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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. | 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. | ||
+ | |||
+ | <b>CAUTION</b>: 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. | ||
==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 Jan. 22, 2018. |
#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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Thomae AW, Schade GO, Padeken J, Borath M, Vetter I, Kremmer E, Heun P, Imhof A, (2013) "A pair of centromeric proteins mediates reproductive isolation in Drosophila species." <i>Dev Cell</i> <b>27</b>(4):412–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24239514 24239514]; doi: [https://dx.doi.org/10.1016/j.devcel.2013.10.001 10.1016/j.devcel.2013.10.001]; GPMDB: [http://gpmdb.org/data/keyword/24239514 51]. | #Thomae AW, Schade GO, Padeken J, Borath M, Vetter I, Kremmer E, Heun P, Imhof A, (2013) "A pair of centromeric proteins mediates reproductive isolation in Drosophila species." <i>Dev Cell</i> <b>27</b>(4):412–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24239514 24239514]; doi: [https://dx.doi.org/10.1016/j.devcel.2013.10.001 10.1016/j.devcel.2013.10.001]; GPMDB: [http://gpmdb.org/data/keyword/24239514 51]. | ||
#Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, Forshed J, Käll L, Lehtiö J, (2014) "HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics." <i>Nat Methods</i> <b>11</b>(1):59–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24240322 24240322]; doi: [https://dx.doi.org/10.1038/nmeth.2732 10.1038/nmeth.2732]; GPMDB: [http://gpmdb.org/data/keyword/24240322 2592]. | #Branca RM, Orre LM, Johansson HJ, Granholm V, Huss M, Pérez-Bercoff Å, Forshed J, Käll L, Lehtiö J, (2014) "HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics." <i>Nat Methods</i> <b>11</b>(1):59–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24240322 24240322]; doi: [https://dx.doi.org/10.1038/nmeth.2732 10.1038/nmeth.2732]; GPMDB: [http://gpmdb.org/data/keyword/24240322 2592]. | ||
+ | #Schaab C, Oppermann FS, Klammer M, Pfeifer H, Tebbe A, Oellerich T, Krauter J, Levis M, Perl AE, Daub H, Steffen B, Godl K, Serve H, (2014) "Global phosphoproteome analysis of human bone marrow reveals predictive phosphorylation markers for the treatment of acute myeloid leukemia with quizartinib." <i>Leukemia</i> <b>28</b>(3):716–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24247654 24247654]; doi: [https://dx.doi.org/10.1038/leu.2013.347 10.1038/leu.2013.347]; GPMDB: [http://gpmdb.org/data/keyword/24247654 22]. | ||
#Drake JM, Graham NA, Lee JK, Stoyanova T, Faltermeier CM, Sud S, Titz B, Huang J, Pienta KJ, Graeber TG, Witte ON, (2013) "Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinase targets." <i>Proc Natl Acad Sci U S A</i> <b>110</b>(49):E4762–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24248375 24248375]; doi: [https://dx.doi.org/10.1073/pnas.1319948110 10.1073/pnas.1319948110]; GPMDB: [http://gpmdb.org/data/keyword/24248375 87]. | #Drake JM, Graham NA, Lee JK, Stoyanova T, Faltermeier CM, Sud S, Titz B, Huang J, Pienta KJ, Graeber TG, Witte ON, (2013) "Metastatic castration-resistant prostate cancer reveals intrapatient similarity and interpatient heterogeneity of therapeutic kinase targets." <i>Proc Natl Acad Sci U S A</i> <b>110</b>(49):E4762–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24248375 24248375]; doi: [https://dx.doi.org/10.1073/pnas.1319948110 10.1073/pnas.1319948110]; GPMDB: [http://gpmdb.org/data/keyword/24248375 87]. | ||
#Chang C, Li L, Zhang C, Wu S, Guo K, Zi J, Chen Z, Jiang J, Ma J, Yu Q, Fan F, Qin P, Han M, Su N, Chen T, Wang K, Zhai L, Zhang T, Ying W, Xu Z, Zhang Y, Liu Y, Liu X, Zhong F, Shen H, Wang Q, Hou G, Zhao H, Li G, Liu S, Gu W, Wang G, Wang T, Zhang G, Qian X, Li N, He QY, Lin L, Yang P, Zhu Y, He F, Xu P, (2014) "Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP." <i>J Proteome Res</i> <b>13</b>(1):38–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24256510 24256510]; doi: [https://dx.doi.org/10.1021/pr4009018 10.1021/pr4009018]; GPMDB: [http://gpmdb.org/data/keyword/24256510 216]. | #Chang C, Li L, Zhang C, Wu S, Guo K, Zi J, Chen Z, Jiang J, Ma J, Yu Q, Fan F, Qin P, Han M, Su N, Chen T, Wang K, Zhai L, Zhang T, Ying W, Xu Z, Zhang Y, Liu Y, Liu X, Zhong F, Shen H, Wang Q, Hou G, Zhao H, Li G, Liu S, Gu W, Wang G, Wang T, Zhang G, Qian X, Li N, He QY, Lin L, Yang P, Zhu Y, He F, Xu P, (2014) "Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP." <i>J Proteome Res</i> <b>13</b>(1):38–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24256510 24256510]; doi: [https://dx.doi.org/10.1021/pr4009018 10.1021/pr4009018]; GPMDB: [http://gpmdb.org/data/keyword/24256510 216]. | ||
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#Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium., Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. | #Hosp F, Vossfeldt H, Heinig M, Vasiljevic D, Arumughan A, Wyler E, Genetic and Environmental Risk for Alzheimer’s Disease GERAD1 Consortium., Landthaler M, Hubner N, Wanker EE, Lannfelt L, Ingelsson M, Lalowski M, Voigt A, Selbach M, (2015) "Quantitative interaction proteomics of neurodegenerative disease proteins." <i>Cell Rep</i> <b>11</b>(7):1134–46; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25959826 25959826]; doi: [https://dx.doi.org/10.1016/j.celrep.2015.04.030 10.1016/j.celrep.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25959826 122]. | ||
#Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR, (2015) "Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data." <i>J Proteome Res</i> <b>14</b>(9):3541–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25961807 25961807]; doi: [https://dx.doi.org/10.1021/pr5011394 10.1021/pr5011394]; GPMDB: [http://gpmdb.org/data/keyword/25961807 77]. | #Tay AP, Pang CN, Twine NA, Hart-Smith G, Harkness L, Kassem M, Wilkins MR, (2015) "Proteomic Validation of Transcript Isoforms, Including Those Assembled from RNA-Seq Data." <i>J Proteome Res</i> <b>14</b>(9):3541–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25961807 25961807]; doi: [https://dx.doi.org/10.1021/pr5011394 10.1021/pr5011394]; GPMDB: [http://gpmdb.org/data/keyword/25961807 77]. | ||
