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==Data from publications== | ==Data from publications== | ||
- | The following is a 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 July | + | The following is a 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 July 17, 2016. |
#Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | #Speer CA, Whitmire WM, (1989) "Shedding of the immunodominant P20 surface antigen of Eimeria bovis sporozoites." <i>Infect Immun</i> <b>57</b>(3):999–1001; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2645217 2645217]; GPMDB: [http://gpmdb.org/data/keyword/2645217 66]. | ||
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#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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/25086240 44]. | ||
#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: [http://gpmdb.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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/25096996 11]. | ||
#Zhang B, Pirmoradian M, Chernobrovkin A, Zubarev RA, (2014) "DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry." <i>Mol Cell Proteomics</i> <b>13</b>(11):3211–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25100859 25100859]; doi: [https://dx.doi.org/10.1074/mcp.O114.038877 10.1074/mcp.O114.038877]; GPMDB: [http://gpmdb.org/data/keyword/25100859 7]. | #Zhang B, Pirmoradian M, Chernobrovkin A, Zubarev RA, (2014) "DeMix workflow for efficient identification of cofragmented peptides in high resolution data-dependent tandem mass spectrometry." <i>Mol Cell Proteomics</i> <b>13</b>(11):3211–23; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25100859 25100859]; doi: [https://dx.doi.org/10.1074/mcp.O114.038877 10.1074/mcp.O114.038877]; GPMDB: [http://gpmdb.org/data/keyword/25100859 7]. | ||
#Wallin MT, Oh U, Nyalwidhe J, Semmes J, Kislinger T, Coffman P, Kurtzke JF, Jacobson S, (2015) "Serum proteomic analysis of a pre-symptomatic multiple sclerosis cohort." <i>Eur J Neurol</i> <b>22</b>(3):591–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25104396 25104396]; doi: [https://dx.doi.org/10.1111/ene.12534 10.1111/ene.12534]; GPMDB: [http://gpmdb.org/data/keyword/25104396 104]. | #Wallin MT, Oh U, Nyalwidhe J, Semmes J, Kislinger T, Coffman P, Kurtzke JF, Jacobson S, (2015) "Serum proteomic analysis of a pre-symptomatic multiple sclerosis cohort." <i>Eur J Neurol</i> <b>22</b>(3):591–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25104396 25104396]; doi: [https://dx.doi.org/10.1111/ene.12534 10.1111/ene.12534]; GPMDB: [http://gpmdb.org/data/keyword/25104396 104]. | ||
Line 710: | Line 711: | ||
#Shin J, Kim HJ, Kim G, Song M, Woo SJ, Lee ST, Kim H, Lee C, (2014) "Discovery of melanotransferrin as a serological marker of colorectal cancer by secretome analysis and quantitative proteomics." <i>J Proteome Res</i> <b>13</b>(11):4919–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25216327 25216327]; doi: [https://dx.doi.org/10.1021/pr500790f 10.1021/pr500790f]; GPMDB: [http://gpmdb.org/data/keyword/25216327 34]. | #Shin J, Kim HJ, Kim G, Song M, Woo SJ, Lee ST, Kim H, Lee C, (2014) "Discovery of melanotransferrin as a serological marker of colorectal cancer by secretome analysis and quantitative proteomics." <i>J Proteome Res</i> <b>13</b>(11):4919–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25216327 25216327]; doi: [https://dx.doi.org/10.1021/pr500790f 10.1021/pr500790f]; GPMDB: [http://gpmdb.org/data/keyword/25216327 34]. | ||
#Hendriks IA, D'Souza RC, Yang B, Verlaan-de Vries M, Mann M, Vertegaal AC, (2014) "Uncovering global SUMOylation signaling networks in a site-specific manner." <i>Nat Struct Mol Biol</i> <b>21</b>(10):927–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25218447 25218447]; doi: [https://dx.doi.org/10.1038/nsmb.2890 10.1038/nsmb.2890]; GPMDB: [http://gpmdb.org/data/keyword/25218447 32]. | #Hendriks IA, D'Souza RC, Yang B, Verlaan-de Vries M, Mann M, Vertegaal AC, (2014) "Uncovering global SUMOylation signaling networks in a site-specific manner." <i>Nat Struct Mol Biol</i> <b>21</b>(10):927–36; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25218447 25218447]; doi: [https://dx.doi.org/10.1038/nsmb.2890 10.1038/nsmb.2890]; GPMDB: [http://gpmdb.org/data/keyword/25218447 32]. | ||
+ | #Wiese H, Gelis L, Wiese S, Reichenbach C, Jovancevic N, Osterloh M, Meyer HE, Neuhaus EM, Hatt HH, Radziwill G, Warscheid B, (2015) "Quantitative phosphoproteomics reveals the protein tyrosine kinase Pyk2 as a central effector of olfactory receptor signaling in prostate cancer cells." <i>Biochim Biophys Acta</i> <b>1854</b>(6):632–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25219547 25219547]; doi: [https://dx.doi.org/10.1016/j.bbapap.2014.09.002 10.1016/j.bbapap.2014.09.002]; GPMDB: [http://gpmdb.org/data/keyword/25219547 191]. | ||
#Negroni L, Taouji S, Arma D, Pallares-Lupon N, Leong K, Beausang LA, Latterich M, Bossé R, Balabaud C, Schmitter JM, Bioulac-Sage P, Zucman-Rossi J, Rosenbaum J, Chevet E, (2014) "Integrative quantitative proteomics unveils proteostasis imbalance in human hepatocellular carcinoma developed on nonfibrotic livers." <i>Mol Cell Proteomics</i> <b>13</b>(12):3473–83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225353 25225353]; doi: [https://dx.doi.org/10.1074/mcp.M114.043174 10.1074/mcp.M114.043174]; GPMDB: [http://gpmdb.org/data/keyword/25225353 8]. | #Negroni L, Taouji S, Arma D, Pallares-Lupon N, Leong K, Beausang LA, Latterich M, Bossé R, Balabaud C, Schmitter JM, Bioulac-Sage P, Zucman-Rossi J, Rosenbaum J, Chevet E, (2014) "Integrative quantitative proteomics unveils proteostasis imbalance in human hepatocellular carcinoma developed on nonfibrotic livers." <i>Mol Cell Proteomics</i> <b>13</b>(12):3473–83; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225353 25225353]; doi: [https://dx.doi.org/10.1074/mcp.M114.043174 10.1074/mcp.M114.043174]; GPMDB: [http://gpmdb.org/data/keyword/25225353 8]. | ||
#Wiśniewski JR, Hein MY, Cox J, Mann M, (2014) "A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards." <i>Mol Cell Proteomics</i> <b>13</b>(12):3497–506; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225357 25225357]; doi: [https://dx.doi.org/10.1074/mcp.M113.037309 10.1074/mcp.M113.037309]; GPMDB: [http://gpmdb.org/data/keyword/25225357 69]. | #Wiśniewski JR, Hein MY, Cox J, Mann M, (2014) "A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards." <i>Mol Cell Proteomics</i> <b>13</b>(12):3497–506; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25225357 25225357]; doi: [https://dx.doi.org/10.1074/mcp.M113.037309 10.1074/mcp.M113.037309]; GPMDB: [http://gpmdb.org/data/keyword/25225357 69]. | ||
Line 719: | Line 721: | ||
#Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | #Wu X, Renuse S, Sahasrabuddhe NA, Zahari MS, Chaerkady R, Kim MS, Nirujogi RS, Mohseni M, Kumar P, Raju R, Zhong J, Yang J, Neiswinger J, Jeong JS, Newman R, Powers MA, Somani BL, Gabrielson E, Sukumar S, Stearns V, Qian J, Zhu H, Vogelstein B, Park BH, Pandey A, (2014) "Activation of diverse signalling pathways by oncogenic PIK3CA mutations." <i>Nat Commun</i> <b>5</b>:4961; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25247763 25247763]; doi: [https://dx.doi.org/10.1038/ncomms5961 10.1038/ncomms5961]; GPMDB: [http://gpmdb.org/data/keyword/25247763 91]. | ||
#van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM, (2014) "SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs." <i>EMBO J</i> <b>33</b>(22):2643–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25257309 25257309]; doi: [https://dx.doi.org/10.15252/embj.201488202 10.15252/embj.201488202]; GPMDB: [http://gpmdb.org/data/keyword/25257309 2]. | #van der Lelij P, Stocsits RR, Ladurner R, Petzold G, Kreidl E, Koch B, Schmitz J, Neumann B, Ellenberg J, Peters JM, (2014) "SNW1 enables sister chromatid cohesion by mediating the splicing of sororin and APC2 pre-mRNAs." <i>EMBO J</i> <b>33</b>(22):2643–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25257309 25257309]; doi: [https://dx.doi.org/10.15252/embj.201488202 10.15252/embj.201488202]; GPMDB: [http://gpmdb.org/data/keyword/25257309 2]. | ||
+ | #Cortes LK, Vainauskas S, Dai N, McClung CM, Shah M, Benner JS, Corrêa IR Jr, VerBerkmoes NC, Taron CH, (2014) "Proteomic identification of mammalian cell surface derived glycosylphosphatidylinositol-anchored proteins through selective glycan enrichment." <i>Proteomics</i> <b>14</b>(21-22):2471–84; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25262930 25262930]; doi: [https://dx.doi.org/10.1002/pmic.201400148 10.1002/pmic.201400148]; GPMDB: [http://gpmdb.org/data/keyword/25262930 36]. | ||
