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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of April 19, 2020. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/12177431 498]. | ||
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#Jean Beltran PM, Mathias RA, Cristea IM, (2016) "A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection." <i>Cell Syst</i> <b>3</b>(4):361–373.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27641956 27641956]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.012 10.1016/j.cels.2016.08.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27641956 45]. | #Jean Beltran PM, Mathias RA, Cristea IM, (2016) "A Portrait of the Human Organelle Proteome In Space and Time during Cytomegalovirus Infection." <i>Cell Syst</i> <b>3</b>(4):361–373.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27641956 27641956]; doi: [https://dx.doi.org/10.1016/j.cels.2016.08.012 10.1016/j.cels.2016.08.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27641956 45]. | ||
#Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27642623 18]. | #Athanason MG, Stevens SM Jr, Burkhardt BR, (2016) "Hepatic SILAC proteomic data from PANDER transgenic model." <i>Data Brief</i> <b>9</b>:159–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642623 27642623]; doi: [https://dx.doi.org/10.1016/j.dib.2016.08.017 10.1016/j.dib.2016.08.017]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27642623 18]. | ||
+ | #Bian Y, Li L, Dong M, Liu X, Kaneko T, Cheng K, Liu H, Voss C, Cao X, Wang Y, Litchfield D, Ye M, Li SS, Zou H, (2016) "Ultra-deep tyrosine phosphoproteomics enabled by a phosphotyrosine superbinder." <i>Nat Chem Biol</i> <b>12</b>(11):959–966; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27642862 27642862]; doi: [https://dx.doi.org/10.1038/nchembio.2178 10.1038/nchembio.2178]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27642862 215]. | ||
#Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i> <b>15</b>(12):4304–4317; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27643528 28]. | #Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I, (2016) "Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves." <i>J Proteome Res</i> <b>15</b>(12):4304–4317; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27643528 27643528]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00348 10.1021/acs.jproteome.6b00348]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27643528 28]. | ||
#Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2017) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i> <b>72</b>(1):115–127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27650186 42]. | #Kubicek-Sutherland JZ, Lofton H, Vestergaard M, Hjort K, Ingmer H, Andersson DI, (2017) "Antimicrobial peptide exposure selects for Staphylococcus aureus resistance to human defence peptides." <i>J Antimicrob Chemother</i> <b>72</b>(1):115–127; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27650186 27650186]; doi: [https://dx.doi.org/10.1093/jac/dkw381 10.1093/jac/dkw381]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/27650186 42]. | ||
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#Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." <i>Nat Commun</i> <b>10</b>(1):1519; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30944321 30944321]; doi: [https://dx.doi.org/10.1038/s41467-019-09469-3 10.1038/s41467-019-09469-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30944321 3]. | #Yang M, Vesterlund M, Siavelis I, Moura-Castro LH, Castor A, Fioretos T, Jafari R, Lilljebjörn H, Odom DT, Olsson L, Ravi N, Woodward EL, Harewood L, Lehtiö J, Paulsson K, (2019) "Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia." <i>Nat Commun</i> <b>10</b>(1):1519; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30944321 30944321]; doi: [https://dx.doi.org/10.1038/s41467-019-09469-3 10.1038/s41467-019-09469-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30944321 3]. | ||
#Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." <i>Nat Commun</i> <b>10</b>(1):1600; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30962452 30962452]; doi: [https://dx.doi.org/10.1038/s41467-019-09018-y 10.1038/s41467-019-09018-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30962452 12]. | #Johansson HJ, Socciarelli F, Vacanti NM, Haugen MH, Zhu Y, Siavelis I, Fernandez-Woodbridge A, Aure MR, Sennblad B, Vesterlund M, Branca RM, Orre LM, Huss M, Fredlund E, Beraki E, Garred Ø, Boekel J, Sauer T, Zhao W, Nord S, Höglander EK, Jans DC, Brismar H, Haukaas TH, Bathen TF, Schlichting E, Naume B, Consortia Oslo Breast Cancer Research Consortium (OSBREAC)., Luders T, Borgen E, Kristensen VN, Russnes HG, Lingjærde OC, Mills GB, Sahlberg KK, Børresen-Dale AL, Lehtiö J, (2019) "Breast cancer quantitative proteome and proteogenomic landscape." <i>Nat Commun</i> <b>10</b>(1):1600; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30962452 30962452]; doi: [https://dx.doi.org/10.1038/s41467-019-09018-y 10.1038/s41467-019-09018-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30962452 12]. | ||