+ | #Drissi R, Dubois ML, Douziech M, Boisvert FM, (2015) "Quantitative Proteomics Reveals Dynamic Interactions of the Minichromosome Maintenance Complex (MCM) in the Cellular Response to Etoposide Induced DNA Damage." <i>Mol Cell Proteomics</i> <b>14</b>(7):2002–13; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963833 25963833]; doi: [https://dx.doi.org/10.1074/mcp.M115.048991 10.1074/mcp.M115.048991]; GPMDB: [http://gpmdb.org/data/keyword/25963833 48]. | ||
#Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [http://gpmdb.org/data/keyword/25963923 18]. | #Koch H, Busto ME, Kramer K, Médard G, Kuster B, (2015) "Chemical Proteomics Uncovers EPHA2 as a Mechanism of Acquired Resistance to Small Molecule EGFR Kinase Inhibition." <i>J Proteome Res</i> <b>14</b>(6):2617–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25963923 25963923]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00161 10.1021/acs.jproteome.5b00161]; GPMDB: [http://gpmdb.org/data/keyword/25963923 18]. | ||
#Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL, (2015) "Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C." <i>Nat Commun</i> <b>6</b>:7108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25964121 25964121]; doi: [https://dx.doi.org/10.1038/ncomms8108 10.1038/ncomms8108]; GPMDB: [http://gpmdb.org/data/keyword/25964121 2]. | #Watanabe S, Tan D, Lakshminarasimhan M, Washburn MP, Hong EJ, Walz T, Peterson CL, (2015) "Structural analyses of the chromatin remodelling enzymes INO80-C and SWR-C." <i>Nat Commun</i> <b>6</b>:7108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25964121 25964121]; doi: [https://dx.doi.org/10.1038/ncomms8108 10.1038/ncomms8108]; GPMDB: [http://gpmdb.org/data/keyword/25964121 2]. | ||
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#Murphy JP, Stepanova E, Everley RA, Paulo JA, Gygi SP, (2015) "Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>14</b>(9):2454–65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26077900 26077900]; doi: [https://dx.doi.org/10.1074/mcp.M114.045849 10.1074/mcp.M114.045849]; GPMDB: [http://gpmdb.org/data/keyword/26077900 66]. | #Murphy JP, Stepanova E, Everley RA, Paulo JA, Gygi SP, (2015) "Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae." <i>Mol Cell Proteomics</i> <b>14</b>(9):2454–65; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26077900 26077900]; doi: [https://dx.doi.org/10.1074/mcp.M114.045849 10.1074/mcp.M114.045849]; GPMDB: [http://gpmdb.org/data/keyword/26077900 66]. | ||
#Wiśniewski JR, Gizak A, Rakus D, (2015) "Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways." <i>J Proteome Res</i> <b>14</b>(8):3263–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26080680 26080680]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00276 10.1021/acs.jproteome.5b00276]; GPMDB: [http://gpmdb.org/data/keyword/26080680 18]. | #Wiśniewski JR, Gizak A, Rakus D, (2015) "Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways." <i>J Proteome Res</i> <b>14</b>(8):3263–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26080680 26080680]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00276 10.1021/acs.jproteome.5b00276]; GPMDB: [http://gpmdb.org/data/keyword/26080680 18]. | ||
+ | #Yagoub D, Hart-Smith G, Moecking J, Erce MA, Wilkins MR, (2015) "Yeast proteins Gar1p, Nop1p, Npl3p, Nsr1p, and Rps2p are natively methylated and are substrates of the arginine methyltransferase Hmt1p." <i>Proteomics</i> <b>15</b>(18):3209–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26081071 26081071]; doi: [https://dx.doi.org/10.1002/pmic.201500075 10.1002/pmic.201500075]; GPMDB: [http://gpmdb.org/data/keyword/26081071 7]. | ||
#Mui MZ, Zhou Y, Blanchette P, Chughtai N, Knight JF, Gruosso T, Papadakis AI, Huang S, Park M, Gingras AC, Branton PE, (2015) "The Human Adenovirus Type 5 E4orf4 Protein Targets Two Phosphatase Regulators of the Hippo Signaling Pathway." <i>J Virol</i> <b>89</b>(17):8855–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26085163 26085163]; doi: [https://dx.doi.org/10.1128/JVI.03710-14 10.1128/JVI.03710-14]; GPMDB: [http://gpmdb.org/data/keyword/26085163 16]. | #Mui MZ, Zhou Y, Blanchette P, Chughtai N, Knight JF, Gruosso T, Papadakis AI, Huang S, Park M, Gingras AC, Branton PE, (2015) "The Human Adenovirus Type 5 E4orf4 Protein Targets Two Phosphatase Regulators of the Hippo Signaling Pathway." <i>J Virol</i> <b>89</b>(17):8855–70; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26085163 26085163]; doi: [https://dx.doi.org/10.1128/JVI.03710-14 10.1128/JVI.03710-14]; GPMDB: [http://gpmdb.org/data/keyword/26085163 16]. | ||
#Cehofski LJ, Kruse A, Kjærgaard B, Stensballe A, Honoré B, Vorum H, (2015) "Proteins involved in focal adhesion signaling pathways are differentially regulated in experimental branch retinal vein occlusion." <i>Exp Eye Res</i> <b>138</b>:87–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26086079 26086079]; doi: [https://dx.doi.org/10.1016/j.exer.2015.06.011 10.1016/j.exer.2015.06.011]; GPMDB: [http://gpmdb.org/data/keyword/26086079 48]. | #Cehofski LJ, Kruse A, Kjærgaard B, Stensballe A, Honoré B, Vorum H, (2015) "Proteins involved in focal adhesion signaling pathways are differentially regulated in experimental branch retinal vein occlusion." <i>Exp Eye Res</i> <b>138</b>:87–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26086079 26086079]; doi: [https://dx.doi.org/10.1016/j.exer.2015.06.011 10.1016/j.exer.2015.06.011]; GPMDB: [http://gpmdb.org/data/keyword/26086079 48]. | ||
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#Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A, (2015) "Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer." <i>Mol Cell Proteomics</i> <b>14</b>(11):2887–900; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330541 26330541]; doi: [https://dx.doi.org/10.1074/mcp.M115.050484 10.1074/mcp.M115.050484]; GPMDB: [http://gpmdb.org/data/keyword/26330541 29]. | #Wu X, Zahari MS, Renuse S, Nirujogi RS, Kim MS, Manda SS, Stearns V, Gabrielson E, Sukumar S, Pandey A, (2015) "Phosphoproteomic Analysis Identifies Focal Adhesion Kinase 2 (FAK2) as a Potential Therapeutic Target for Tamoxifen Resistance in Breast Cancer." <i>Mol Cell Proteomics</i> <b>14</b>(11):2887–900; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330541 26330541]; doi: [https://dx.doi.org/10.1074/mcp.M115.050484 10.1074/mcp.M115.050484]; GPMDB: [http://gpmdb.org/data/keyword/26330541 29]. | ||