#Zhong J, Martinez M, Sengupta S, Lee A, Wu X, Chaerkady R, Chatterjee A, O'Meally RN, Cole RN, Pandey A, Zachara NE, (2015) "Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway." <i>Proteomics</i> <b>15</b>(2-3):591–607; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25263469 25263469]; doi: [https://dx.doi.org/10.1002/pmic.201400339 10.1002/pmic.201400339]; GPMDB: [http://gpmdb.org/data/keyword/25263469 6]. | #Zhong J, Martinez M, Sengupta S, Lee A, Wu X, Chaerkady R, Chatterjee A, O'Meally RN, Cole RN, Pandey A, Zachara NE, (2015) "Quantitative phosphoproteomics reveals crosstalk between phosphorylation and O-GlcNAc in the DNA damage response pathway." <i>Proteomics</i> <b>15</b>(2-3):591–607; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25263469 25263469]; doi: [https://dx.doi.org/10.1002/pmic.201400339 10.1002/pmic.201400339]; GPMDB: [http://gpmdb.org/data/keyword/25263469 6]. | ||
#Navarro MN, Goebel J, Hukelmann JL, Cantrell DA, (2014) "Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks." <i>Mol Cell Proteomics</i> <b>13</b>(12):3544–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25266776 25266776]; doi: [https://dx.doi.org/10.1074/mcp.M113.037242 10.1074/mcp.M113.037242]; GPMDB: [http://gpmdb.org/data/keyword/25266776 274]. | #Navarro MN, Goebel J, Hukelmann JL, Cantrell DA, (2014) "Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks." <i>Mol Cell Proteomics</i> <b>13</b>(12):3544–57; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25266776 25266776]; doi: [https://dx.doi.org/10.1074/mcp.M113.037242 10.1074/mcp.M113.037242]; GPMDB: [http://gpmdb.org/data/keyword/25266776 274]. | ||
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#Savitski MM, Reinhard FB, Franken H, Werner T, Savitski MF, Eberhard D, Martinez Molina D, Jafari R, Dovega RB, Klaeger S, Kuster B, Nordlund P, Bantscheff M, Drewes G, (2014) "Tracking cancer drugs in living cells by thermal profiling of the proteome." <i>Science</i> <b>346</b>(6205):1255784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25278616 25278616]; doi: [https://dx.doi.org/10.1126/science.1255784 10.1126/science.1255784]; GPMDB: [http://gpmdb.org/data/keyword/25278616 403]. | #Savitski MM, Reinhard FB, Franken H, Werner T, Savitski MF, Eberhard D, Martinez Molina D, Jafari R, Dovega RB, Klaeger S, Kuster B, Nordlund P, Bantscheff M, Drewes G, (2014) "Tracking cancer drugs in living cells by thermal profiling of the proteome." <i>Science</i> <b>346</b>(6205):1255784; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25278616 25278616]; doi: [https://dx.doi.org/10.1126/science.1255784 10.1126/science.1255784]; GPMDB: [http://gpmdb.org/data/keyword/25278616 403]. | ||
#Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M, (2014) "Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach." <i>J Biotechnol</i> <b>192 Pt A</b>:204–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25281541 25281541]; doi: [https://dx.doi.org/10.1016/j.jbiotec.2014.08.028 10.1016/j.jbiotec.2014.08.028]; GPMDB: [http://gpmdb.org/data/keyword/25281541 120]. | #Handtke S, Volland S, Methling K, Albrecht D, Becher D, Nehls J, Bongaerts J, Maurer KH, Lalk M, Liesegang H, Voigt B, Daniel R, Hecker M, (2014) "Cell physiology of the biotechnological relevant bacterium Bacillus pumilus-an omics-based approach." <i>J Biotechnol</i> <b>192 Pt A</b>:204–14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25281541 25281541]; doi: [https://dx.doi.org/10.1016/j.jbiotec.2014.08.028 10.1016/j.jbiotec.2014.08.028]; GPMDB: [http://gpmdb.org/data/keyword/25281541 120]. | ||
+ | #Bhargava M, Becker TL, Viken KJ, Jagtap PD, Dey S, Steinbach MS, Wu B, Kumar V, Bitterman PB, Ingbar DH, Wendt CH, (2014) "Proteomic profiles in acute respiratory distress syndrome differentiates survivors from non-survivors." <i>PLoS One</i> <b>9</b>(10):e109713; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25290099 25290099]; doi: [https://dx.doi.org/10.1371/journal.pone.0109713 10.1371/journal.pone.0109713]; GPMDB: [http://gpmdb.org/data/keyword/25290099 15]. | ||
#Qi L, Liu Z, Wang J, Cui Y, Guo Y, Zhou T, Zhou Z, Guo X, Xue Y, Sha J, (2014) "Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis." <i>Mol Cell Proteomics</i> <b>13</b>(12):3626–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25293948 25293948]; doi: [https://dx.doi.org/10.1074/mcp.M114.039073 10.1074/mcp.M114.039073]; GPMDB: [http://gpmdb.org/data/keyword/25293948 59]. | #Qi L, Liu Z, Wang J, Cui Y, Guo Y, Zhou T, Zhou Z, Guo X, Xue Y, Sha J, (2014) "Systematic analysis of the phosphoproteome and kinase-substrate networks in the mouse testis." <i>Mol Cell Proteomics</i> <b>13</b>(12):3626–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25293948 25293948]; doi: [https://dx.doi.org/10.1074/mcp.M114.039073 10.1074/mcp.M114.039073]; GPMDB: [http://gpmdb.org/data/keyword/25293948 59]. | ||
#Tan H, Wu Z, Wang H, Bai B, Li Y, Wang X, Zhai B, Beach TG, Peng J, (2015) "Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome." <i>Proteomics</i> <b>15</b>(2-3):500–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25307156 25307156]; doi: [https://dx.doi.org/10.1002/pmic.201400171 10.1002/pmic.201400171]; GPMDB: [http://gpmdb.org/data/keyword/25307156 3]. | #Tan H, Wu Z, Wang H, Bai B, Li Y, Wang X, Zhai B, Beach TG, Peng J, (2015) "Refined phosphopeptide enrichment by phosphate additive and the analysis of human brain phosphoproteome." <i>Proteomics</i> <b>15</b>(2-3):500–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25307156 25307156]; doi: [https://dx.doi.org/10.1002/pmic.201400171 10.1002/pmic.201400171]; GPMDB: [http://gpmdb.org/data/keyword/25307156 3]. | ||
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#Helgeland E, Breivik LE, Vaudel M, Svendsen ØS, Garberg H, Nordrehaug JE, Berven FS, Jonassen AK, (2014) "Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution." <i>PLoS One</i> <b>9</b>(10):e109279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25333471 25333471]; doi: [https://dx.doi.org/10.1371/journal.pone.0109279 10.1371/journal.pone.0109279]; GPMDB: [http://gpmdb.org/data/keyword/25333471 146]. | #Helgeland E, Breivik LE, Vaudel M, Svendsen ØS, Garberg H, Nordrehaug JE, Berven FS, Jonassen AK, (2014) "Exploring the human plasma proteome for humoral mediators of remote ischemic preconditioning--a word of caution." <i>PLoS One</i> <b>9</b>(10):e109279; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25333471 25333471]; doi: [https://dx.doi.org/10.1371/journal.pone.0109279 10.1371/journal.pone.0109279]; GPMDB: [http://gpmdb.org/data/keyword/25333471 146]. | ||
#Batth TS, Francavilla C, Olsen JV, (2014) "Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics." <i>J Proteome Res</i> <b>13</b>(12):6176–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25338131 25338131]; doi: [https://dx.doi.org/10.1021/pr500893m 10.1021/pr500893m]; GPMDB: [http://gpmdb.org/data/keyword/25338131 11]. | #Batth TS, Francavilla C, Olsen JV, (2014) "Off-line high-pH reversed-phase fractionation for in-depth phosphoproteomics." <i>J Proteome Res</i> <b>13</b>(12):6176–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25338131 25338131]; doi: [https://dx.doi.org/10.1021/pr500893m 10.1021/pr500893m]; GPMDB: [http://gpmdb.org/data/keyword/25338131 11]. | ||
+ | #Fang NN, Chan GT, Zhu M, Comyn SA, Persaud A, Deshaies RJ, Rotin D, Gsponer J, Mayor T, (2014) "Rsp5/Nedd4 is the main ubiquitin ligase that targets cytosolic misfolded proteins following heat stress." <i>Nat Cell Biol</i> <b>16</b>(12):1227–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25344756 25344756]; doi: [https://dx.doi.org/10.1038/ncb3054 10.1038/ncb3054]; GPMDB: [http://gpmdb.org/data/keyword/25344756 9]. | ||
#Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TS, Pandey A, (2014) "Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host." <i>Proteomics</i> <b>14</b>(23-24):2769–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25346215 25346215]; doi: [https://dx.doi.org/10.1002/pmic.201400267 10.1002/pmic.201400267]; GPMDB: [http://gpmdb.org/data/keyword/25346215 105]. | #Renuse S, Madugundu AK, Kumar P, Nair BG, Gowda H, Prasad TS, Pandey A, (2014) "Proteomic analysis and genome annotation of Pichia pastoris, a recombinant protein expression host." <i>Proteomics</i> <b>14</b>(23-24):2769–79; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25346215 25346215]; doi: [https://dx.doi.org/10.1002/pmic.201400267 10.1002/pmic.201400267]; GPMDB: [http://gpmdb.org/data/keyword/25346215 105]. | ||
