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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of October | + | 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 October 28, 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: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Lardi M, Aguilar C, Pedrioli A, Omasits U, Suppiger A, Cárcamo-Oyarce G, Schmid N, Ahrens CH, Eberl L, Pessi G, (2015) "σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111." <i>Appl Environ Microbiol</i> <b>81</b>(12):4077–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841012 25841012]; doi: [https://dx.doi.org/10.1128/AEM.00694-15 10.1128/AEM.00694-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841012 40]. | #Lardi M, Aguilar C, Pedrioli A, Omasits U, Suppiger A, Cárcamo-Oyarce G, Schmid N, Ahrens CH, Eberl L, Pessi G, (2015) "σ54-Dependent Response to Nitrogen Limitation and Virulence in Burkholderia cenocepacia Strain H111." <i>Appl Environ Microbiol</i> <b>81</b>(12):4077–89; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841012 25841012]; doi: [https://dx.doi.org/10.1128/AEM.00694-15 10.1128/AEM.00694-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841012 40]. | ||
#Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841592 31]. | #Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR, (2015) "Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines." <i>J Proteomics</i> <b>127</b>(Pt B):247–58; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25841592 25841592]; doi: [https://dx.doi.org/10.1016/j.jprot.2015.03.019 10.1016/j.jprot.2015.03.019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25841592 31]. | ||
- | #Krishnan RK, Nolte H, Sun T, Kaur H, Sreenivasan K, Looso M, Offermanns S, Krüger M, Swiercz JM, (2015) "Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate." <i>Nat Commun</i> <b>6</b>:6658; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25849741 25849741]; doi: [https://dx.doi.org/10.1038/ncomms7658 10.1038/ncomms7658]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25849741 | + | #Krishnan RK, Nolte H, Sun T, Kaur H, Sreenivasan K, Looso M, Offermanns S, Krüger M, Swiercz JM, (2015) "Quantitative analysis of the TNF-α-induced phosphoproteome reveals AEG-1/MTDH/LYRIC as an IKKβ substrate." <i>Nat Commun</i> <b>6</b>:6658; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25849741 25849741]; doi: [https://dx.doi.org/10.1038/ncomms7658 10.1038/ncomms7658]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25849741 53]. |
#Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25850434 12]. | #Krisp C, Yang H, van Soest R, Molloy MP, (2015) "Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics." <i>Mol Cell Proteomics</i> <b>14</b>(6):1708–19; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850434 25850434]; doi: [https://dx.doi.org/10.1074/mcp.M114.046425 10.1074/mcp.M114.046425]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25850434 12]. | ||
#Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG, (2015) "A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells." <i>Mol Cell Proteomics</i> <b>14</b>(6):1599–615; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850435 25850435]; doi: [https://dx.doi.org/10.1074/mcp.M114.047233 10.1074/mcp.M114.047233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25850435 255]. | #Stuart SA, Houel S, Lee T, Wang N, Old WM, Ahn NG, (2015) "A Phosphoproteomic Comparison of B-RAFV600E and MKK1/2 Inhibitors in Melanoma Cells." <i>Mol Cell Proteomics</i> <b>14</b>(6):1599–615; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/25850435 25850435]; doi: [https://dx.doi.org/10.1074/mcp.M114.047233 10.1074/mcp.M114.047233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/25850435 255]. | ||
Line 1,303: | Line 1,303: | ||
#Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW, (2016) "Comprehensive Identification of RNA-Binding Domains in Human Cells." <i>Mol Cell</i> <b>63</b>(4):696–710; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27453046 27453046]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.06.029 10.1016/j.molcel.2016.06.029]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27453046 12]. | #Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW, (2016) "Comprehensive Identification of RNA-Binding Domains in Human Cells." <i>Mol Cell</i> <b>63</b>(4):696–710; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27453046 27453046]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.06.029 10.1016/j.molcel.2016.06.029]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27453046 12]. | ||