#Duhamel M, Rodet F, Delhem N, Vanden Abeele F, Kobeissy F, Nataf S, Pays L, Desjardins R, Gagnon H, Wisztorski M, Fournier I, Day R, Salzet M, (2015) "Molecular Consequences of Proprotein Convertase 1/3 (PC1/3) Inhibition in Macrophages for Application to Cancer Immunotherapy: A Proteomic Study." <i>Mol Cell Proteomics</i> <b>14</b>(11):2857–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330543 26330543]; doi: [https://dx.doi.org/10.1074/mcp.M115.052480 10.1074/mcp.M115.052480]; GPMDB: [http://gpmdb.org/data/keyword/26330543 18]. | #Duhamel M, Rodet F, Delhem N, Vanden Abeele F, Kobeissy F, Nataf S, Pays L, Desjardins R, Gagnon H, Wisztorski M, Fournier I, Day R, Salzet M, (2015) "Molecular Consequences of Proprotein Convertase 1/3 (PC1/3) Inhibition in Macrophages for Application to Cancer Immunotherapy: A Proteomic Study." <i>Mol Cell Proteomics</i> <b>14</b>(11):2857–77; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26330543 26330543]; doi: [https://dx.doi.org/10.1074/mcp.M115.052480 10.1074/mcp.M115.052480]; GPMDB: [http://gpmdb.org/data/keyword/26330543 18]. | ||
+ | #Liebensteiner MG, Pinkse MW, Nijsse B, Verhaert PD, Tsesmetzis N, Stams AJ, Lomans BP, (2015) "Perchlorate and chlorate reduction by the Crenarchaeon Aeropyrum pernix and two thermophilic Firmicutes." <i>Environ Microbiol Rep</i> <b>7</b>(6):936–45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26332065 26332065]; doi: [https://dx.doi.org/10.1111/1758-2229.12335 10.1111/1758-2229.12335]; GPMDB: [http://gpmdb.org/data/keyword/26332065 12]. | ||
#Lluch-Senar M, Cozzuto L, Cano J, Delgado J, Llórens-Rico V, Pereyre S, Bebear C, Serrano L, (2015) "Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors." <i>PLoS One</i> <b>10</b>(9):e0137354; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26335586 26335586]; doi: [https://dx.doi.org/10.1371/journal.pone.0137354 10.1371/journal.pone.0137354]; GPMDB: [http://gpmdb.org/data/keyword/26335586 25]. | #Lluch-Senar M, Cozzuto L, Cano J, Delgado J, Llórens-Rico V, Pereyre S, Bebear C, Serrano L, (2015) "Comparative "-omics" in Mycoplasma pneumoniae Clinical Isolates Reveals Key Virulence Factors." <i>PLoS One</i> <b>10</b>(9):e0137354; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26335586 26335586]; doi: [https://dx.doi.org/10.1371/journal.pone.0137354 10.1371/journal.pone.0137354]; GPMDB: [http://gpmdb.org/data/keyword/26335586 25]. | ||
#White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | #White CH, Johnston HE, Moesker B, Manousopoulou A, Margolis DM, Richman DD, Spina CA, Garbis SD, Woelk CH, Beliakova-Bethell N, (2015) "Mixed effects of suberoylanilide hydroxamic acid (SAHA) on the host transcriptome and proteome and their implications for HIV reactivation from latency." <i>Antiviral Res</i> <b>123</b>:78–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26343910 26343910]; doi: [https://dx.doi.org/10.1016/j.antiviral.2015.09.002 10.1016/j.antiviral.2015.09.002]; GPMDB: [http://gpmdb.org/data/keyword/26343910 172]. | ||
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#Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | #Liu T, Tian CF, Chen WX, (2015) "Site-Specific Ser/Thr/Tyr Phosphoproteome of Sinorhizobium meliloti at Stationary Phase." <i>PLoS One</i> <b>10</b>(9):e0139143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26401955 26401955]; doi: [https://dx.doi.org/10.1371/journal.pone.0139143 10.1371/journal.pone.0139143]; GPMDB: [http://gpmdb.org/data/keyword/26401955 2]. | ||
#Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | #Li S, Dislich B, Brakebusch CH, Lichtenthaler SF, Brocker T, (2015) "Control of Homeostasis and Dendritic Cell Survival by the GTPase RhoA." <i>J Immunol</i> <b>195</b>(9):4244–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26408665 26408665]; doi: [https://dx.doi.org/10.4049/jimmunol.1500676 10.4049/jimmunol.1500676]; GPMDB: [http://gpmdb.org/data/keyword/26408665 60]. | ||
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+ | #Glatter T, Ahrné E, Schmidt A, (2015) "Comparison of Different Sample Preparation Protocols Reveals Lysis Buffer-Specific Extraction Biases in Gram-Negative Bacteria and Human Cells." <i>J Proteome Res</i> <b>14</b>(11):4472–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26412744 26412744]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00654 10.1021/acs.jproteome.5b00654]; GPMDB: [http://gpmdb.org/data/keyword/26412744 901]. | ||
#Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | #Hadley KC, Rakhit R, Guo H, Sun Y, Jonkman JE, McLaurin J, Hazrati LN, Emili A, Chakrabartty A, (2015) "Determining composition of micron-scale protein deposits in neurodegenerative disease by spatially targeted optical microproteomics." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26418743 26418743]; doi: [https://dx.doi.org/10.7554/eLife.09579 10.7554/eLife.09579]; GPMDB: [http://gpmdb.org/data/keyword/26418743 12]. | ||
#Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | #Gallart-Palau X, Serra A, Wong AS, Sandin S, Lai MK, Chen CP, Kon OL, Sze SK, (2015) "Extracellular vesicles are rapidly purified from human plasma by PRotein Organic Solvent PRecipitation (PROSPR)." <i>Sci Rep</i> <b>5</b>:14664; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26419333 26419333]; doi: [https://dx.doi.org/10.1038/srep14664 10.1038/srep14664]; GPMDB: [http://gpmdb.org/data/keyword/26419333 172]. | ||
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#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | ||
#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | ||
+ | #Hintermair C, Voß K, Forné I, Heidemann M, Flatley A, Kremmer E, Imhof A, Eick D, (2016) "Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression." <i>Sci Rep</i> <b>6</b>:27401; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27264542 27264542]; doi: [https://dx.doi.org/10.1038/srep27401 10.1038/srep27401]; GPMDB: [http://gpmdb.org/data/keyword/27264542 63]. | ||
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i> <b>7</b>(28):43868–43893; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i> <b>7</b>(28):43868–43893; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | ||
#Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | #Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | ||