#Marino F, Cristobal A, Binai NA, Bache N, Heck AJ, Mohammed S, (2014) "Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system." <i>Analyst</i> <b>139</b>(24):6520–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25346955 25346955]; doi: [https://dx.doi.org/10.1039/c4an01568a 10.1039/c4an01568a]; GPMDB: [http://gpmdb.org/data/keyword/25346955 38]. | #Marino F, Cristobal A, Binai NA, Bache N, Heck AJ, Mohammed S, (2014) "Characterization and usage of the EASY-spray technology as part of an online 2D SCX-RP ultra-high pressure system." <i>Analyst</i> <b>139</b>(24):6520–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25346955 25346955]; doi: [https://dx.doi.org/10.1039/c4an01568a 10.1039/c4an01568a]; GPMDB: [http://gpmdb.org/data/keyword/25346955 38]. | ||
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#Li L, Wei Y, To C, Zhu CQ, Tong J, Pham NA, Taylor P, Ignatchenko V, Ignatchenko A, Zhang W, Wang D, Yanagawa N, Li M, Pintilie M, Liu G, Muthuswamy L, Shepherd FA, Tsao MS, Kislinger T, Moran MF, (2014) "Integrated omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact." <i>Nat Commun</i> <b>5</b>:5469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25429762 25429762]; doi: [https://dx.doi.org/10.1038/ncomms6469 10.1038/ncomms6469]; GPMDB: [http://gpmdb.org/data/keyword/25429762 33]. | #Li L, Wei Y, To C, Zhu CQ, Tong J, Pham NA, Taylor P, Ignatchenko V, Ignatchenko A, Zhang W, Wang D, Yanagawa N, Li M, Pintilie M, Liu G, Muthuswamy L, Shepherd FA, Tsao MS, Kislinger T, Moran MF, (2014) "Integrated omic analysis of lung cancer reveals metabolism proteome signatures with prognostic impact." <i>Nat Commun</i> <b>5</b>:5469; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25429762 25429762]; doi: [https://dx.doi.org/10.1038/ncomms6469 10.1038/ncomms6469]; GPMDB: [http://gpmdb.org/data/keyword/25429762 33]. | ||
#Hagen L, Sharma A, Aas PA, Slupphaug G, (2015) "Off-target responses in the HeLa proteome subsequent to transient plasmid-mediated transfection." <i>Biochim Biophys Acta</i> <b>1854</b>(1):84–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25448019 25448019]; doi: [https://dx.doi.org/10.1016/j.bbapap.2014.10.016 10.1016/j.bbapap.2014.10.016]; GPMDB: [http://gpmdb.org/data/keyword/25448019 27]. | #Hagen L, Sharma A, Aas PA, Slupphaug G, (2015) "Off-target responses in the HeLa proteome subsequent to transient plasmid-mediated transfection." <i>Biochim Biophys Acta</i> <b>1854</b>(1):84–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25448019 25448019]; doi: [https://dx.doi.org/10.1016/j.bbapap.2014.10.016 10.1016/j.bbapap.2014.10.016]; GPMDB: [http://gpmdb.org/data/keyword/25448019 27]. | ||
+ | #Tummala KS, Gomes AL, Yilmaz M, Graña O, Bakiri L, Ruppen I, Ximénez-Embún P, Sheshappanavar V, Rodriguez-Justo M, Pisano DG, Wagner EF, Djouder N, (2014) "Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage." <i>Cancer Cell</i> <b>26</b>(6):826–39; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25453901 25453901]; doi: [https://dx.doi.org/10.1016/j.ccell.2014.10.002 10.1016/j.ccell.2014.10.002]; GPMDB: [http://gpmdb.org/data/keyword/25453901 46]. | ||
+ | #Guo Z, Neilson LJ, Zhong H, Murray PS, Zanivan S, Zaidel-Bar R, (2014) "E-cadherin interactome complexity and robustness resolved by quantitative proteomics." <i>Sci Signal</i> <b>7</b>(354):rs7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25468996 25468996]; doi: [https://dx.doi.org/10.1126/scisignal.2005473 10.1126/scisignal.2005473]; GPMDB: [http://gpmdb.org/data/keyword/25468996 90]. | ||
#Wiśniewski JR, Koepsell H, Gizak A, Rakus D, (2015) "Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions." <i>Proteomics</i> <b>15</b>(7):1316–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475432 25475432]; doi: [https://dx.doi.org/10.1002/pmic.201400456 10.1002/pmic.201400456]; GPMDB: [http://gpmdb.org/data/keyword/25475432 44]. | #Wiśniewski JR, Koepsell H, Gizak A, Rakus D, (2015) "Absolute protein quantification allows differentiation of cell-specific metabolic routes and functions." <i>Proteomics</i> <b>15</b>(7):1316–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475432 25475432]; doi: [https://dx.doi.org/10.1002/pmic.201400456 10.1002/pmic.201400456]; GPMDB: [http://gpmdb.org/data/keyword/25475432 44]. | ||
#Schnell G, Boeuf A, Jaulhac B, Boulanger N, Collin E, Barthel C, De Martino S, Ehret-Sabatier L, (2015) "Proteomic analysis of three Borrelia burgdorferi sensu lato native species and disseminating clones: relevance for Lyme vaccine design." <i>Proteomics</i> <b>15</b>(7):1280–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475896 25475896]; doi: [https://dx.doi.org/10.1002/pmic.201400177 10.1002/pmic.201400177]; GPMDB: [http://gpmdb.org/data/keyword/25475896 6]. | #Schnell G, Boeuf A, Jaulhac B, Boulanger N, Collin E, Barthel C, De Martino S, Ehret-Sabatier L, (2015) "Proteomic analysis of three Borrelia burgdorferi sensu lato native species and disseminating clones: relevance for Lyme vaccine design." <i>Proteomics</i> <b>15</b>(7):1280–90; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25475896 25475896]; doi: [https://dx.doi.org/10.1002/pmic.201400177 10.1002/pmic.201400177]; GPMDB: [http://gpmdb.org/data/keyword/25475896 6]. | ||
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#Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM, (2014) "Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity." <i>Cell</i> <b>159</b>(7):1615–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25525879 25525879]; doi: [https://dx.doi.org/10.1016/j.cell.2014.11.046 10.1016/j.cell.2014.11.046]; GPMDB: [http://gpmdb.org/data/keyword/25525879 24]. | #Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM, (2014) "Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity." <i>Cell</i> <b>159</b>(7):1615–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25525879 25525879]; doi: [https://dx.doi.org/10.1016/j.cell.2014.11.046 10.1016/j.cell.2014.11.046]; GPMDB: [http://gpmdb.org/data/keyword/25525879 24]. | ||
#Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, Béchet D, (2014) "Proteomics of muscle chronological ageing in post-menopausal women." <i>BMC Genomics</i> <b>15</b>:1165; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25532418 25532418]; doi: [https://dx.doi.org/10.1186/1471-2164-15-1165 10.1186/1471-2164-15-1165]; GPMDB: [http://gpmdb.org/data/keyword/25532418 98]. | #Gueugneau M, Coudy-Gandilhon C, Gourbeyre O, Chambon C, Combaret L, Polge C, Taillandier D, Attaix D, Friguet B, Maier AB, Butler-Browne G, Béchet D, (2014) "Proteomics of muscle chronological ageing in post-menopausal women." <i>BMC Genomics</i> <b>15</b>:1165; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25532418 25532418]; doi: [https://dx.doi.org/10.1186/1471-2164-15-1165 10.1186/1471-2164-15-1165]; GPMDB: [http://gpmdb.org/data/keyword/25532418 98]. | ||
+ | #Rotival M, Ko JH, Srivastava PK, Kerloc'h A, Montoya A, Mauro C, Faull P, Cutillas PR, Petretto E, Behmoaras J, (2015) "Integrating phosphoproteome and transcriptome reveals new determinants of macrophage multinucleation." <i>Mol Cell Proteomics</i> <b>14</b>(3):484–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25532521 25532521]; doi: [https://dx.doi.org/10.1074/mcp.M114.043836 10.1074/mcp.M114.043836]; GPMDB: [http://gpmdb.org/data/keyword/25532521 15]. | ||
#Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM, (2015) "Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling." <i>Mol Cell</i> <b>57</b>(2):273–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25533186 25533186]; doi: [https://dx.doi.org/10.1016/j.molcel.2014.11.016 10.1016/j.molcel.2014.11.016]; GPMDB: [http://gpmdb.org/data/keyword/25533186 12]. | #Hustedt N, Seeber A, Sack R, Tsai-Pflugfelder M, Bhullar B, Vlaming H, van Leeuwen F, Guénolé A, van Attikum H, Srivas R, Ideker T, Shimada K, Gasser SM, (2015) "Yeast PP4 interacts with ATR homolog Ddc2-Mec1 and regulates checkpoint signaling." <i>Mol Cell</i> <b>57</b>(2):273–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25533186 25533186]; doi: [https://dx.doi.org/10.1016/j.molcel.2014.11.016 10.1016/j.molcel.2014.11.016]; GPMDB: [http://gpmdb.org/data/keyword/25533186 12]. | ||
