ubiquitylation-dependent phase separation of the proteasome." <i>Nature</i> <b>578</b>(7794):296–300; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32025036 32025036]; doi: [https://dx.doi.org/10.1038/s41586-020-1982-9 10.1038/s41586-020-1982-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32025036 6]. | ||
+ | #Pini T, Parks J, Russ J, Dzieciatkowska M, Hansen KC, Schoolcraft WB, Katz-Jaffe M, (2020) "Obesity significantly alters the human sperm proteome, with potential implications for fertility." <i>J Assist Reprod Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32026202 32026202]; doi: [https://dx.doi.org/10.1007/s10815-020-01707-8 10.1007/s10815-020-01707-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32026202 20]. | ||
+ | #Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA, (2020) "Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32027144 32027144]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00704 10.1021/acs.jproteome.9b00704]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32027144 2]. | ||
+ | #Eldridge MJG, Pereira JM, Impens F, Hamon MA, (2020) "Active nuclear import of the deacetylase Sirtuin-2 is controlled by its C-terminus and importins." <i>Sci Rep</i> <b>10</b>(1):2034; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32042025 32042025]; doi: [https://dx.doi.org/10.1038/s41598-020-58397-6 10.1038/s41598-020-58397-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32042025 6]. | ||
+ | #Zhao Q, Laverdure JP, Lanoix J, Durette C, Coté C, Bonneil E, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C, (2020) "Proteogenomics uncovers a vast repertoire of shared tumor-specific antigens in ovarian cancer." <i>Cancer Immunol Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32047025 32047025]; doi: [https://dx.doi.org/10.1158/2326-6066.CIR-19-0541 10.1158/2326-6066.CIR-19-0541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32047025 12]. | ||
+ | #Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR, (2020) "Human Mast Cell Proteome Reveals Unique Lineage, Putative Functions, and Structural Basis for Cell Ablation." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32049054 32049054]; doi: [https://dx.doi.org/10.1016/j.immuni.2020.01.012 10.1016/j.immuni.2020.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32049054 12]. | ||
+ | #Ray S, Valekunja UK, Stangherlin A, Howell SA, Snijders AP, Damodaran G, Reddy AB, (2020) "Circadian rhythms in the absence of the clock gene <i>Bmal1</i>." <i>Science</i> <b>367</b>(6479):800–806; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32054765 32054765]; doi: [https://dx.doi.org/10.1126/science.aaw7365 10.1126/science.aaw7365]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32054765 40]. | ||
+ | #Kosok M, Alli-Shaik A, Bay BH, Gunaratne J, (2020) "Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer." <i>iScience</i> <b>23</b>(2):100868; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32058975 32058975]; doi: [https://dx.doi.org/10.1016/j.isci.2020.100868 10.1016/j.isci.2020.100868]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32058975 1]. | ||
+ | #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, Clinical Proteomic Tumor Analysis Consortium., (2020) "Proteogenomic Characterization of Endometrial Carcinoma." <i>Cell</i> <b>180</b>(4):729–748.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32059776 32059776]; doi: [https://dx.doi.org/10.1016/j.cell.2020.01.026 10.1016/j.cell.2020.01.026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32059776 208]. | ||
+ | #Kalaora S, Lee JS, Barnea E, Levy R, Greenberg P, Alon M, Yagel G, Bar Eli G, Oren R, Peri A, Patkar S, Bitton L, Rosenberg SA, Lotem M, Levin Y, Admon A, Ruppin E, Samuels Y, (2020) "Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma." <i>Nat Commun</i> <b>11</b>(1):896; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32060274 32060274]; doi: [https://dx.doi.org/10.1038/s41467-020-14639-9 10.1038/s41467-020-14639-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32060274 30]. | ||
+ | #Kurimchak AM, Herrera-Montávez C, Brown J, Johnson KJ, Sodi V, Srivastava N, Kumar V, Deihimi S, O'Brien S, Peri S, Mantia-Smaldone GM, Jain A, Winters RM, Cai KQ, Chernoff J, Connolly DC, Duncan JS, (2020) "Functional proteomics interrogation of the kinome identifies MRCKA as a therapeutic target in high-grade serous ovarian carcinoma." <i>Sci Signal</i> <b>13</b>(619):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32071169 32071169]; doi: [https://dx.doi.org/10.1126/scisignal.aax8238 10.1126/scisignal.aax8238]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32071169 51]. | ||
+ | #Touzelet O, Broadbent L, Armstrong SD, Aljabr W, Cloutman-Green E, Power UF, Hiscox JA, (2020) "The secretome profiling of a pediatric airway epithelium infected with hRSV identified aberrant apical/basolateral trafficking and novel immune modulating (CXCL6, CXCL16, CSF3) and antiviral (CEACAM1) proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32075873 32075873]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001546 10.1074/mcp.RA119.001546]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32075873 15]. | ||
+ | #Peters F, Tellkamp F, Brodesser S, Wachsmuth E, Tosetti B, Karow U, Bloch W, Utermöhlen O, Krönke M, Niessen CM, (2020) "Murine Epidermal Ceramide Synthase 4 is a Key Regulator of Skin Barrier Homeostasis." <i>J Invest Dermatol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32092351 32092351]; doi: [https://dx.doi.org/10.1016/j.jid.2020.02.006 10.1016/j.jid.2020.02.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32092351 40]. | ||
+ | #Fan Y, Cheng Y, Li Y, Chen B, Wang Z, Wei T, Zhang H, Guo Y, Wang Q, Wei Y, Chen F, Sha J, Guo X, Wang L, (2020) "Phosphoproteomic Analysis of Neonatal Regenerative Myocardium Revealed Important Roles of CHK1 via Activating mTORC1/P70S6K Pathway." <i>Circulation</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32098494 32098494]; doi: [https://dx.doi.org/10.1161/CIRCULATIONAHA.119.040747 10.1161/CIRCULATIONAHA.119.040747]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32098494 31]. | ||
+ | #Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129078 32129078]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00772 10.1021/acs.jproteome.9b00772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129078 16]. |
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 March 8, 2020.