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#Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | #Naboulsi W, Bracht T, Megger DA, Reis H, Ahrens M, Turewicz M, Eisenacher M, Tautges S, Canbay AE, Meyer HE, Weber F, Baba HA, Sitek B, (2016) "Quantitative proteome analysis reveals the correlation between endocytosis-associated proteins and hepatocellular carcinoma dedifferentiation." <i>Biochim Biophys Acta</i> <b>1864</b>(11):1579–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27519163 27519163]; doi: [https://dx.doi.org/10.1016/j.bbapap.2016.08.005 10.1016/j.bbapap.2016.08.005]; GPMDB: [http://gpmdb.org/data/keyword/27519163 36]. | ||
#Rasmussen MH, Lyskjær I, Jersie-Christensen RR, Tarpgaard LS, Primdal-Bengtson B, Nielsen MM, Pedersen JS, Hansen TP, Hansen F, Olsen JV, Pfeiffer P, Ørntoft TF, Andersen CL, (2016) "miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells." <i>Nat Commun</i> <b>7</b>:12436; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27526785 27526785]; doi: [https://dx.doi.org/10.1038/ncomms12436 10.1038/ncomms12436]; GPMDB: [http://gpmdb.org/data/keyword/27526785 24]. | #Rasmussen MH, Lyskjær I, Jersie-Christensen RR, Tarpgaard LS, Primdal-Bengtson B, Nielsen MM, Pedersen JS, Hansen TP, Hansen F, Olsen JV, Pfeiffer P, Ørntoft TF, Andersen CL, (2016) "miR-625-3p regulates oxaliplatin resistance by targeting MAP2K6-p38 signalling in human colorectal adenocarcinoma cells." <i>Nat Commun</i> <b>7</b>:12436; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27526785 27526785]; doi: [https://dx.doi.org/10.1038/ncomms12436 10.1038/ncomms12436]; GPMDB: [http://gpmdb.org/data/keyword/27526785 24]. | ||
+ | #Chatterjee S, Stupp GS, Park SK, Ducom JC, Yates JR 3rd, Su AI, Wolan DW, (2016) "A comprehensive and scalable database search system for metaproteomics." <i>BMC Genomics</i> <b>17</b>(1):642; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27528457 27528457]; doi: [https://dx.doi.org/10.1186/s12864-016-2855-3 10.1186/s12864-016-2855-3]; GPMDB: [http://gpmdb.org/data/keyword/27528457 28]. | ||
#Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases." <i>J Biol Chem</i> <b>291</b>(41):21571–21583; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27531744 27531744]; doi: [https://dx.doi.org/10.1074/jbc.M116.748897 10.1074/jbc.M116.748897]; GPMDB: [http://gpmdb.org/data/keyword/27531744 6]. | #Liu L, Phua YW, Lee RS, Ma X, Jenkins Y, Novy K, Humphrey ES, Chan H, Shearer R, Ong PC, Dai W, Saunders DN, Lucet IS, Daly RJ, (2016) "Homo- and Heterotypic Association Regulates Signaling by the SgK269/PEAK1 and SgK223 Pseudokinases." <i>J Biol Chem</i> <b>291</b>(41):21571–21583; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27531744 27531744]; doi: [https://dx.doi.org/10.1074/jbc.M116.748897 10.1074/jbc.M116.748897]; GPMDB: [http://gpmdb.org/data/keyword/27531744 6]. | ||
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#Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | #Mauri M, Kirchner M, Aharoni R, Ciolli Mattioli C, van den Bruck D, Gutkovitch N, Modepalli V, Selbach M, Moran Y, Chekulaeva M, (2016) "Conservation of miRNA-mediated silencing mechanisms across 600 million years of animal evolution." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27604873 27604873]; doi: [https://dx.doi.org/10.1093/nar/gkw792 10.1093/nar/gkw792]; GPMDB: [http://gpmdb.org/data/keyword/27604873 35]. | ||
#Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | #Lee J, McKinney KQ, Pavlopoulos AJ, Han MH, Kim SH, Kim HJ, Hwang S, (2016) "Exosomal proteome analysis of cerebrospinal fluid detects biosignatures of neuromyelitis optica and multiple sclerosis." <i>Clin Chim Acta</i> <b>462</b>:118–126; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27609124 27609124]; doi: [https://dx.doi.org/10.1016/j.cca.2016.09.001 10.1016/j.cca.2016.09.001]; GPMDB: [http://gpmdb.org/data/keyword/27609124 24]. | ||
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#Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | #Subramanian S, Souleimanov A, Smith DL, (2016) "Proteomic Studies on the Effects of Lipo-Chitooligosaccharide and Thuricin 17 under Unstressed and Salt Stressed Conditions in Arabidopsis thaliana." <i>Front Plant Sci</i> <b>7</b>:1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27625672 27625672]; doi: [https://dx.doi.org/10.3389/fpls.2016.01314 10.3389/fpls.2016.01314]; GPMDB: [http://gpmdb.org/data/keyword/27625672 36]. | ||
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+ | #Smirnov A, Förstner KU, Holmqvist E, Otto A, Günster R, Becher D, Reinhardt R, Vogel J, (2016) "Grad-seq guides the discovery of ProQ as a major small RNA-binding protein." <i>Proc Natl Acad Sci U S A</i> <b>113</b>(41):11591–11596; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27671629 27671629]; doi: [https://dx.doi.org/10.1073/pnas.1609981113 10.1073/pnas.1609981113]; GPMDB: [http://gpmdb.org/data/keyword/27671629 200]. | ||
#Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i> <b>515</b>:33–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 10]. | #Lyon SM, Mayampurath A, Rogers MR, Wolfgeher DJ, Fisher SM, Volchenboum SL, He TC, Reid RR, (2016) "A method for whole protein isolation from human cranial bone." <i>Anal Biochem</i> <b>515</b>:33–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27677936 27677936]; doi: [https://dx.doi.org/10.1016/j.ab.2016.09.021 10.1016/j.ab.2016.09.021]; GPMDB: [http://gpmdb.org/data/keyword/27677936 10]. | ||
#Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i> <b>115</b>(9):1078–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 8]. | #Larkin SE, Johnston HE, Jackson TR, Jamieson DG, Roumeliotis TI, Mockridge CI, Michael A, Manousopoulou A, Papachristou EK, Brown MD, Clarke NW, Pandha H, Aukim-Hastie CL, Cragg MS, Garbis SD, Townsend PA, (2016) "Detection of candidate biomarkers of prostate cancer progression in serum: a depletion-free 3D LC/MS quantitative proteomics pilot study." <i>Br J Cancer</i> <b>115</b>(9):1078–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27685442 27685442]; doi: [https://dx.doi.org/10.1038/bjc.2016.291 10.1038/bjc.2016.291]; GPMDB: [http://gpmdb.org/data/keyword/27685442 8]. | ||
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#Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | #Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | ||
#Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | #Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | ||
+ | #Yu P, Hahne H, Wilhelm M, Kuster B, (2017) "Ethylene glycol improves electrospray ionization efficiency in bottom-up proteomics." <i>Anal Bioanal Chem</i> <b>409</b>(4):1049–1057; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27766361 27766361]; doi: [https://dx.doi.org/10.1007/s00216-016-0023-x 10.1007/s00216-016-0023-x]; GPMDB: [http://gpmdb.org/data/keyword/27766361 147]. | ||
+ | #Isogai T, van der Kammen R, Bleijerveld OB, Goerdayal SS, Argenzio E, Altelaar AF, Innocenti M, (2016) "Quantitative Proteomics Illuminates a Functional Interaction between mDia2 and the Proteasome." <i>J Proteome Res</i> <b>15</b>(12):4624–4637; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27769112 27769112]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00718 10.1021/acs.jproteome.6b00718]; GPMDB: [http://gpmdb.org/data/keyword/27769112 44]. | ||
#Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | ||
#Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | #Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | ||
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#Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | #Sheppard C, Blombach F, Belsom A, Schulz S, Daviter T, Smollett K, Mahieu E, Erdmann S, Tinnefeld P, Garrett R, Grohmann D, Rappsilber J, Werner F, (2016) "Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP." <i>Nat Commun</i> <b>7</b>:13595; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27882920 27882920]; doi: [https://dx.doi.org/10.1038/ncomms13595 10.1038/ncomms13595]; GPMDB: [http://gpmdb.org/data/keyword/27882920 9]. | ||
#Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [http://gpmdb.org/data/keyword/27894104 898]. | #Hurwitz SN, Rider MA, Bundy JL, Liu X, Singh RK, Meckes DG Jr, (2016) "Proteomic profiling of NCI-60 extracellular vesicles uncovers common protein cargo and cancer type-specific biomarkers." <i>Oncotarget</i> <b>7</b>(52):86999–87015; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27894104 27894104]; doi: [https://dx.doi.org/10.18632/oncotarget.13569 10.18632/oncotarget.13569]; GPMDB: [http://gpmdb.org/data/keyword/27894104 898]. | ||
+ | #Gonneaud A, Jones C, Turgeon N, Lévesque D, Asselin C, Boudreau F, Boisvert FM, (2016) "A SILAC-Based Method for Quantitative Proteomic Analysis of Intestinal Organoids." <i>Sci Rep</i> <b>6</b>:38195; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27901089 27901089]; doi: [https://dx.doi.org/10.1038/srep38195 10.1038/srep38195]; GPMDB: [http://gpmdb.org/data/keyword/27901089 38]. | ||
#Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M, (2016) "Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry." <i>PLoS One</i> <b>11</b>(12):e0167138; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27907059 27907059]; doi: [https://dx.doi.org/10.1371/journal.pone.0167138 10.1371/journal.pone.0167138]; GPMDB: [http://gpmdb.org/data/keyword/27907059 3]. | #Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M, (2016) "Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry." <i>PLoS One</i> <b>11</b>(12):e0167138; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27907059 27907059]; doi: [https://dx.doi.org/10.1371/journal.pone.0167138 10.1371/journal.pone.0167138]; GPMDB: [http://gpmdb.org/data/keyword/27907059 3]. | ||
#Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | #Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT, (2016) "A proteomic approach to analyse the aspirin-mediated lysine acetylome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27913581 27913581]; doi: [https://dx.doi.org/10.1074/mcp.O116.065219 10.1074/mcp.O116.065219]; GPMDB: [http://gpmdb.org/data/keyword/27913581 40]. | ||
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#Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | #Godfrey M, Touati SA, Kataria M, Jones A, Snijders AP, Uhlmann F, (2017) "PP2A<sup>Cdc55</sup> Phosphatase Imposes Ordered Cell-Cycle Phosphorylation by Opposing Threonine Phosphorylation." <i>Mol Cell</i> <b>65</b>(3):393–402.e3; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28132839 28132839]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.12.018 10.1016/j.molcel.2016.12.018]; GPMDB: [http://gpmdb.org/data/keyword/28132839 120]. | ||
#Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | #Zolg DP, Wilhelm M, Schnatbaum K, Zerweck J, Knaute T, Delanghe B, Bailey DJ, Gessulat S, Ehrlich HC, Weininger M, Yu P, Schlegl J, Kramer K, Schmidt T, Kusebauch U, Deutsch EW, Aebersold R, Moritz RL, Wenschuh H, Moehring T, Aiche S, Huhmer A, Reimer U, Kuster B, (2017) "Building ProteomeTools based on a complete synthetic human proteome." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28135259 28135259]; doi: [https://dx.doi.org/10.1038/nmeth.4153 10.1038/nmeth.4153]; GPMDB: [http://gpmdb.org/data/keyword/28135259 1095]. | ||
+ | #Abe Y, Nagano M, Tada A, Adachi J, Tomonaga T, (2017) "Deep Phosphotyrosine Proteomics by Optimization of Phosphotyrosine Enrichment and MS/MS Parameters." <i>J Proteome Res</i> <b>16</b>(2):1077–1086; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28152594 28152594]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00576 10.1021/acs.jproteome.6b00576]; GPMDB: [http://gpmdb.org/data/keyword/28152594 41]. | ||
#Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | #Jung SY, Choi JM, Rousseaux MW, Malovannaya A, Kim JJ, Kutzera J, Wang Y, Huang Y, Zhu W, Maity S, Zoghbi HY, Qin J, (2017) "An anatomically resolved mouse brain proteome reveals Parkinson disease-relevant pathways." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28153913 28153913]; doi: [https://dx.doi.org/10.1074/mcp.M116.061440 10.1074/mcp.M116.061440]; GPMDB: [http://gpmdb.org/data/keyword/28153913 610]. | ||
#Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL, (2017) "Homer1a drives homeostatic scaling-down of excitatory synapses during sleep." <i>Science</i> <b>355</b>(6324):511–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28154077 28154077]; doi: [https://dx.doi.org/10.1126/science.aai8355 10.1126/science.aai8355]; GPMDB: [http://gpmdb.org/data/keyword/28154077 25]. | #Diering GH, Nirujogi RS, Roth RH, Worley PF, Pandey A, Huganir RL, (2017) "Homer1a drives homeostatic scaling-down of excitatory synapses during sleep." <i>Science</i> <b>355</b>(6324):511–515; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28154077 28154077]; doi: [https://dx.doi.org/10.1126/science.aai8355 10.1126/science.aai8355]; GPMDB: [http://gpmdb.org/data/keyword/28154077 25]. | ||