#Paster W, Bruger AM, Katsch K, Grégoire C, Roncagalli R, Fu G, Gascoigne NR, Nika K, Cohnen A, Feller SM, Simister PC, Molder KC, Cordoba SP, Dushek O, Malissen B, Acuto O, (2015) "A THEMIS:SHP1 complex promotes T-cell survival." <i>EMBO J</i> <b>34</b>(3):393–409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25535246 25535246]; doi: [https://dx.doi.org/10.15252/embj.201387725 10.15252/embj.201387725]; GPMDB: [http://gpmdb.org/data/keyword/25535246 15]. | #Paster W, Bruger AM, Katsch K, Grégoire C, Roncagalli R, Fu G, Gascoigne NR, Nika K, Cohnen A, Feller SM, Simister PC, Molder KC, Cordoba SP, Dushek O, Malissen B, Acuto O, (2015) "A THEMIS:SHP1 complex promotes T-cell survival." <i>EMBO J</i> <b>34</b>(3):393–409; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25535246 25535246]; doi: [https://dx.doi.org/10.15252/embj.201387725 10.15252/embj.201387725]; GPMDB: [http://gpmdb.org/data/keyword/25535246 15]. | ||
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#Boj SF, Hwang CI, Baker LA, Chio II, Engle DD, Corbo V, Jager M, Ponz-Sarvise M, Tiriac H, Spector MS, Gracanin A, Oni T, Yu KH, van Boxtel R, Huch M, Rivera KD, Wilson JP, Feigin ME, Öhlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Borel Rinkes IH, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA, (2015) "Organoid models of human and mouse ductal pancreatic cancer." <i>Cell</i> <b>160</b>(1-2):324–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25557080 25557080]; doi: [https://dx.doi.org/10.1016/j.cell.2014.12.021 10.1016/j.cell.2014.12.021]; GPMDB: [http://gpmdb.org/data/keyword/25557080 4]. | #Boj SF, Hwang CI, Baker LA, Chio II, Engle DD, Corbo V, Jager M, Ponz-Sarvise M, Tiriac H, Spector MS, Gracanin A, Oni T, Yu KH, van Boxtel R, Huch M, Rivera KD, Wilson JP, Feigin ME, Öhlund D, Handly-Santana A, Ardito-Abraham CM, Ludwig M, Elyada E, Alagesan B, Biffi G, Yordanov GN, Delcuze B, Creighton B, Wright K, Park Y, Morsink FH, Molenaar IQ, Borel Rinkes IH, Cuppen E, Hao Y, Jin Y, Nijman IJ, Iacobuzio-Donahue C, Leach SD, Pappin DJ, Hammell M, Klimstra DS, Basturk O, Hruban RH, Offerhaus GJ, Vries RG, Clevers H, Tuveson DA, (2015) "Organoid models of human and mouse ductal pancreatic cancer." <i>Cell</i> <b>160</b>(1-2):324–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25557080 25557080]; doi: [https://dx.doi.org/10.1016/j.cell.2014.12.021 10.1016/j.cell.2014.12.021]; GPMDB: [http://gpmdb.org/data/keyword/25557080 4]. | ||
#Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R, (2015) "Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry." <i>Mol Cell Proteomics</i> <b>14</b>(3):739–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561506 25561506]; doi: [https://dx.doi.org/10.1074/mcp.M113.035550 10.1074/mcp.M113.035550]; GPMDB: [http://gpmdb.org/data/keyword/25561506 46]. | #Selevsek N, Chang CY, Gillet LC, Navarro P, Bernhardt OM, Reiter L, Cheng LY, Vitek O, Aebersold R, (2015) "Reproducible and consistent quantification of the Saccharomyces cerevisiae proteome by SWATH-mass spectrometry." <i>Mol Cell Proteomics</i> <b>14</b>(3):739–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561506 25561506]; doi: [https://dx.doi.org/10.1074/mcp.M113.035550 10.1074/mcp.M113.035550]; GPMDB: [http://gpmdb.org/data/keyword/25561506 46]. | ||
+ | #Fabre B, Lambour T, Garrigues L, Amalric F, Vigneron N, Menneteau T, Stella A, Monsarrat B, Van den Eynde B, Burlet-Schiltz O, Bousquet-Dubouch MP, (2015) "Deciphering preferential interactions within supramolecular protein complexes: the proteasome case." <i>Mol Syst Biol</i> <b>11</b>(1):771; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25561571 25561571]; GPMDB: [http://gpmdb.org/data/keyword/25561571 84]. | ||
#Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM, (2015) "The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response." <i>PLoS Genet</i> <b>11</b>(1):e1004903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25569619 25569619]; doi: [https://dx.doi.org/10.1371/journal.pgen.1004903 10.1371/journal.pgen.1004903]; GPMDB: [http://gpmdb.org/data/keyword/25569619 20]. | #Kershaw CJ, Costello JL, Castelli LM, Talavera D, Rowe W, Sims PF, Ashe MP, Hubbard SJ, Pavitt GD, Grant CM, (2015) "The yeast La related protein Slf1p is a key activator of translation during the oxidative stress response." <i>PLoS Genet</i> <b>11</b>(1):e1004903; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25569619 25569619]; doi: [https://dx.doi.org/10.1371/journal.pgen.1004903 10.1371/journal.pgen.1004903]; GPMDB: [http://gpmdb.org/data/keyword/25569619 20]. | ||
#Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42]. | #Zappacosta F, Scott GF, Huddleston MJ, Annan RS, (2015) "An optimized platform for hydrophilic interaction chromatography-immobilized metal affinity chromatography enables deep coverage of the rat liver phosphoproteome." <i>J Proteome Res</i> <b>14</b>(2):997–1009; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25575281 25575281]; doi: [https://dx.doi.org/10.1021/pr501025e 10.1021/pr501025e]; GPMDB: [http://gpmdb.org/data/keyword/25575281 42]. | ||
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#Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M, (2015) "Single muscle fiber proteomics reveals unexpected mitochondrial specialization." <i>EMBO Rep</i> <b>16</b>(3):387–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643707 25643707]; doi: [https://dx.doi.org/10.15252/embr.201439757 10.15252/embr.201439757]; GPMDB: [http://gpmdb.org/data/keyword/25643707 89]. | #Murgia M, Nagaraj N, Deshmukh AS, Zeiler M, Cancellara P, Moretti I, Reggiani C, Schiaffino S, Mann M, (2015) "Single muscle fiber proteomics reveals unexpected mitochondrial specialization." <i>EMBO Rep</i> <b>16</b>(3):387–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25643707 25643707]; doi: [https://dx.doi.org/10.15252/embr.201439757 10.15252/embr.201439757]; GPMDB: [http://gpmdb.org/data/keyword/25643707 89]. | ||
#Eagle GL, Zhuang J, Jenkins RE, Till KJ, Jithesh PV, Lin K, Johnson GG, Oates M, Park K, Kitteringham NR, Pettitt AR, (2015) "Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia." <i>Mol Cell Proteomics</i> <b>14</b>(4):933–45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25645933 25645933]; doi: [https://dx.doi.org/10.1074/mcp.M114.044479 10.1074/mcp.M114.044479]; GPMDB: [http://gpmdb.org/data/keyword/25645933 3]. | #Eagle GL, Zhuang J, Jenkins RE, Till KJ, Jithesh PV, Lin K, Johnson GG, Oates M, Park K, Kitteringham NR, Pettitt AR, (2015) "Total proteome analysis identifies migration defects as a major pathogenetic factor in immunoglobulin heavy chain variable region (IGHV)-unmutated chronic lymphocytic leukemia." <i>Mol Cell Proteomics</i> <b>14</b>(4):933–45; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25645933 25645933]; doi: [https://dx.doi.org/10.1074/mcp.M114.044479 10.1074/mcp.M114.044479]; GPMDB: [http://gpmdb.org/data/keyword/25645933 3]. | ||
+ | #Walker MP, Stopford CM, Cederlund M, Fang F, Jahn C, Rabinowitz AD, Goldfarb D, Graham DM, Yan F, Deal AM, Fedoriw Y, Richards KL, Davis IJ, Weidinger G, Damania B, Major MB, (2015) "FOXP1 potentiates Wnt/β-catenin signaling in diffuse large B cell lymphoma." <i>Sci Signal</i> <b>8</b>(362):ra12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25650440 25650440]; doi: [https://dx.doi.org/10.1126/scisignal.2005654 10.1126/scisignal.2005654]; GPMDB: [http://gpmdb.org/data/keyword/25650440 8]. | ||
#Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E, (2015) "Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription." <i>EMBO Rep</i> <b>16</b>(3):332–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25652260 25652260]; doi: [https://dx.doi.org/10.15252/embr.201439123 10.15252/embr.201439123]; GPMDB: [http://gpmdb.org/data/keyword/25652260 6]. | #Marza E, Taouji S, Barroso K, Raymond AA, Guignard L, Bonneu M, Pallares-Lupon N, Dupuy JW, Fernandez-Zapico ME, Rosenbaum J, Palladino F, Dupuy D, Chevet E, (2015) "Genome-wide screen identifies a novel p97/CDC-48-dependent pathway regulating ER-stress-induced gene transcription." <i>EMBO Rep</i> <b>16</b>(3):332–40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25652260 25652260]; doi: [https://dx.doi.org/10.15252/embr.201439123 10.15252/embr.201439123]; GPMDB: [http://gpmdb.org/data/keyword/25652260 6]. | ||
#Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | #Corradini E, Burgers PP, Plank M, Heck AJ, Scholten A, (2015) "Huntingtin-associated protein 1 (HAP1) is a cGMP-dependent kinase anchoring protein (GKAP) specific for the cGMP-dependent protein kinase Iβ isoform." <i>J Biol Chem</i> <b>290</b>(12):7887–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25653285 25653285]; doi: [https://dx.doi.org/10.1074/jbc.M114.622613 10.1074/jbc.M114.622613]; GPMDB: [http://gpmdb.org/data/keyword/25653285 6]. | ||
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#Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC, (2015) "Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering." <i>Mol Cell Proteomics</i> <b>14</b>(4):961–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660013 25660013]; doi: [https://dx.doi.org/10.1074/mcp.M114.045260 10.1074/mcp.M114.045260]; GPMDB: [http://gpmdb.org/data/keyword/25660013 60]. | #Hill RC, Calle EA, Dzieciatkowska M, Niklason LE, Hansen KC, (2015) "Quantification of extracellular matrix proteins from a rat lung scaffold to provide a molecular readout for tissue engineering." <i>Mol Cell Proteomics</i> <b>14</b>(4):961–73; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660013 25660013]; doi: [https://dx.doi.org/10.1074/mcp.M114.045260 10.1074/mcp.M114.045260]; GPMDB: [http://gpmdb.org/data/keyword/25660013 60]. | ||
#Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B, (2015) "Optimized chemical proteomics assay for kinase inhibitor profiling." <i>J Proteome Res</i> <b>14</b>(3):1574–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660469 25660469]; doi: [https://dx.doi.org/10.1021/pr5012608 10.1021/pr5012608]; GPMDB: [http://gpmdb.org/data/keyword/25660469 126]. | #Médard G, Pachl F, Ruprecht B, Klaeger S, Heinzlmeir S, Helm D, Qiao H, Ku X, Wilhelm M, Kuehne T, Wu Z, Dittmann A, Hopf C, Kramer K, Kuster B, (2015) "Optimized chemical proteomics assay for kinase inhibitor profiling." <i>J Proteome Res</i> <b>14</b>(3):1574–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25660469 25660469]; doi: [https://dx.doi.org/10.1021/pr5012608 10.1021/pr5012608]; GPMDB: [http://gpmdb.org/data/keyword/25660469 126]. | ||
+ | #Krahmer J, Hindle MM, Martin SF, Le Bihan T, Millar AJ, (2015) "Sample preparation for phosphoproteomic analysis of circadian time series in Arabidopsis thaliana." <i>Methods Enzymol</i> <b>551</b>:405–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25662467 25662467]; doi: [https://dx.doi.org/10.1016/bs.mie.2014.10.022 10.1016/bs.mie.2014.10.022]; GPMDB: [http://gpmdb.org/data/keyword/25662467 117]. | ||
#Diner BA, Li T, Greco TM, Crow MS, Fuesler JA, Wang J, Cristea IM, (2015) "The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA." <i>Mol Syst Biol</i> <b>11</b>(1):787; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25665578 25665578]; GPMDB: [http://gpmdb.org/data/keyword/25665578 21]. | #Diner BA, Li T, Greco TM, Crow MS, Fuesler JA, Wang J, Cristea IM, (2015) "The functional interactome of PYHIN immune regulators reveals IFIX is a sensor of viral DNA." <i>Mol Syst Biol</i> <b>11</b>(1):787; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25665578 25665578]; GPMDB: [http://gpmdb.org/data/keyword/25665578 21]. | ||
#Jacques S, Ghesquière B, De Bock PJ, Demol H, Wahni K, Willems P, Messens J, Van Breusegem F, Gevaert K, (2015) "Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress." <i>Mol Cell Proteomics</i> <b>14</b>(5):1217–29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25693801 25693801]; doi: [https://dx.doi.org/10.1074/mcp.M114.043729 10.1074/mcp.M114.043729]; GPMDB: [http://gpmdb.org/data/keyword/25693801 2]. | #Jacques S, Ghesquière B, De Bock PJ, Demol H, Wahni K, Willems P, Messens J, Van Breusegem F, Gevaert K, (2015) "Protein Methionine Sulfoxide Dynamics in Arabidopsis thaliana under Oxidative Stress." <i>Mol Cell Proteomics</i> <b>14</b>(5):1217–29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25693801 25693801]; doi: [https://dx.doi.org/10.1074/mcp.M114.043729 10.1074/mcp.M114.043729]; GPMDB: [http://gpmdb.org/data/keyword/25693801 2]. | ||
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#Franck WL, Gokce E, Randall SM, Oh Y, Eyre A, Muddiman DC, Dean RA, (2015) "Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development." <i>J Proteome Res</i> <b>14</b>(6):2408–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25926025 25926025]; doi: [https://dx.doi.org/10.1021/pr501064q 10.1021/pr501064q]; GPMDB: [http://gpmdb.org/data/keyword/25926025 36]. | #Franck WL, Gokce E, Randall SM, Oh Y, Eyre A, Muddiman DC, Dean RA, (2015) "Phosphoproteome Analysis Links Protein Phosphorylation to Cellular Remodeling and Metabolic Adaptation during Magnaporthe oryzae Appressorium Development." <i>J Proteome Res</i> <b>14</b>(6):2408–24; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25926025 25926025]; doi: [https://dx.doi.org/10.1021/pr501064q 10.1021/pr501064q]; GPMDB: [http://gpmdb.org/data/keyword/25926025 36]. | ||
#Le Bihan T, Hindle M, Martin SF, Barrios-Llerena ME, Krahmer J, Kis K, Millar AJ, van Ooijen G, (2015) "Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri." <i>Proteomics</i> <b>15</b>(23-24):4135–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25930153 25930153]; doi: [https://dx.doi.org/10.1002/pmic.201500086 10.1002/pmic.201500086]; GPMDB: [http://gpmdb.org/data/keyword/25930153 35]. | #Le Bihan T, Hindle M, Martin SF, Barrios-Llerena ME, Krahmer J, Kis K, Millar AJ, van Ooijen G, (2015) "Label-free quantitative analysis of the casein kinase 2-responsive phosphoproteome of the marine minimal model species Ostreococcus tauri." <i>Proteomics</i> <b>15</b>(23-24):4135–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25930153 25930153]; doi: [https://dx.doi.org/10.1002/pmic.201500086 10.1002/pmic.201500086]; GPMDB: [http://gpmdb.org/data/keyword/25930153 35]. | ||
+ | #Mertz J, Tan H, Pagala V, Bai B, Chen PC, Li Y, Cho JH, Shaw T, Wang X, Peng J, (2015) "Sequential Elution Interactome Analysis of the Mind Bomb 1 Ubiquitin Ligase Reveals a Novel Role in Dendritic Spine Outgrowth." <i>Mol Cell Proteomics</i> <b>14</b>(7):1898–910; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931508 25931508]; doi: [https://dx.doi.org/10.1074/mcp.M114.045898 10.1074/mcp.M114.045898]; GPMDB: [http://gpmdb.org/data/keyword/25931508 2]. | ||
#Gadelha C, Zhang W, Chamberlain JW, Chait BT, Wickstead B, Field MC, (2015) "Architecture of a Host-Parasite Interface: Complex Targeting Mechanisms Revealed Through Proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(7):1911–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931509 25931509]; doi: [https://dx.doi.org/10.1074/mcp.M114.047647 10.1074/mcp.M114.047647]; GPMDB: [http://gpmdb.org/data/keyword/25931509 48]. | #Gadelha C, Zhang W, Chamberlain JW, Chait BT, Wickstead B, Field MC, (2015) "Architecture of a Host-Parasite Interface: Complex Targeting Mechanisms Revealed Through Proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(7):1911–26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931509 25931509]; doi: [https://dx.doi.org/10.1074/mcp.M114.047647 10.1074/mcp.M114.047647]; GPMDB: [http://gpmdb.org/data/keyword/25931509 48]. | ||
#Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M, (2015) "DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links." <i>Science</i> <b>348</b>(6234):1253671; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931565 25931565]; doi: [https://dx.doi.org/10.1126/science.1253671 10.1126/science.1253671]; GPMDB: [http://gpmdb.org/data/keyword/25931565 21]. | #Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M, (2015) "DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links." <i>Science</i> <b>348</b>(6234):1253671; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25931565 25931565]; doi: [https://dx.doi.org/10.1126/science.1253671 10.1126/science.1253671]; GPMDB: [http://gpmdb.org/data/keyword/25931565 21]. | ||