- | #Zecha J, Satpathy S, Kanashova T, Avanessian SC, Kane MH, Clauser KR, Mertins P, Carr SA, Kuster B, (2019) "TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach." <i>Mol Cell Proteomics</i> <b>18</b>(7):1468–1478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30967486 30967486]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001385 10.1074/mcp.TIR119.001385]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30967486 | + | #Zecha J, Satpathy S, Kanashova T, Avanessian SC, Kane MH, Clauser KR, Mertins P, Carr SA, Kuster B, (2019) "TMT Labeling for the Masses: A Robust and Cost-efficient, In-solution Labeling Approach." <i>Mol Cell Proteomics</i> <b>18</b>(7):1468–1478; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30967486 30967486]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001385 10.1074/mcp.TIR119.001385]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30967486 28]. |
#Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." <i>Cytotherapy</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30975602 30975602]; doi: [https://dx.doi.org/10.1016/j.jcyt.2019.03.002 10.1016/j.jcyt.2019.03.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30975602 8]. | #Erhart F, Weiss T, Klingenbrunner S, Fischhuber K, Reitermaier R, Halfmann A, Blauensteiner B, Lötsch D, Spiegl-Kreinecker S, Berger W, Sialana FJ, Lubec G, Felzmann T, Dohnal A, Visus C, (2019) "Spheroid glioblastoma culture conditions as antigen source for dendritic cell-based immunotherapy: spheroid proteins are survival-relevant targets but can impair immunogenic interferon γ production." <i>Cytotherapy</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30975602 30975602]; doi: [https://dx.doi.org/10.1016/j.jcyt.2019.03.002 10.1016/j.jcyt.2019.03.002]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30975602 8]. | ||
#Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH, (2019) "Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis." <i>J Proteomics</i> <b>201</b>:104–109; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30978464 30978464]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.04.007 10.1016/j.jprot.2019.04.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30978464 96]. | #Karim N, Durbin-Johnson B, Rocke DM, Salemi M, Phinney BS, Naeem M, Rice RH, (2019) "Proteomic manifestations of genetic defects in autosomal recessive congenital ichthyosis." <i>J Proteomics</i> <b>201</b>:104–109; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30978464 30978464]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.04.007 10.1016/j.jprot.2019.04.007]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30978464 96]. | ||
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#Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 21]. | #Israel S, Ernst M, Psathaki OE, Drexler HCA, Casser E, Suzuki Y, Makalowski W, Boiani M, Fuellen G, Taher L, (2019) "An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo." <i>Sci Rep</i> <b>9</b>(1):13356; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31527703 31527703]; doi: [https://dx.doi.org/10.1038/s41598-019-49817-3 10.1038/s41598-019-49817-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31527703 21]. | ||
#Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M, (2019) "Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis." <i>iScience</i> <b>19</b>:1114–1132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31536960 31536960]; doi: [https://dx.doi.org/10.1016/j.isci.2019.08.057 10.1016/j.isci.2019.08.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31536960 708]. | #Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M, (2019) "Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis." <i>iScience</i> <b>19</b>:1114–1132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31536960 31536960]; doi: [https://dx.doi.org/10.1016/j.isci.2019.08.057 10.1016/j.isci.2019.08.057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31536960 708]. | ||