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#Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | #Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | ||
#Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A, (2017) "Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28210003 28210003]; doi: [https://dx.doi.org/10.1038/leu.2017.61 10.1038/leu.2017.61]; GPMDB: [http://gpmdb.org/data/keyword/28210003 20]. | #Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A, (2017) "Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28210003 28210003]; doi: [https://dx.doi.org/10.1038/leu.2017.61 10.1038/leu.2017.61]; GPMDB: [http://gpmdb.org/data/keyword/28210003 20]. | ||
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#Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, (2017) "Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28217993 28217993]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00645 10.1021/acs.jproteome.6b00645]; GPMDB: [http://gpmdb.org/data/keyword/28217993 54]. | #Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, (2017) "Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28217993 28217993]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00645 10.1021/acs.jproteome.6b00645]; GPMDB: [http://gpmdb.org/data/keyword/28217993 54]. | ||
#Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | #Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | ||
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#Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | #Kliza K, Taumer C, Pinzuti I, Franz-Wachtel M, Kunzelmann S, Stieglitz B, Macek B, Husnjak K, (2017) "Internally tagged ubiquitin: a tool to identify linear polyubiquitin-modified proteins by mass spectrometry." <i>Nat Methods</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28319114 28319114]; doi: [https://dx.doi.org/10.1038/nmeth.4228 10.1038/nmeth.4228]; GPMDB: [http://gpmdb.org/data/keyword/28319114 32]. | ||
+ | #Khodadoust MS, Olsson N, Wagar LE, Haabeth OA, Chen B, Swaminathan K, Rawson K, Liu CL, Steiner D, Lund P, Rao S, Zhang L, Marceau C, Stehr H, Newman AM, Czerwinski DK, Carlton VE, Moorhead M, Faham M, Kohrt HE, Carette J, Green MR, Davis MM, Levy R, Elias JE, Alizadeh AA, (2017) "Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens." <i>Nature</i> <b>543</b>(7647):723–727; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28329770 28329770]; doi: [https://dx.doi.org/10.1038/nature21433 10.1038/nature21433]; GPMDB: [http://gpmdb.org/data/keyword/28329770 147]. | ||
#Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali F, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U, (2017) "Quantitative tyrosine phosphoproteomics of EGFR tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28331001 28331001]; doi: [https://dx.doi.org/10.1074/mcp.M117.067439 10.1074/mcp.M117.067439]; GPMDB: [http://gpmdb.org/data/keyword/28331001 41]. | #Zhang X, Maity T, Kashyap MK, Bansal M, Venugopalan A, Singh S, Awasthi S, Marimuthu A, Jacob HK, Belkina N, Pitts S, Cultraro CM, Gao S, Kirkali F, Biswas R, Chaerkady R, Califano A, Pandey A, Guha U, (2017) "Quantitative tyrosine phosphoproteomics of EGFR tyrosine kinase inhibitor-treated lung adenocarcinoma cells reveals potential novel biomarkers of therapeutic response." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28331001 28331001]; doi: [https://dx.doi.org/10.1074/mcp.M117.067439 10.1074/mcp.M117.067439]; GPMDB: [http://gpmdb.org/data/keyword/28331001 41]. | ||
#Nathan A, Reinhardt P, Kruspe D, Jörß T, Groth M, Nolte H, Habenicht A, Herrmann J, Holschbach V, Toth B, Krüger M, Wang ZQ, Platzer M, Englert C, (2017) "The Wilms tumor protein Wt1 contributes to female fertility by regulating oviductal proteostasis." <i>Hum Mol Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334862 28334862]; doi: [https://dx.doi.org/10.1093/hmg/ddx075 10.1093/hmg/ddx075]; GPMDB: [http://gpmdb.org/data/keyword/28334862 48]. | #Nathan A, Reinhardt P, Kruspe D, Jörß T, Groth M, Nolte H, Habenicht A, Herrmann J, Holschbach V, Toth B, Krüger M, Wang ZQ, Platzer M, Englert C, (2017) "The Wilms tumor protein Wt1 contributes to female fertility by regulating oviductal proteostasis." <i>Hum Mol Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28334862 28334862]; doi: [https://dx.doi.org/10.1093/hmg/ddx075 10.1093/hmg/ddx075]; GPMDB: [http://gpmdb.org/data/keyword/28334862 48]. | ||
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#Casanova R, Xia D, Rulle U, Nanni P, Grossmann J, Vrugt B, Wettstein R, Ballester R, Astolfo A, Weder W, Moch H, Stampanoni M, Beck AH, Soltermann A, (2017) "Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness." <i>Cancer Res</i> <b>77</b>(10):2585–2593; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28364001 28364001]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2363 10.1158/0008-5472.CAN-16-2363]; GPMDB: [http://gpmdb.org/data/keyword/28364001 49]. | #Casanova R, Xia D, Rulle U, Nanni P, Grossmann J, Vrugt B, Wettstein R, Ballester R, Astolfo A, Weder W, Moch H, Stampanoni M, Beck AH, Soltermann A, (2017) "Morphoproteomic Characterization of Lung Squamous Cell Carcinoma Fragmentation, a Histological Marker of Increased Tumor Invasiveness." <i>Cancer Res</i> <b>77</b>(10):2585–2593; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28364001 28364001]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-16-2363 10.1158/0008-5472.CAN-16-2363]; GPMDB: [http://gpmdb.org/data/keyword/28364001 49]. | ||
#Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA, (2017) "ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes." <i>Nat Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368372 28368372]; doi: [https://dx.doi.org/10.1038/ncb3499 10.1038/ncb3499]; GPMDB: [http://gpmdb.org/data/keyword/28368372 146]. | #Chatzinikolaou G, Apostolou Z, Aid-Pavlidis T, Ioannidou A, Karakasilioti I, Papadopoulos GL, Aivaliotis M, Tsekrekou M, Strouboulis J, Kosteas T, Garinis GA, (2017) "ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes." <i>Nat Cell Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368372 28368372]; doi: [https://dx.doi.org/10.1038/ncb3499 10.1038/ncb3499]; GPMDB: [http://gpmdb.org/data/keyword/28368372 146]. | ||