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#Graessel A, Hauck SM, von Toerne C, Kloppmann E, Goldberg T, Koppensteiner H, Schindler M, Knapp B, Krause L, Dietz K, Schmidt-Weber CB, Suttner K, (2015) "A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation." <i>Mol Cell Proteomics</i> <b>14</b>(8):2085–102; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25991687 25991687]; doi: [https://dx.doi.org/10.1074/mcp.M114.045690 10.1074/mcp.M114.045690]; GPMDB: [http://gpmdb.org/data/keyword/25991687 48]. | #Graessel A, Hauck SM, von Toerne C, Kloppmann E, Goldberg T, Koppensteiner H, Schindler M, Knapp B, Krause L, Dietz K, Schmidt-Weber CB, Suttner K, (2015) "A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation." <i>Mol Cell Proteomics</i> <b>14</b>(8):2085–102; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25991687 25991687]; doi: [https://dx.doi.org/10.1074/mcp.M114.045690 10.1074/mcp.M114.045690]; GPMDB: [http://gpmdb.org/data/keyword/25991687 48]. | ||
#Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Stensballe A, Andersen V, (2015) "Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies." <i>Inflamm Bowel Dis</i> <b>21</b>(9):2052–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25993694 25993694]; doi: [https://dx.doi.org/10.1097/MIB.0000000000000460 10.1097/MIB.0000000000000460]; GPMDB: [http://gpmdb.org/data/keyword/25993694 60]. | #Bennike TB, Carlsen TG, Ellingsen T, Bonderup OK, Glerup H, Bøgsted M, Christiansen G, Birkelund S, Stensballe A, Andersen V, (2015) "Neutrophil Extracellular Traps in Ulcerative Colitis: A Proteome Analysis of Intestinal Biopsies." <i>Inflamm Bowel Dis</i> <b>21</b>(9):2052–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25993694 25993694]; doi: [https://dx.doi.org/10.1097/MIB.0000000000000460 10.1097/MIB.0000000000000460]; GPMDB: [http://gpmdb.org/data/keyword/25993694 60]. | ||
+ | #Jehmlich N, Stegmaier P, Golatowski C, Salazar MG, Rischke C, Henke M, Völker U, (2015) "Differences in the whole saliva baseline proteome profile associated with development of oral mucositis in head and neck cancer patients undergoing radiotherapy." <i>J Proteomics</i> <b>125</b>:98–103; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25997676 25997676]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.04.030 10.1016/j.jprot.2015.04.030]; GPMDB: [http://gpmdb.org/data/keyword/25997676 56]. | ||
#Kharlampieva D, Manuvera V, Podgorny O, Grafskaia E, Kovalchuk S, Pobeguts O, Altukhov I, Govorun V, Lazarev V, (2015) "Recombinant fragilysin isoforms cause E-cadherin cleavage of intact cells and do not cleave isolated E-cadherin." <i>Microb Pathog</i> <b>83-84</b>:47–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25998017 25998017]; doi: [https://dx.doi.org/10.1016/j.micpath.2015.05.003 10.1016/j.micpath.2015.05.003]; GPMDB: [http://gpmdb.org/data/keyword/25998017 23]. | #Kharlampieva D, Manuvera V, Podgorny O, Grafskaia E, Kovalchuk S, Pobeguts O, Altukhov I, Govorun V, Lazarev V, (2015) "Recombinant fragilysin isoforms cause E-cadherin cleavage of intact cells and do not cleave isolated E-cadherin." <i>Microb Pathog</i> <b>83-84</b>:47–56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25998017 25998017]; doi: [https://dx.doi.org/10.1016/j.micpath.2015.05.003 10.1016/j.micpath.2015.05.003]; GPMDB: [http://gpmdb.org/data/keyword/25998017 23]. | ||
#Chen Y, Yang F, Sun Z, Wang Q, Mi K, Deng H, (2015) "Proteomic Analysis of Drug-Resistant Mycobacteria: Co-Evolution of Copper and INH Resistance." <i>PLoS One</i> <b>10</b>(6):e0127788; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26035302 26035302]; doi: [https://dx.doi.org/10.1371/journal.pone.0127788 10.1371/journal.pone.0127788]; GPMDB: [http://gpmdb.org/data/keyword/26035302 1]. | #Chen Y, Yang F, Sun Z, Wang Q, Mi K, Deng H, (2015) "Proteomic Analysis of Drug-Resistant Mycobacteria: Co-Evolution of Copper and INH Resistance." <i>PLoS One</i> <b>10</b>(6):e0127788; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26035302 26035302]; doi: [https://dx.doi.org/10.1371/journal.pone.0127788 10.1371/journal.pone.0127788]; GPMDB: [http://gpmdb.org/data/keyword/26035302 1]. | ||
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#Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 54]. | #Higgins R, Gendron JM, Rising L, Mak R, Webb K, Kaiser SE, Zuzow N, Riviere P, Yang B, Fenech E, Tang X, Lindsay SA, Christianson JC, Hampton RY, Wasserman SA, Bennett EJ, (2015) "The Unfolded Protein Response Triggers Site-Specific Regulatory Ubiquitylation of 40S Ribosomal Proteins." <i>Mol Cell</i> <b>59</b>(1):35–49; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26051182 26051182]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.04.026 10.1016/j.molcel.2015.04.026]; GPMDB: [http://gpmdb.org/data/keyword/26051182 54]. | ||
#Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S, (2015) "Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis." <i>J Proteomics</i> <b>126</b>:54–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26054784 26054784]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.037 10.1016/j.jprot.2015.05.037]; GPMDB: [http://gpmdb.org/data/keyword/26054784 15]. | #Sethi MK, Thaysen-Andersen M, Kim H, Park CK, Baker MS, Packer NH, Paik YK, Hancock WS, Fanayan S, (2015) "Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis." <i>J Proteomics</i> <b>126</b>:54–67; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26054784 26054784]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.05.037 10.1016/j.jprot.2015.05.037]; GPMDB: [http://gpmdb.org/data/keyword/26054784 15]. | ||
+ | #Cifani P, Kirik U, Waldemarson S, James P, (2015) "Molecular Portrait of Breast-Cancer-Derived Cell Lines Reveals Poor Similarity with Tumors." <i>J Proteome Res</i> <b>14</b>(7):2819–27; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055192 26055192]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b00375 10.1021/acs.jproteome.5b00375]; GPMDB: [http://gpmdb.org/data/keyword/26055192 9]. | ||
#McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | #McCloy RA, Parker BL, Rogers S, Chaudhuri R, Gayevskiy V, Hoffman NJ, Ali N, Watkins DN, Daly RJ, James DE, Lorca T, Castro A, Burgess A, (2015) "Global Phosphoproteomic Mapping of Early Mitotic Exit in Human Cells Identifies Novel Substrate Dephosphorylation Motifs." <i>Mol Cell Proteomics</i> <b>14</b>(8):2194–212; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26055452 26055452]; doi: [https://dx.doi.org/10.1074/mcp.M114.046938 10.1074/mcp.M114.046938]; GPMDB: [http://gpmdb.org/data/keyword/26055452 29]. | ||
#Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. | #Mulvey CM, Schröter C, Gatto L, Dikicioglu D, Fidaner IB, Christoforou A, Deery MJ, Cho LT, Niakan KK, Martinez-Arias A, Lilley KS, (2015) "Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells." <i>Stem Cells</i> <b>33</b>(9):2712–25; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26059426 26059426]; doi: [https://dx.doi.org/10.1002/stem.2067 10.1002/stem.2067]; GPMDB: [http://gpmdb.org/data/keyword/26059426 7]. | ||
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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]. | ||
+ | #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]. | ||
#Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A, (2015) "Panorama of ancient metazoan macromolecular complexes." <i>Nature</i> <b>525</b>(7569):339–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26344197 26344197]; doi: [https://dx.doi.org/10.1038/nature14877 10.1038/nature14877]; GPMDB: [http://gpmdb.org/data/keyword/26344197 4066]. | #Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A, (2015) "Panorama of ancient metazoan macromolecular complexes." <i>Nature</i> <b>525</b>(7569):339–44; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26344197 26344197]; doi: [https://dx.doi.org/10.1038/nature14877 10.1038/nature14877]; GPMDB: [http://gpmdb.org/data/keyword/26344197 4066]. | ||
#Borgdorff H, Gautam R, Armstrong SD, Xia D, Ndayisaba GF, van Teijlingen NH, Geijtenbeek TB, Wastling JM, van de Wijgert JH, (2016) "Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier." <i>Mucosal Immunol</i> <b>9</b>(3):621–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26349657 26349657]; doi: [https://dx.doi.org/10.1038/mi.2015.86 10.1038/mi.2015.86]; GPMDB: [http://gpmdb.org/data/keyword/26349657 50]. | #Borgdorff H, Gautam R, Armstrong SD, Xia D, Ndayisaba GF, van Teijlingen NH, Geijtenbeek TB, Wastling JM, van de Wijgert JH, (2016) "Cervicovaginal microbiome dysbiosis is associated with proteome changes related to alterations of the cervicovaginal mucosal barrier." <i>Mucosal Immunol</i> <b>9</b>(3):621–33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26349657 26349657]; doi: [https://dx.doi.org/10.1038/mi.2015.86 10.1038/mi.2015.86]; GPMDB: [http://gpmdb.org/data/keyword/26349657 50]. | ||