+ | #Lim MY, Paulo JA, Gygi SP, (2019) "Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model." <i>J Proteome Res</i> <b>18</b>(11):4020–4026; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31547658 31547658]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00492 10.1021/acs.jproteome.9b00492]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31547658 40]. | ||
#Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | #Uckeley ZM, Moeller R, Kühn LI, Nilsson E, Robens C, Lasswitz L, Lindqvist R, Lenman A, Passos V, Voss Y, Sommerauer C, Kampmann M, Goffinet C, Meissner F, Överby AK, Lozach PY, Gerold G, (2019) "Quantitative proteomics of Uukuniemi virus - host cell interactions reveals GBF1 as proviral host factor for phleboviruses." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31570497 31570497]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001631 10.1074/mcp.RA119.001631]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31570497 20]. | ||
#Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | #Kawahara R, Recuero S, Nogueira FCS, Domont GB, Leite KRM, Srougi M, Thaysen-Andersen M, Palmisano G, (2019) "Tissue Proteome Signatures Associated with Five Grades of Prostate Cancer and Benign Prostatic Hyperplasia." <i>Proteomics</i> <b></b>:e1900174; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31576646 31576646]; doi: [https://dx.doi.org/10.1002/pmic.201900174 10.1002/pmic.201900174]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31576646 5]. | ||
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#Rispoli LA, Edwards JL, Pohler KG, Russell S, Somiari RI, Payton RR, Schrick FN, (2019) "Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows." <i>PLoS One</i> <b>14</b>(12):e0227095; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31887207 31887207]; doi: [https://dx.doi.org/10.1371/journal.pone.0227095 10.1371/journal.pone.0227095]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31887207 5]. | #Rispoli LA, Edwards JL, Pohler KG, Russell S, Somiari RI, Payton RR, Schrick FN, (2019) "Heat-induced hyperthermia impacts the follicular fluid proteome of the periovulatory follicle in lactating dairy cows." <i>PLoS One</i> <b>14</b>(12):e0227095; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31887207 31887207]; doi: [https://dx.doi.org/10.1371/journal.pone.0227095 10.1371/journal.pone.0227095]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31887207 5]. | ||
#Róka B, Tod P, Kaucsár T, Vizovišek M, Vidmar R, Turk B, Fonović M, Szénási G, Hamar P, (2019) "The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice." <i>Int J Mol Sci</i> <b>21</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31892161 31892161]; doi: [https://dx.doi.org/10.3390/ijms21010200 10.3390/ijms21010200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31892161 120]. | #Róka B, Tod P, Kaucsár T, Vizovišek M, Vidmar R, Turk B, Fonović M, Szénási G, Hamar P, (2019) "The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice." <i>Int J Mol Sci</i> <b>21</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31892161 31892161]; doi: [https://dx.doi.org/10.3390/ijms21010200 10.3390/ijms21010200]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31892161 120]. | ||
+ | #Isobe K, Raghuram V, Krishnan L, Chou CL, Yang CR, Knepper MA, (2020) "CRISPR-Cas9/phosphoproteomics identifies multiple noncanonical targets of myosin light chain kinase." <i>Am J Physiol Renal Physiol</i> <b>318</b>(3):F600–F616; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31904282 31904282]; doi: [https://dx.doi.org/10.1152/ajprenal.00431.2019 10.1152/ajprenal.00431.2019]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31904282 75]. | ||
#Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | #Hose J, Escalante LE, Clowers KJ, Dutcher HA, Robinson D, Bouriakov V, Coon JJ, Shishkova E, Gasch AP, (2020) "The genetic basis of aneuploidy tolerance in wild yeast." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31909711 31909711]; doi: [https://dx.doi.org/10.7554/eLife.52063 10.7554/eLife.52063]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31909711 24]. | ||
#Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | #Bian Y, Zheng R, Bayer FP, Wong C, Chang YC, Meng C, Zolg DP, Reinecke M, Zecha J, Wiechmann S, Heinzlmeir S, Scherr J, Hemmer B, Baynham M, Gingras AC, Boychenko O, Kuster B, (2020) "Robust, reproducible and quantitative analysis of thousands of proteomes by micro-flow LC-MS/MS." <i>Nat Commun</i> <b>11</b>(1):157; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31919466 31919466]; doi: [https://dx.doi.org/10.1038/s41467-019-13973-x 10.1038/s41467-019-13973-x]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31919466 2175]. | ||