#Thomsen MS, Birkelund S, Burkhart A, Stensballe A, Moos T, (2016) "Synthesis and deposition of basement membrane proteins by primary brain capillary endothelial cells in a murine model of the blood-brain barrier." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27456748 27456748]; doi: [https://dx.doi.org/10.1111/jnc.13747 10.1111/jnc.13747]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27456748 12]. | #Thomsen MS, Birkelund S, Burkhart A, Stensballe A, Moos T, (2016) "Synthesis and deposition of basement membrane proteins by primary brain capillary endothelial cells in a murine model of the blood-brain barrier." <i>J Neurochem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27456748 27456748]; doi: [https://dx.doi.org/10.1111/jnc.13747 10.1111/jnc.13747]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27456748 12]. | ||
+ | #Zhao Y, Tian B, Sadygov RG, Zhang Y, Brasier AR, (2016) "Integrative proteomic analysis reveals reprograming tumor necrosis factor signaling in epithelial mesenchymal transition." <i>J Proteomics</i> <b>148</b>:126–38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27461979 27461979]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.014 10.1016/j.jprot.2016.07.014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27461979 30]. | ||
#Osinalde N, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Blagoev B, Kratchmarova I, (2016) "Characterization of Receptor-Associated Protein Complex Assembly in Interleukin (IL)-2- and IL-15-Activated T-Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27463037 27463037]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00233 10.1021/acs.jproteome.6b00233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27463037 55]. | #Osinalde N, Sanchez-Quiles V, Akimov V, Aloria K, Arizmendi JM, Blagoev B, Kratchmarova I, (2016) "Characterization of Receptor-Associated Protein Complex Assembly in Interleukin (IL)-2- and IL-15-Activated T-Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27463037 27463037]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00233 10.1021/acs.jproteome.6b00233]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27463037 55]. | ||
#Liu Z, Wang F, Chen J, Zhou Y, Zou H, (2016) "Modulating the selectivity of affinity absorbents to multi-phosphopeptides by a competitive substitution strategy." <i>J Chromatogr A</i> <b>1461</b>:35–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27470094 27470094]; doi: [https://dx.doi.org/10.1016/j.chroma.2016.07.042 10.1016/j.chroma.2016.07.042]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27470094 9]. | #Liu Z, Wang F, Chen J, Zhou Y, Zou H, (2016) "Modulating the selectivity of affinity absorbents to multi-phosphopeptides by a competitive substitution strategy." <i>J Chromatogr A</i> <b>1461</b>:35–41; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27470094 27470094]; doi: [https://dx.doi.org/10.1016/j.chroma.2016.07.042 10.1016/j.chroma.2016.07.042]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27470094 9]. | ||
Line 1,774: | Line 1,775: | ||
#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: [https://gpmdb.thegpm.org/data/keyword/29229923 28]. | #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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29233185 263]. | #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: [https://gpmdb.thegpm.org/data/keyword/29233185 263]. | ||
+ | #Maumus M, Manferdini C, Toupet K, Chuchana P, Casteilla L, Gachet M, Jorgensen C, Lisignoli G, Noël D, (2017) "Thrombospondin-1 Partly Mediates the Cartilage Protective Effect of Adipose-Derived Mesenchymal Stem Cells in Osteoarthritis." <i>Front Immunol</i> <b>8</b>:1638; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29238343 29238343]; doi: [https://dx.doi.org/10.3389/fimmu.2017.01638 10.3389/fimmu.2017.01638]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29238343 120]. | ||
#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: [https://gpmdb.thegpm.org/data/keyword/29242379 121]. | #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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29248718 15]. | #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: [https://gpmdb.thegpm.org/data/keyword/29248718 15]. | ||
Line 1,865: | Line 1,867: | ||
#Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29773673 29773673]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000720 10.1074/mcp.RA118.000720]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29773673 30]. | #Di Lorenzo G, Voltolini Velho R, Winter D, Thelen M, Ahmadi S, Schweizer M, De Pace R, Cornils K, Yorgan TA, Grüb S, Hermans-Borgmeyer I, Schinke T, Müller-Loennies S, Braulke T, Pohl S, (2018) "Lysosomal proteome and secretome analysis identifies missorted enzymes and their non-degraded substrates in mucolipidosis III mouse cells." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29773673 29773673]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000720 10.1074/mcp.RA118.000720]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29773673 30]. | ||
#Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29776966 29776966]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000620 10.1074/mcp.RA118.000620]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29776966 9]. | #Wang H, Cheng Q, Li X, Hu F, Han L, Zhang H, Li L, Ge J, Ying X, Guo X, Wang Q, (2018) "Loss of TIGAR induces oxidative stress and meiotic defects in oocytes from obese mice." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29776966 29776966]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000620 10.1074/mcp.RA118.000620]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29776966 9]. | ||
+ | #Guo J, Zhang T, Guo Y, Sun T, Li H, Zhang X, Yin H, Cao G, Yin Y, Wang H, Shi L, Guo X, Sha J, Eppig JJ, Su YQ, (2018) "Oocyte stage-specific effects of MTOR determine granulosa cell fate and oocyte quality in mice." <i>Proc Natl Acad Sci U S A</i> <b>115</b>(23):E5326–E5333; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29784807 29784807]; doi: [https://dx.doi.org/10.1073/pnas.1800352115 10.1073/pnas.1800352115]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29784807 30]. | ||
#Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D, (2018) "Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens." <i>Proteomics</i> <b>18</b>(12):e1700465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29786170 29786170]; doi: [https://dx.doi.org/10.1002/pmic.201700465 10.1002/pmic.201700465]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29786170 66]. | #Ternette N, Olde Nordkamp MJM, Müller J, Anderson AP, Nicastri A, Hill AVS, Kessler BM, Li D, (2018) "Immunopeptidomic Profiling of HLA-A2-Positive Triple Negative Breast Cancer Identifies Potential Immunotherapy Target Antigens." <i>Proteomics</i> <b>18</b>(12):e1700465; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29786170 29786170]; doi: [https://dx.doi.org/10.1002/pmic.201700465 10.1002/pmic.201700465]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29786170 66]. | ||
#Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29789417 29789417]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-17-1745 10.1158/0008-5472.CAN-17-1745]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29789417 530]. | #Löffler MW, Kowalewski DJ, Backert L, Bernhardt J, Adam P, Schuster H, Dengler F, Backes D, Kopp HG, Beckert S, Wagner S, Königsrainer I, Kohlbacher O, Kanz L, Königsrainer A, Rammensee HG, Stevanovic S, Haen SP, (2018) "Mapping the HLA ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation." <i>Cancer Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29789417 29789417]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-17-1745 10.1158/0008-5472.CAN-17-1745]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29789417 530]. | ||
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#Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ, (2018) "Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria." <i>Nat Commun</i> <b>9</b>(1):2558; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967381 29967381]; doi: [https://dx.doi.org/10.1038/s41467-018-05007-9 10.1038/s41467-018-05007-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967381 18]. | #Pietras Z, Wojcik MA, Borowski LS, Szewczyk M, Kulinski TM, Cysewski D, Stepien PP, Dziembowski A, Szczesny RJ, (2018) "Dedicated surveillance mechanism controls G-quadruplex forming non-coding RNAs in human mitochondria." <i>Nat Commun</i> <b>9</b>(1):2558; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967381 29967381]; doi: [https://dx.doi.org/10.1038/s41467-018-05007-9 10.1038/s41467-018-05007-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967381 18]. | ||
#Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B, (2018) "UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites." <i>Nat Struct Mol Biol</i> <b>25</b>(7):631–640; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967540 29967540]; doi: [https://dx.doi.org/10.1038/s41594-018-0084-y 10.1038/s41594-018-0084-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967540 136]. | #Akimov V, Barrio-Hernandez I, Hansen SVF, Hallenborg P, Pedersen AK, Bekker-Jensen DB, Puglia M, Christensen SDK, Vanselow JT, Nielsen MM, Kratchmarova I, Kelstrup CD, Olsen JV, Blagoev B, (2018) "UbiSite approach for comprehensive mapping of lysine and N-terminal ubiquitination sites." <i>Nat Struct Mol Biol</i> <b>25</b>(7):631–640; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29967540 29967540]; doi: [https://dx.doi.org/10.1038/s41594-018-0084-y 10.1038/s41594-018-0084-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29967540 136]. | ||