+ | #Wu X, Zahari MS, Ma B, Liu R, Renuse S, Sahasrabuddhe NA, Chen L, Chaerkady R, Kim MS, Zhong J, Jelinek C, Barbhuiya MA, Leal-Rojas P, Yang Y, Kashyap MK, Marimuthu A, Ling M, Fackler MJ, Merino V, Zhang Z, Zahnow CA, Gabrielson E, Stearns V, Roa JC, Sukumar S, Gill PS, Pandey A, (2015) "Global phosphotyrosine survey in triple-negative breast cancer reveals activation of multiple tyrosine kinase signaling pathways." <i>Oncotarget</i> <b>6</b>(30):29143–60; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26356563 26356563]; doi: [https://dx.doi.org/10.18632/oncotarget.5020 10.18632/oncotarget.5020]; GPMDB: [http://gpmdb.org/data/keyword/26356563 27]. | ||
#Weinert BT, Moustafa T, Iesmantavicius V, Zechner R, Choudhary C, (2015) "Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions." <i>EMBO J</i> <b>34</b>(21):2620–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26358839 26358839]; doi: [https://dx.doi.org/10.15252/embj.201591271 10.15252/embj.201591271]; GPMDB: [http://gpmdb.org/data/keyword/26358839 142]. | #Weinert BT, Moustafa T, Iesmantavicius V, Zechner R, Choudhary C, (2015) "Analysis of acetylation stoichiometry suggests that SIRT3 repairs nonenzymatic acetylation lesions." <i>EMBO J</i> <b>34</b>(21):2620–32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26358839 26358839]; doi: [https://dx.doi.org/10.15252/embj.201591271 10.15252/embj.201591271]; GPMDB: [http://gpmdb.org/data/keyword/26358839 142]. | ||
#Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | #Grundner-Culemann K, Dybowski JN, Klammer M, Tebbe A, Schaab C, Daub H, (2016) "Comparative proteome analysis across non-small cell lung cancer cell lines." <i>J Proteomics</i> <b>130</b>:1–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26361996 26361996]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.09.003 10.1016/j.jprot.2015.09.003]; GPMDB: [http://gpmdb.org/data/keyword/26361996 23]. | ||
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#Clark DJ, Fondrie WE, Liao Z, Hanson PI, Fulton A, Mao L, Yang AJ, (2015) "Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis." <i>Anal Chem</i> <b>87</b>(20):10462–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378940 26378940]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b02586 10.1021/acs.analchem.5b02586]; GPMDB: [http://gpmdb.org/data/keyword/26378940 2]. | #Clark DJ, Fondrie WE, Liao Z, Hanson PI, Fulton A, Mao L, Yang AJ, (2015) "Redefining the Breast Cancer Exosome Proteome by Tandem Mass Tag Quantitative Proteomics and Multivariate Cluster Analysis." <i>Anal Chem</i> <b>87</b>(20):10462–9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26378940 26378940]; doi: [https://dx.doi.org/10.1021/acs.analchem.5b02586 10.1021/acs.analchem.5b02586]; GPMDB: [http://gpmdb.org/data/keyword/26378940 2]. | ||
#Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | #Kieselbach T, Zijnge V, Granström E, Oscarsson J, (2015) "Proteomics of Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles." <i>PLoS One</i> <b>10</b>(9):e0138591; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26381655 26381655]; doi: [https://dx.doi.org/10.1371/journal.pone.0138591 10.1371/journal.pone.0138591]; GPMDB: [http://gpmdb.org/data/keyword/26381655 5]. | ||
+ | #Goris T, Schiffmann CL, Gadkari J, Schubert T, Seifert J, Jehmlich N, von Bergen M, Diekert G, (2015) "Proteomics of the organohalide-respiring Epsilonproteobacterium Sulfurospirillum multivorans adapted to tetrachloroethene and other energy substrates." <i>Sci Rep</i> <b>5</b>:13794; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26387727 26387727]; doi: [https://dx.doi.org/10.1038/srep13794 10.1038/srep13794]; GPMDB: [http://gpmdb.org/data/keyword/26387727 36]. | ||
+ | #Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R, (2015) "Kinome-wide decoding of network-attacking mutations rewiring cancer signaling." <i>Cell</i> <b>163</b>(1):202–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26388441 26388441]; doi: [https://dx.doi.org/10.1016/j.cell.2015.08.056 10.1016/j.cell.2015.08.056]; GPMDB: [http://gpmdb.org/data/keyword/26388441 3]. | ||
#Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | #Paulo JA, O'Connell JD, Gaun A, Gygi SP, (2015) "Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae." <i>Mol Biol Cell</i> <b>26</b>(22):4063–74; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26399295 26399295]; doi: [https://dx.doi.org/10.1091/mbc.E15-07-0499 10.1091/mbc.E15-07-0499]; GPMDB: [http://gpmdb.org/data/keyword/26399295 1]. | ||
#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]. | ||
- | #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 | + | #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 746]. |
#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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#Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin M, (2016) "Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen." <i>Mol Cell Proteomics</i> <b>15</b>(3):1032–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | #Kozlov SV, Waardenberg AJ, Engholm-Keller K, Arthur JW, Graham ME, Lavin M, (2016) "Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen." <i>Mol Cell Proteomics</i> <b>15</b>(3):1032–47; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26699800 26699800]; doi: [https://dx.doi.org/10.1074/mcp.M115.055723 10.1074/mcp.M115.055723]; GPMDB: [http://gpmdb.org/data/keyword/26699800 141]. | ||
#El Ouaamari A, Dirice E, Gedeon N, Hu J, Zhou JY, Shirakawa J, Hou L, Goodman J, Karampelias C, Qiang G, Boucher J, Martinez R, Gritsenko MA, De Jesus DF, Kahraman S, Bhatt S, Smith RD, Beer HD, Jungtrakoon P, Gong Y, Goldfine AB, Liew CW, Doria A, Andersson O, Qian WJ, Remold-O'Donnell E, Kulkarni RN, (2016) "SerpinB1 Promotes Pancreatic β Cell Proliferation." <i>Cell Metab</i> <b>23</b>(1):194–205; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26701651 26701651]; doi: [https://dx.doi.org/10.1016/j.cmet.2015.12.001 10.1016/j.cmet.2015.12.001]; GPMDB: [http://gpmdb.org/data/keyword/26701651 4]. | #El Ouaamari A, Dirice E, Gedeon N, Hu J, Zhou JY, Shirakawa J, Hou L, Goodman J, Karampelias C, Qiang G, Boucher J, Martinez R, Gritsenko MA, De Jesus DF, Kahraman S, Bhatt S, Smith RD, Beer HD, Jungtrakoon P, Gong Y, Goldfine AB, Liew CW, Doria A, Andersson O, Qian WJ, Remold-O'Donnell E, Kulkarni RN, (2016) "SerpinB1 Promotes Pancreatic β Cell Proliferation." <i>Cell Metab</i> <b>23</b>(1):194–205; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26701651 26701651]; doi: [https://dx.doi.org/10.1016/j.cmet.2015.12.001 10.1016/j.cmet.2015.12.001]; GPMDB: [http://gpmdb.org/data/keyword/26701651 4]. | ||
+ | #Chong WM, Hsu SC, Kao WT, Lo CW, Lee KY, Shao JS, Chen YH, Chang J, Chen SS, Yu MJ, (2016) "Phosphoproteomics Identified an NS5A Phosphorylation Site Involved in Hepatitis C Virus Replication." <i>J Biol Chem</i> <b>291</b>(8):3918–31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702051 26702051]; doi: [https://dx.doi.org/10.1074/jbc.M115.675413 10.1074/jbc.M115.675413]; GPMDB: [http://gpmdb.org/data/keyword/26702051 27]. | ||
#Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | #Lluch-Senar M, Mancuso FM, Climente-González H, Peña-Paz MI, Sabido E, Serrano L, (2016) "Rescuing discarded spectra: Full comprehensive analysis of a minimal proteome." <i>Proteomics</i> <b>16</b>(4):554–63; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26702875 26702875]; doi: [https://dx.doi.org/10.1002/pmic.201500187 10.1002/pmic.201500187]; GPMDB: [http://gpmdb.org/data/keyword/26702875 2]. | ||
#Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | #Thierry E, Guilligay D, Kosinski J, Bock T, Gaudon S, Round A, Pflug A, Hengrung N, El Omari K, Baudin F, Hart DJ, Beck M, Cusack S, (2016) "Influenza Polymerase Can Adopt an Alternative Configuration Involving a Radical Repacking of PB2 Domains." <i>Mol Cell</i> <b>61</b>(1):125–37; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26711008 26711008]; doi: [https://dx.doi.org/10.1016/j.molcel.2015.11.016 10.1016/j.molcel.2015.11.016]; GPMDB: [http://gpmdb.org/data/keyword/26711008 44]. | ||