+ | #Bai B, Wang X, Li Y, Chen PC, Yu K, Dey KK, Yarbro JM, Han X, Lutz BM, Rao S, Jiao Y, Sifford JM, Han J, Wang M, Tan H, Shaw TI, Cho JH, Zhou S, Wang H, Niu M, Mancieri A, Messler KA, Sun X, Wu Z, Pagala V, High AA, Bi W, Zhang H, Chi H, Haroutunian V, Zhang B, Beach TG, Yu G, Peng J, (2020) "Deep Multilayer Brain Proteomics Identifies Molecular Networks in Alzheimer's Disease Progression." <i>Neuron</i> <b>105</b>(6):975–991.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31926610 31926610]; doi: [https://dx.doi.org/10.1016/j.neuron.2019.12.015 10.1016/j.neuron.2019.12.015]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31926610 58]. | ||
#Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR, (2020) "Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31959955 31959955]; doi: [https://dx.doi.org/10.1038/s41587-019-0391-9 10.1038/s41587-019-0391-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31959955 874]. | #Hijazi M, Smith R, Rajeeve V, Bessant C, Cutillas PR, (2020) "Reconstructing kinase network topologies from phosphoproteomics data reveals cancer-associated rewiring." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31959955 31959955]; doi: [https://dx.doi.org/10.1038/s41587-019-0391-9 10.1038/s41587-019-0391-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31959955 874]. | ||
#Xu K, Yang L, Zhang L, Qi H, (2020) "Lack of AKAP3 disrupts integrity of the subcellular structure and proteome of mouse sperm and causes male sterility." <i>Development</i> <b>147</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31969357 31969357]; doi: [https://dx.doi.org/10.1242/dev.181057 10.1242/dev.181057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31969357 3]. | #Xu K, Yang L, Zhang L, Qi H, (2020) "Lack of AKAP3 disrupts integrity of the subcellular structure and proteome of mouse sperm and causes male sterility." <i>Development</i> <b>147</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31969357 31969357]; doi: [https://dx.doi.org/10.1242/dev.181057 10.1242/dev.181057]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31969357 3]. | ||
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#Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." <i>J Proteomics</i> <b>216</b>:103670; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31991189 31991189]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103670 10.1016/j.jprot.2020.103670]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31991189 48]. | #Gonnet J, Poncelet L, Meriaux C, Gonçalves E, Weiss L, Tchitchek N, Pedruzzi E, Soria A, Boccara D, Vogt A, Bonduelle O, Hamm G, Ait-Belkacem R, Stauber J, Fournier I, Wisztorski M, Combadiere B, (2020) "Mechanisms of innate events during skin reaction following intradermal injection of seasonal influenza vaccine." <i>J Proteomics</i> <b>216</b>:103670; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31991189 31991189]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103670 10.1016/j.jprot.2020.103670]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31991189 48]. | ||
#Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH, Krawczyk B, Rist W, Simon E, (2020) "Biomarker discovery for chronic liver diseases by multi-omics - a preclinical case study." <i>Sci Rep</i> <b>10</b>(1):1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31992752 31992752]; doi: [https://dx.doi.org/10.1038/s41598-020-58030-6 10.1038/s41598-020-58030-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31992752 4]. | #Veyel D, Wenger K, Broermann A, Bretschneider T, Luippold AH, Krawczyk B, Rist W, Simon E, (2020) "Biomarker discovery for chronic liver diseases by multi-omics - a preclinical case study." <i>Sci Rep</i> <b>10</b>(1):1314; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31992752 31992752]; doi: [https://dx.doi.org/10.1038/s41598-020-58030-6 10.1038/s41598-020-58030-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31992752 4]. | ||
+ | #Lindberg T, de Ávila RI, Zeller KS, Levander F, Eriksson D, Chawade A, Lindstedt M, (2020) "An integrated transcriptomic- and proteomic-based approach to evaluate the human skin sensitization potential of glyphosate and its commercial agrochemical formulations." <i>J Proteomics</i> <b>217</b>:103647; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32006680 32006680]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103647 10.1016/j.jprot.2020.103647]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32006680 21]. | ||