+ | #Schaible B, Rodriguez J, Garcia A, von Kriegsheim A, McClean S, Hickey C, Keogh CE, Brown E, Schaffer K, Broquet A, Taylor CT, (2017) "Hypoxia Reduces the Pathogenicity of Pseudomonas aeruginosa by Decreasing the Expression of Multiple Virulence Factors." <i>J Infect Dis</i> <b>215</b>(9):1459–1467; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28368464 28368464]; doi: [https://dx.doi.org/10.1093/infdis/jix139 10.1093/infdis/jix139]; GPMDB: [http://gpmdb.org/data/keyword/28368464 18]. | ||
#Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A, (2017) "Proteomic analysis of regulatory T cells reveals the importance of Themis1 in the control of their suppressive function." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373295 28373295]; doi: [https://dx.doi.org/10.1074/mcp.M116.062745 10.1074/mcp.M116.062745]; GPMDB: [http://gpmdb.org/data/keyword/28373295 26]. | #Duguet F, Locard-Paulet M, Marcellin M, Chaoui K, Bernard I, Andreoletti O, Lesourne R, Burlet-Schiltz O, Gonzalez de Peredo A, Saoudi A, (2017) "Proteomic analysis of regulatory T cells reveals the importance of Themis1 in the control of their suppressive function." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373295 28373295]; doi: [https://dx.doi.org/10.1074/mcp.M116.062745 10.1074/mcp.M116.062745]; GPMDB: [http://gpmdb.org/data/keyword/28373295 26]. | ||
#Namuduri AV, Heras G, Mi J, Cacciani N, Hörnaeus K, Konzer A, Bergström Lind S, Larsson L, Gastaldello S, (2017) "A proteomic approach to identify alterations in the SUMO network during controlled mechanical ventilation in rat diaphragm muscle." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373296 28373296]; doi: [https://dx.doi.org/10.1074/mcp.M116.066159 10.1074/mcp.M116.066159]; GPMDB: [http://gpmdb.org/data/keyword/28373296 80]. | #Namuduri AV, Heras G, Mi J, Cacciani N, Hörnaeus K, Konzer A, Bergström Lind S, Larsson L, Gastaldello S, (2017) "A proteomic approach to identify alterations in the SUMO network during controlled mechanical ventilation in rat diaphragm muscle." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28373296 28373296]; doi: [https://dx.doi.org/10.1074/mcp.M116.066159 10.1074/mcp.M116.066159]; GPMDB: [http://gpmdb.org/data/keyword/28373296 80]. | ||
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#Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [http://gpmdb.org/data/keyword/28388408 3]. | ||
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+ | #Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M, (2017) "A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29128334 29128334]; doi: [https://dx.doi.org/10.1016/j.cels.2017.10.010 10.1016/j.cels.2017.10.010]; GPMDB: [http://gpmdb.org/data/keyword/29128334 109]. | ||
+ | #García-Berrocoso T, Llombart V, Colàs-Campàs L, Hainard A, Licker V, Penalba A, Ramiro L, Simats A, Bustamante A, Martínez-Saez E, Canals F, Sanchez JC, Montaner J, (2017) "Single Cell Immuno-laser Microdissection Coupled to Label-free Proteomics to Reveal the Proteotypes of Human Brain Cells After Ischemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133510 29133510]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000419 10.1074/mcp.RA117.000419]; GPMDB: [http://gpmdb.org/data/keyword/29133510 102]. | ||
+ | #Negretti NM, Gourley CR, Clair G, Adkins JN, Konkel ME, (2017) "The food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species." <i>Sci Rep</i> <b>7</b>(1):15455; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133896 29133896]; doi: [https://dx.doi.org/10.1038/s41598-017-15379-5 10.1038/s41598-017-15379-5]; GPMDB: [http://gpmdb.org/data/keyword/29133896 8]. | ||
+ | #Doll S, Dreßen M, Geyer PE, Itzhak DN, Braun C, Doppler SA, Meier F, Deutsch MA, Lahm H, Lange R, Krane M, Mann M, (2017) "Region and cell-type resolved quantitative proteomic map of the human heart." <i>Nat Commun</i> <b>8</b>(1):1469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29133944 29133944]; doi: [https://dx.doi.org/10.1038/s41467-017-01747-2 10.1038/s41467-017-01747-2]; GPMDB: [http://gpmdb.org/data/keyword/29133944 159]. | ||
+ | #Anders F, Liu A, Mann C, Teister J, Lauzi J, Thanos S, Grus FH, Pfeiffer N, Prokosch V, (2017) "The Small Heat Shock Protein α-Crystallin B Shows Neuroprotective Properties in a Glaucoma Animal Model." <i>Int J Mol Sci</i> <b>18</b>(11):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29135941 29135941]; doi: [https://dx.doi.org/10.3390/ijms18112418 10.3390/ijms18112418]; GPMDB: [http://gpmdb.org/data/keyword/29135941 8]. | ||
+ | #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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/29141914 121]. | ||
+ | #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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/29145658 4]. | ||
+ | #Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS, (2017) "Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29155090 29155090]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.008 10.1016/j.jprot.2017.11.008]; GPMDB: [http://gpmdb.org/data/keyword/29155090 21]. | ||
+ | #Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O, Nyström A, Kern JS, (2017) "Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas." <i>Matrix Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29158163 29158163]; doi: [https://dx.doi.org/10.1016/j.matbio.2017.11.004 10.1016/j.matbio.2017.11.004]; GPMDB: [http://gpmdb.org/data/keyword/29158163 24]. | ||
+ | #Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM, (2017) "Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29164889 29164889]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00329 10.1021/acs.jproteome.7b00329]; GPMDB: [http://gpmdb.org/data/keyword/29164889 18]. | ||
+ | #Hosp F, Gutiérrez-Ángel S, Schaefer MH, Cox J, Meissner F, Hipp MS, Hartl FU, Klein R, Dudanova I, Mann M, (2017) "Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function." <i>Cell Rep</i> <b>21</b>(8):2291–2303; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29166617 29166617]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.10.097 10.1016/j.celrep.2017.10.097]; GPMDB: [http://gpmdb.org/data/keyword/29166617 196]. | ||