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#Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | #Virant-Klun I, Leicht S, Hughes C, Krijgsveld J, (2016) "Identification of maturation-specific proteins by single-cell proteomics of human oocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27215607 27215607]; doi: [https://dx.doi.org/10.1074/mcp.M115.056887 10.1074/mcp.M115.056887]; GPMDB: [http://gpmdb.org/data/keyword/27215607 18]. | ||
#Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | #Yu J, Storer BE, Kushekhar K, Abu Zaid M, Zhang Q, Gafken PR, Ogata Y, Martin PJ, Flowers ME, Hansen JA, Arora M, Cutler C, Jagasia M, Pidala J, Hamilton BK, Chen GL, Pusic I, Lee SJ, Paczesny S, (2016) "Biomarker Panel for Chronic Graft-Versus-Host Disease." <i>J Clin Oncol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27217465 27217465]; doi: [https://dx.doi.org/10.1200/JCO.2015.65.9615 10.1200/JCO.2015.65.9615]; GPMDB: [http://gpmdb.org/data/keyword/27217465 3]. | ||
- | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic | + | #Wang B, Pfeiffer MJ, Drexler HC, Fuellen G, Boiani M, (2016) "Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27225728 27225728]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01083 10.1021/acs.jproteome.5b01083]; GPMDB: [http://gpmdb.org/data/keyword/27225728 14]. |
#Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | #Lodrini M, Poschmann G, Schmidt V, Wünschel J, Dreidax D, Witt O, Höfer T, Meyer HE, Stühler K, Eggert A, Deubzer HE, (2016) "Minichromosome Maintenance Complex Is a Critical Node in the miR-183 Signaling Network of MYCN-Amplified Neuroblastoma Cells." <i>J Proteome Res</i> <b>15</b>(7):2178–86; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27239679 27239679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00134 10.1021/acs.jproteome.6b00134]; GPMDB: [http://gpmdb.org/data/keyword/27239679 12]. | ||
#Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | #Bullen JW, Tchernyshyov I, Holewinski RJ, DeVine L, Wu F, Venkatraman V, Kass DL, Cole RN, Van Eyk J, Semenza GL, (2016) "Protein kinase A-dependent phosphorylation stimulates the transcriptional activity of hypoxia-inducible factor 1." <i>Sci Signal</i> <b>9</b>(430):ra56; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27245613 27245613]; doi: [https://dx.doi.org/10.1126/scisignal.aaf0583 10.1126/scisignal.aaf0583]; GPMDB: [http://gpmdb.org/data/keyword/27245613 14]. | ||
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#Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | #Wiśniewski JR, Mann M, (2016) "A Proteomics Approach to the Protein Normalization Problem: Selection of Unvarying Proteins for MS-Based Proteomics and Western Blotting." <i>J Proteome Res</i> <b>15</b>(7):2321–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27297043 27297043]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00403 10.1021/acs.jproteome.6b00403]; GPMDB: [http://gpmdb.org/data/keyword/27297043 64]. | ||
#Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | #Rakus D, Gizak A, Wiśniewski JR, (2016) "Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27302655 27302655]; doi: [https://dx.doi.org/10.1021/acs.jproteome.5b01149 10.1021/acs.jproteome.5b01149]; GPMDB: [http://gpmdb.org/data/keyword/27302655 60]. | ||
- | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 | + | #Chick JM, Munger SC, Simecek P, Huttlin EL, Choi K, Gatti DM, Raghupathy N, Svenson KL, Churchill GA, Gygi SP, (2016) "Defining the consequences of genetic variation on a proteome-wide scale." <i>Nature</i> <b>534</b>(7608):500–5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27309819 27309819]; doi: [https://dx.doi.org/10.1038/nature18270 10.1038/nature18270]; GPMDB: [http://gpmdb.org/data/keyword/27309819 27]. |
#Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | #Szklanna PB, Foy M, Wynne K, Byrne D, Maguire PB, (2016) "Analysis of the proteins associated with platelet detergent resistant membranes." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27329341 27329341]; doi: [https://dx.doi.org/10.1002/pmic.201500309 10.1002/pmic.201500309]; GPMDB: [http://gpmdb.org/data/keyword/27329341 18]. | ||
- | #Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 | + | #Ahrné E, Glatter T, Viganò C, Schubert CV, Nigg EA, Schmidt A, (2016) "Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27345528 27345528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00066 10.1021/acs.jproteome.6b00066]; GPMDB: [http://gpmdb.org/data/keyword/27345528 41]. |
- | #Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG, (2016) "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27364158 27364158]; doi: [https://dx.doi.org/10.1074/mcp.M116.060582 10.1074/mcp.M116.060582]; GPMDB: [http://gpmdb.org/data/keyword/27364158 | + | #Chaubey PM, Hofstetter L, Roschitzki B, Stieger B, (2016) "Proteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver." <i>PLoS One</i> <b>11</b>(6):e0158033; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27347675 27347675]; doi: [https://dx.doi.org/10.1371/journal.pone.0158033 10.1371/journal.pone.0158033]; GPMDB: [http://gpmdb.org/data/keyword/27347675 60]. |
+ | #Rinschen MM, Schroeter CB, Koehler S, Ising C, Schermer B, Kann M, Benzing T, Brinkkoetter PT, (2016) "Quantitative deep-mapping of the cultured podocyte proteome uncovers shifts in proteostatic mechanisms during differentiation." <i>Am J Physiol Cell Physiol</i> <b></b>:ajpcell.00121.2016; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27357545 27357545]; doi: [https://dx.doi.org/10.1152/ajpcell.00121.2016 10.1152/ajpcell.00121.2016]; GPMDB: [http://gpmdb.org/data/keyword/27357545 3]. | ||
+ | #Dudekula K, Le Bihan T, (2016) "Data from quantitative label free proteomics analysis of rat spleen." <i>Data Brief</i> <b>8</b>:494–500; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27358910 27358910]; doi: [https://dx.doi.org/10.1016/j.dib.2016.05.058 10.1016/j.dib.2016.05.058]; GPMDB: [http://gpmdb.org/data/keyword/27358910 17]. | ||
+ | #Carrier M, Joint M, Lutzing R, Page A, Rochette-Egly C, (2016) "Phosphoproteome and Transcriptome of RA-Responsive and RA-Resistant Breast Cancer Cell Lines." <i>PLoS One</i> <b>11</b>(6):e0157290; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27362937 27362937]; doi: [https://dx.doi.org/10.1371/journal.pone.0157290 10.1371/journal.pone.0157290]; GPMDB: [http://gpmdb.org/data/keyword/27362937 6]. | ||
+ | #Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG, (2016) "Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27364158 27364158]; doi: [https://dx.doi.org/10.1074/mcp.M116.060582 10.1074/mcp.M116.060582]; GPMDB: [http://gpmdb.org/data/keyword/27364158 90]. | ||
+ | #Luo Y, Jacobs EY, Greco TM, Mohammed KD, Tong T, Keegan S, Binley JM, Cristea IM, Fenyö D, Rout MP, Chait BT, Muesing MA, (2016) "HIV-host interactome revealed directly from infected cells." <i>Nat Microbiol</i> <b>1</b>(7):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27375898 27375898]; doi: [https://dx.doi.org/10.1038/nmicrobiol.2016.68 10.1038/nmicrobiol.2016.68]; GPMDB: [http://gpmdb.org/data/keyword/27375898 53]. | ||
+ | #Carabetta VJ, Greco TM, Tanner AW, Cristea IM, Dubnau D, (2016) "Temporal Regulation of the <i>Bacillus subtilis</i> Acetylome and Evidence for a Role of MreB Acetylation in Cell Wall Growth." <i>mSystems</i> <b>1</b>(3):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27376153 27376153]; doi: [https://dx.doi.org/10.1128/mSystems.00005-16 10.1128/mSystems.00005-16]; GPMDB: [http://gpmdb.org/data/keyword/27376153 30]. | ||
+ | #Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A, (2016) "Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila." <i>Nat Commun</i> <b>7</b>:12128; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27378189 27378189]; doi: [https://dx.doi.org/10.1038/ncomms12128 10.1038/ncomms12128]; GPMDB: [http://gpmdb.org/data/keyword/27378189 25]. | ||
+ | #Hampoelz B, Mackmull MT, Machado P, Ronchi P, Bui KH, Schieber N, Santarella-Mellwig R, Necakov A, Andrés-Pons A, Philippe JM, Lecuit T, Schwab Y, Beck M, (2016) "Pre-assembled Nuclear Pores Insert into the Nuclear Envelope during Early Development." <i>Cell</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27397507 27397507]; doi: [https://dx.doi.org/10.1016/j.cell.2016.06.015 10.1016/j.cell.2016.06.015]; GPMDB: [http://gpmdb.org/data/keyword/27397507 18]. |
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 pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a 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 July 17, 2016.