#Yasuda S, Tsuchiya H, Kaiho A, Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernández-Busnadiego R, Tanaka K, Saeki Y, (2020) "Stress- and ubiquitylation-dependent phase separation of the proteasome." <i>Nature</i> <b>578</b>(7794):296–300; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32025036 32025036]; doi: [https://dx.doi.org/10.1038/s41586-020-1982-9 10.1038/s41586-020-1982-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32025036 6]. | #Yasuda S, Tsuchiya H, Kaiho A, Guo Q, Ikeuchi K, Endo A, Arai N, Ohtake F, Murata S, Inada T, Baumeister W, Fernández-Busnadiego R, Tanaka K, Saeki Y, (2020) "Stress- and ubiquitylation-dependent phase separation of the proteasome." <i>Nature</i> <b>578</b>(7794):296–300; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32025036 32025036]; doi: [https://dx.doi.org/10.1038/s41586-020-1982-9 10.1038/s41586-020-1982-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32025036 6]. | ||
#Pini T, Parks J, Russ J, Dzieciatkowska M, Hansen KC, Schoolcraft WB, Katz-Jaffe M, (2020) "Obesity significantly alters the human sperm proteome, with potential implications for fertility." <i>J Assist Reprod Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32026202 32026202]; doi: [https://dx.doi.org/10.1007/s10815-020-01707-8 10.1007/s10815-020-01707-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32026202 20]. | #Pini T, Parks J, Russ J, Dzieciatkowska M, Hansen KC, Schoolcraft WB, Katz-Jaffe M, (2020) "Obesity significantly alters the human sperm proteome, with potential implications for fertility." <i>J Assist Reprod Genet</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32026202 32026202]; doi: [https://dx.doi.org/10.1007/s10815-020-01707-8 10.1007/s10815-020-01707-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32026202 20]. | ||
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#Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR, (2020) "Human Mast Cell Proteome Reveals Unique Lineage, Putative Functions, and Structural Basis for Cell Ablation." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32049054 32049054]; doi: [https://dx.doi.org/10.1016/j.immuni.2020.01.012 10.1016/j.immuni.2020.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32049054 12]. | #Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR, (2020) "Human Mast Cell Proteome Reveals Unique Lineage, Putative Functions, and Structural Basis for Cell Ablation." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32049054 32049054]; doi: [https://dx.doi.org/10.1016/j.immuni.2020.01.012 10.1016/j.immuni.2020.01.012]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32049054 12]. | ||
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+ | #Subbannayya Y, Pinto SM, Mohanty V, Dagamajalu S, Prasad TSK, Murthy KR, (2020) "What Makes Cornea Immunologically Unique and Privileged? Mechanistic Clues from a High-Resolution Proteomic Landscape of the Human Cornea." <i>OMICS</i> <b>24</b>(3):129–139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32125911 32125911]; doi: [https://dx.doi.org/10.1089/omi.2019.0190 10.1089/omi.2019.0190]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32125911 2]. | ||
#Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129078 32129078]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00772 10.1021/acs.jproteome.9b00772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129078 16]. | #Ding H, Fazelinia H, Spruce LA, Weiss DA, Zderic SA, Seeholzer SH, (2020) "Urine proteomics: Evaluation of different sample preparation workflows for quantitative, reproducible and improved depth of analysis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129078 32129078]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00772 10.1021/acs.jproteome.9b00772]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129078 16]. | ||
+ | #Bernatik O, Pejskova P, Vyslouzil D, Hanakova K, Zdrahal Z, Cajanek L, (2020) "Phosphorylation of multiple proteins involved in ciliogenesis by Tau Tubulin kinase 2." <i>Mol Biol Cell</i> <b></b>:mbcE19060334; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129703 32129703]; doi: [https://dx.doi.org/10.1091/mbc.E19-06-0334 10.1091/mbc.E19-06-0334]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129703 165]. | ||
+ | #Montellese C, van den Heuvel J, Ashiono C, Dörner K, Melnik A, Jonas S, Zemp I, Picotti P, Gillet LC, Kutay U, (2020) "USP16 counteracts mono-ubiquitination of RPS27a and promotes maturation of the 40S ribosomal subunit." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32129764 32129764]; doi: [https://dx.doi.org/10.7554/eLife.54435 10.7554/eLife.54435]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32129764 18]. | ||