+ | #Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A, (2017) "Global landscape of cell envelope protein complexes in Escherichia coli." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29176613 29176613]; doi: [https://dx.doi.org/10.1038/nbt.4024 10.1038/nbt.4024]; GPMDB: [http://gpmdb.org/data/keyword/29176613 2972]. | ||
+ | #Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV, (2018) "Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics." <i>J Proteome Res</i> <b>17</b>(1):727–738; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183128 29183128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00602 10.1021/acs.jproteome.7b00602]; GPMDB: [http://gpmdb.org/data/keyword/29183128 107]. | ||
+ | #Winter DL, Hart-Smith G, Wilkins MR, (2018) "Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification." <i>J Mol Biol</i> <b>430</b>(1):102–118; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183786 29183786]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.11.009 10.1016/j.jmb.2017.11.009]; GPMDB: [http://gpmdb.org/data/keyword/29183786 18]. | ||
+ | #Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | ||
+ | #Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | ||
+ | #Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | ||
+ | #Herzog R, Boehm M, Unterwurzacher M, Wagner A, Parapatics K, Majek P, Mueller AC, Lichtenauer A, Bennett KL, Alper SL, Vychytil A, Aufricht C, Kratochwill K, (2017) "Effects of alanyl-glutamine treatment on the peritoneal dialysis effluent proteome reveal pathomechanism-associated molecular signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208752 29208752]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000186 10.1074/mcp.RA117.000186]; GPMDB: [http://gpmdb.org/data/keyword/29208752 10]. | ||
+ | #Wierer M, Prestel M, Schiller H, Yan G, Schaab C, Azghandi S, Werner J, Kessler T, Malik R, Murgia M, Aherrahrou Z, Schunkert H, Dichgans M, Mann M, (2017) "Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208753 29208753]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000315 10.1074/mcp.RA117.000315]; GPMDB: [http://gpmdb.org/data/keyword/29208753 156]. | ||
+ | #Stachowicz A, Siudut J, Suski M, Olszanecki R, Korbut R, Undas A, Wiśniewski JR, (2017) "Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism." <i>Clin Proteomics</i> <b>14</b>:38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29209155 29209155]; doi: [https://dx.doi.org/10.1186/s12014-017-9173-x 10.1186/s12014-017-9173-x]; GPMDB: [http://gpmdb.org/data/keyword/29209155 36]. | ||
+ | #Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY, (2017) "MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29215871 29215871]; doi: [https://dx.doi.org/10.1021/acs.analchem.7b03544 10.1021/acs.analchem.7b03544]; GPMDB: [http://gpmdb.org/data/keyword/29215871 3]. | ||
+ | #Sobocińska J, Roszczenko-Jasińska P, Zaręba-Kozioł M, Hromada-Judycka A, Matveichuk OV, Traczyk G, Łukasiuk K, Kwiatkowska K, (2017) "LPS upregulates palmitoylated enzymes of the phosphatidylinositol cycle. An insight from proteomic studies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29217618 29217618]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000050 10.1074/mcp.RA117.000050]; GPMDB: [http://gpmdb.org/data/keyword/29217618 12]. | ||
+ | #Holthoff ER, Byrum SD, Mackintosh SG, Kelly T, Tackett AJ, Quick CM, Post SR, (2017) "Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1." <i>Clin Proteomics</i> <b>14</b>:40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29225558 29225558]; doi: [https://dx.doi.org/10.1186/s12014-017-9175-8 10.1186/s12014-017-9175-8]; GPMDB: [http://gpmdb.org/data/keyword/29225558 414]. | ||
+ | #Stewart NA, Gerlach RF, Gowland RL, Gron KJ, Montgomery J, (2017) "Sex determination of human remains from peptides in tooth enamel." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(52):13649–13654; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29229823 29229823]; doi: [https://dx.doi.org/10.1073/pnas.1714926115 10.1073/pnas.1714926115]; GPMDB: [http://gpmdb.org/data/keyword/29229823 13]. | ||
+ | #Bizzotto S, Uzquiano A, Dingli F, Ershov D, Houllier A, Arras G, Richards M, Loew D, Minc N, Croquelois A, Houdusse A, Francis F, (2017) "Eml1 loss impairs apical progenitor spindle length and soma shape in the developing cerebral cortex." <i>Sci Rep</i> <b>7</b>(1):17308; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29229923 29229923]; doi: [https://dx.doi.org/10.1038/s41598-017-15253-4 10.1038/s41598-017-15253-4]; GPMDB: [http://gpmdb.org/data/keyword/29229923 28]. | ||
+ | #Alli-Shaik A, Wee S, Lim LHK, Gunaratne J, (2017) "Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells." <i>Breast Cancer Res</i> <b>19</b>(1):132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29233185 29233185]; doi: [https://dx.doi.org/10.1186/s13058-017-0924-4 10.1186/s13058-017-0924-4]; GPMDB: [http://gpmdb.org/data/keyword/29233185 263]. | ||
+ | #Chong C, Marino F, Pak HS, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M, (2017) "High-throughput and sensitive immunopeptidomics platform reveals profound IFNγ-mediated remodeling of the HLA ligandome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29242379 29242379]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000383 10.1074/mcp.TIR117.000383]; GPMDB: [http://gpmdb.org/data/keyword/29242379 121]. | ||
+ | #Müller AK, Föll M, Heckelmann B, Kiefer S, Werner M, Schilling O, Biniossek ML, Jilg CA, Drendel V, (2017) "Proteomic Characterization of Prostate Cancer to Distinguish Nonmetastasizing and Metastasizing Primary Tumors and Lymph Node Metastases." <i>Neoplasia</i> <b>20</b>(2):140–151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29248718 29248718]; doi: [https://dx.doi.org/10.1016/j.neo.2017.10.009 10.1016/j.neo.2017.10.009]; GPMDB: [http://gpmdb.org/data/keyword/29248718 15]. | ||
+ | #Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [http://gpmdb.org/data/keyword/29251727 33]. | ||
+ | #Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [http://gpmdb.org/data/keyword/29270287 12]. | ||
+ | #Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | ||
+ | #Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 5]. |
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 Jan. 22, 2018.