+ | #Tölle RC, Gaggioli C, Dengjel J, (2018) "Three-Dimensional Cell Culture Conditions Affect the Proteome of Cancer-Associated Fibroblasts." <i>J Proteome Res</i> <b>17</b>(8):2780–2789; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29989826 29989826]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00237 10.1021/acs.jproteome.8b00237]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29989826 318]. | ||
#Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | #Sureka R, Wadhwa R, Thakur SS, Pathak RU, Mishra RK, (2018) "Comparison of Nuclear Matrix and Mitotic Chromosome Scaffold proteins in Drosophila S2 cells - Transmission of hallmarks of nuclear organization through mitosis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29991507 29991507]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000591 10.1074/mcp.RA118.000591]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29991507 6]. | ||
#Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | #Kim D, Liu Y, Oberly S, Freire R, Smolka MB, (2018) "ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30010936 30010936]; doi: [https://dx.doi.org/10.1093/nar/gky625 10.1093/nar/gky625]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30010936 2]. | ||
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#Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | #Shraibman B, Barnea E, Melamed Kadosh D, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, Von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2018) "Identification of tumor antigens among the HLA peptidomes of Glioblastoma tumors and plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30072578 30072578]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000792 10.1074/mcp.RA118.000792]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30072578 75]. | ||
#Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | #Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | ||
+ | #Kozono S, Lin YM, Seo HS, Pinch B, Lian X, Qiu C, Herbert MK, Chen CH, Tan L, Gao ZJ, Massefski W, Doctor ZM, Jackson BP, Chen Y, Dhe-Paganon S, Lu KP, Zhou XZ, (2018) "Arsenic targets Pin1 and cooperates with retinoic acid to inhibit cancer-driving pathways and tumor-initiating cells." <i>Nat Commun</i> <b>9</b>(1):3069; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30093655 30093655]; doi: [https://dx.doi.org/10.1038/s41467-018-05402-2 10.1038/s41467-018-05402-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30093655 12]. | ||
#Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M, (2018) "Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)." <i>Proteomics</i> <b></b>:e1800101; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30094954 30094954]; doi: [https://dx.doi.org/10.1002/pmic.201800101 10.1002/pmic.201800101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30094954 54]. | #Kumar G, Hummel K, Razzazi-Fazeli E, El-Matbouli M, (2018) "Proteome Profiles of Head Kidney and Spleen of Rainbow Trout (Oncorhynchus Mykiss)." <i>Proteomics</i> <b></b>:e1800101; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30094954 30094954]; doi: [https://dx.doi.org/10.1002/pmic.201800101 10.1002/pmic.201800101]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30094954 54]. | ||
#Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | #Schiza C, Korbakis D, Panteleli E, Jarvi K, Drabovich AP, Diamandis EP, (2018) "Discovery of a human testis-specific protein complex TEX101-DPEP3 and selection of its disrupting antibodies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30097533 30097533]; doi: [https://dx.doi.org/10.1074/mcp.RA118.000749 10.1074/mcp.RA118.000749]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30097533 44]. | ||
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#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
+ | #Sun J, Shi J, Wang Y, Chen Y, Li Y, Kong D, Chang L, Liu F, Lv Z, Zhou Y, He F, Zhang Y, Xu P, (2018) "Multiproteases Combined with High-pH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30280576 30280576]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00397 10.1021/acs.jproteome.8b00397]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30280576 72]. |
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 October 28, 2018.