+ | #Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P, (2020) "Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics." <i>J Proteome Res</i> <b>19</b>(4):1718–1730; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32134668 32134668]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00862 10.1021/acs.jproteome.9b00862]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32134668 25]. | ||
+ | #Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C, (2020) "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." <i>Molecules</i> <b>25</b>(5):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32138239 32138239]; doi: [https://dx.doi.org/10.3390/molecules25051125 10.3390/molecules25051125]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32138239 2]. | ||
+ | #Parker BL, Kiens B, Wojtaszewski JFP, Richter EA, James DE, (2020) "Quantification of exercise-regulated ubiquitin signaling in human skeletal muscle identifies protein modification cross talk via NEDDylation." <i>FASEB J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32141134 32141134]; doi: [https://dx.doi.org/10.1096/fj.202000075R 10.1096/fj.202000075R]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32141134 45]. | ||
+ | #Dietachmayr M, Rathakrishnan A, Karpiuk O, von Zweydorf F, Engleitner T, Fernández-Sáiz V, Schenk P, Ueffing M, Rad R, Eilers M, Gloeckner CJ, Clemm von Hohenberg K, Bassermann F, (2020) "Antagonistic activities of CDC14B and CDK1 on USP9X regulate WT1-dependent mitotic transcription and survival." <i>Nat Commun</i> <b>11</b>(1):1268; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32152317 32152317]; doi: [https://dx.doi.org/10.1038/s41467-020-15059-5 10.1038/s41467-020-15059-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32152317 3]. | ||
+ | #Wan X, Vomund AN, Peterson OJ, Chervonsky AV, Lichti CF, Unanue ER, (2020) "The MHC-II peptidome of pancreatic islets identifies key features of autoimmune peptides." <i>Nat Immunol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32152506 32152506]; doi: [https://dx.doi.org/10.1038/s41590-020-0623-7 10.1038/s41590-020-0623-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32152506 9]. | ||
+ | #Coscia F, Doll S, Bech JM, Schweizer L, Mund A, Lengyel E, Lindebjerg J, Madsen GI, Moreira JMA, Mann M, (2020) "A streamlined mass spectrometry-based proteomics workflow for large scale FFPE tissue analysis." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32154592 32154592]; doi: [https://dx.doi.org/10.1002/path.5420 10.1002/path.5420]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32154592 52]. | ||
+ | #Yin CF, Kao SC, Hsu CL, Chang YW, Cheung CHY, Huang HC, Juan HF, (2020) "Phosphoproteome Analysis Reveals Dynamic Heat Shock Protein 27 Phosphorylation in Tanshinone IIA-Induced Cell Death." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32154729 32154729]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00836 10.1021/acs.jproteome.9b00836]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32154729 168]. | ||
+ | #Wegrzyn AB, Herzog K, Gerding A, Kwiatkowski M, Wolters JC, Dolga AM, van Lint AEM, Wanders RJA, Waterham HR, Bakker BM, (2020) "Fibroblast-specific genome-scale modelling predicts an imbalance in amino acid metabolism in Refsum disease." <i>FEBS J</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32160399 32160399]; doi: [https://dx.doi.org/10.1111/febs.15292 10.1111/febs.15292]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32160399 71]. | ||
+ | #Chen L, Shi H, Koftori D, Sekine T, Nicastri A, Ternette N, Bowness P, (2020) "Identification of an unconventional sub-peptidome bound to the Behçet's disease - associated HLA-B*51:01 that is regulated by endoplasmic reticulum aminopeptidase 1 (ERAP1)." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32161166 32161166]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001617 10.1074/mcp.RA119.001617]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32161166 11]. | ||
+ | #Ooi CP, Benz C, Urbaniak MD, (2020) "Phosphoproteomic analysis of mammalian infective Trypanosoma brucei subjected to heat shock suggests atypical mechanisms for thermotolerance." <i>J Proteomics</i> <b>219</b>:103735; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32198071 32198071]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103735 10.1016/j.jprot.2020.103735]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32198071 6]. | ||
+ | #Guergues J, Wohlfahrt J, Zhang P, Liu B, Stevens SM Jr, (2020) "Deep proteome profiling reveals novel pathways associated with pro-inflammatory and alcohol-induced microglial activation phenotypes." <i>J Proteomics</i> <b>220</b>:103753; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32200115 32200115]; doi: [https://dx.doi.org/10.1016/j.jprot.2020.103753 10.1016/j.jprot.2020.103753]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32200115 30]. | ||
+ | #Campbell K, Westholm J, Kasvandik S, Di Bartolomeo F, Mormino M, Nielsen J, (2020) "Building blocks are synthesized on demand during the yeast cell cycle." <i>Proc Natl Acad Sci U S A</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32213592 32213592]; doi: [https://dx.doi.org/10.1073/pnas.1919535117 10.1073/pnas.1919535117]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32213592 105]. | ||
+ | #Rinfret Robert C, McManus FP, Lamoliatte F, Thibault P, (2020) "Interplay of Ubiquitin-Like Modifiers Following Arsenic Trioxide Treatment." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32223133 32223133]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00807 10.1021/acs.jproteome.9b00807]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32223133 18]. | ||
+ | #Hör J, Garriss G, Di Giorgio S, Hack LM, Vanselow JT, Förstner KU, Schlosser A, Henriques-Normark B, Vogel J, (2020) "Grad-seq in a Gram-positive bacterium reveals exonucleolytic sRNA activation in competence control." <i>EMBO J</i> <b></b>:e103852; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32227509 32227509]; doi: [https://dx.doi.org/10.15252/embj.2019103852 10.15252/embj.2019103852]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32227509 184]. | ||
+ | #Reustle A, Di Marco M, Meyerhoff C, Nelde A, Walz JS, Winter S, Kandabarau S, Büttner F, Haag M, Backert L, Kowalewski DJ, Rausch S, Hennenlotter J, Stühler V, Scharpf M, Fend F, Stenzl A, Rammensee HG, Bedke J, Stevanović S, Schwab M, Schaeffeler E, (2020) "Integrative -omics and HLA-ligandomics analysis to identify novel drug targets for ccRCC immunotherapy." <i>Genome Med</i> <b>12</b>(1):32; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32228647 32228647]; doi: [https://dx.doi.org/10.1186/s13073-020-00731-8 10.1186/s13073-020-00731-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32228647 849]. | ||
+ | #Atlasi Y, Jafarnejad SM, Gkogkas CG, Vermeulen M, Sonenberg N, Stunnenberg HG, (2020) "The translational landscape of ground state pluripotency." <i>Nat Commun</i> <b>11</b>(1):1617; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32238817 32238817]; doi: [https://dx.doi.org/10.1038/s41467-020-15449-9 10.1038/s41467-020-15449-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32238817 48]. | ||
+ | #Morishita Y, Kabil O, Young KZ, Kellogg AP, Chang A, Arvan P, (2020) "Thyrocyte cell survival and adaptation to chronic endoplasmic reticulum stress due to misfolded thyroglobulin." <i>J Biol Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32241916 32241916]; doi: [https://dx.doi.org/10.1074/jbc.RA120.012656 10.1074/jbc.RA120.012656]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32241916 1]. | ||
+ | #Mizukami H, Hathway B, Procopio N, (2020) "Aquatic Decomposition of Mammalian Corpses: A Forensic Proteomic Approach." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32242669 32242669]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00060 10.1021/acs.jproteome.0c00060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32242669 22]. | ||
+ | #Carter SP, Moran AL, Matallanas D, McManus GJ, Blacque OE, Kennedy BN, (2020) "Genetic Deletion of Zebrafish Rab28 Causes Defective Outer Segment Shedding, but Not Retinal Degeneration." <i>Front Cell Dev Biol</i> <b>8</b>:136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32258030 32258030]; doi: [https://dx.doi.org/10.3389/fcell.2020.00136 10.3389/fcell.2020.00136]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32258030 12]. | ||
+ | #Rohlenova K, Goveia J, García-Caballero M, Subramanian A, Kalucka J, Treps L, Falkenberg KD, de Rooij LPMH, Zheng Y, Lin L, Sokol L, Teuwen LA, Geldhof V, Taverna F, Pircher A, Conradi LC, Khan S, Stegen S, Panovska D, De Smet F, Staal FJT, Mclaughlin RJ, Vinckier S, Van Bergen T, Ectors N, De Haes P, Wang J, Bolund L, Schoonjans L, Karakach TK, Yang H, Carmeliet G, Liu Y, Thienpont B, Dewerchin M, Eelen G, Li X, Luo Y, Carmeliet P, (2020) "Single-Cell RNA Sequencing Maps Endothelial Metabolic Plasticity in Pathological Angiogenesis." <i>Cell Metab</i> <b>31</b>(4):862–877.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32268117 32268117]; doi: [https://dx.doi.org/10.1016/j.cmet.2020.03.009 10.1016/j.cmet.2020.03.009]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32268117 15]. |
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 April 19, 2020.