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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 Jan. | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Jan. 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: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Lum KM, Sato Y, Beyer BA, Plaisted WC, Anglin JL, Lairson LL, Cravatt BF, (2017) "Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Chemical Proteomics." <i>ACS Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28930429 28930429]; doi: [https://dx.doi.org/10.1021/acschembio.7b00581 10.1021/acschembio.7b00581]; GPMDB: [http://gpmdb.org/data/keyword/28930429 43]. | #Lum KM, Sato Y, Beyer BA, Plaisted WC, Anglin JL, Lairson LL, Cravatt BF, (2017) "Mapping Protein Targets of Bioactive Small Molecules Using Lipid-Based Chemical Proteomics." <i>ACS Chem Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28930429 28930429]; doi: [https://dx.doi.org/10.1021/acschembio.7b00581 10.1021/acschembio.7b00581]; GPMDB: [http://gpmdb.org/data/keyword/28930429 43]. | ||
#Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28933694 28933694]; doi: [https://dx.doi.org/10.7554/eLife.26435 10.7554/eLife.26435]; GPMDB: [http://gpmdb.org/data/keyword/28933694 4]. | #Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ, (2017) "Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28933694 28933694]; doi: [https://dx.doi.org/10.7554/eLife.26435 10.7554/eLife.26435]; GPMDB: [http://gpmdb.org/data/keyword/28933694 4]. | ||
+ | #Mackinder LCM, Chen C, Leib RD, Patena W, Blum SR, Rodman M, Ramundo S, Adams CM, Jonikas MC, (2017) "A Spatial Interactome Reveals the Protein Organization of the Algal CO<sub>2</sub>-Concentrating Mechanism." <i>Cell</i> <b>171</b>(1):133–147.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28938113 28938113]; doi: [https://dx.doi.org/10.1016/j.cell.2017.08.044 10.1016/j.cell.2017.08.044]; GPMDB: [http://gpmdb.org/data/keyword/28938113 168]. | ||
#Velásquez E, Nogueira FCS, Velásquez I, Schmitt A, Falkai P, Domont GB, Martins de Souza D, (2017) "Synaptosomal proteome of the orbitofrontal cortex from schizophrenia patients using quantitative label-free and iTRAQ-based shotgun proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28949146 28949146]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00422 10.1021/acs.jproteome.7b00422]; GPMDB: [http://gpmdb.org/data/keyword/28949146 3]. | #Velásquez E, Nogueira FCS, Velásquez I, Schmitt A, Falkai P, Domont GB, Martins de Souza D, (2017) "Synaptosomal proteome of the orbitofrontal cortex from schizophrenia patients using quantitative label-free and iTRAQ-based shotgun proteomics." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28949146 28949146]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00422 10.1021/acs.jproteome.7b00422]; GPMDB: [http://gpmdb.org/data/keyword/28949146 3]. | ||
#Cuijpers SAG, Willemstein E, Vertegaal ACO, (2017) "<b>Converging SUMO and ubiquitin signaling: improved methodology identifies co-modified target proteins</b>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28951443 28951443]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000152 10.1074/mcp.TIR117.000152]; GPMDB: [http://gpmdb.org/data/keyword/28951443 102]. | #Cuijpers SAG, Willemstein E, Vertegaal ACO, (2017) "<b>Converging SUMO and ubiquitin signaling: improved methodology identifies co-modified target proteins</b>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28951443 28951443]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000152 10.1074/mcp.TIR117.000152]; GPMDB: [http://gpmdb.org/data/keyword/28951443 102]. | ||
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#Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982716 28982716]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000020 10.1074/mcp.RA117.000020]; GPMDB: [http://gpmdb.org/data/keyword/28982716 12]. | #Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982716 28982716]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000020 10.1074/mcp.RA117.000020]; GPMDB: [http://gpmdb.org/data/keyword/28982716 12]. | ||
#Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M, Furniss RCD, Dougan G, Dori-Bachash M, Yu L, Clements A, Collins JW, Elinav E, Larrouy-Maumus GJ, Choudhary JS, Frankel G, (2017) "Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo." <i>Cell Metab</i> <b>26</b>(5):738–752.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28988824 28988824]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.09.003 10.1016/j.cmet.2017.09.003]; GPMDB: [http://gpmdb.org/data/keyword/28988824 24]. | #Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M, Furniss RCD, Dougan G, Dori-Bachash M, Yu L, Clements A, Collins JW, Elinav E, Larrouy-Maumus GJ, Choudhary JS, Frankel G, (2017) "Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo." <i>Cell Metab</i> <b>26</b>(5):738–752.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28988824 28988824]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.09.003 10.1016/j.cmet.2017.09.003]; GPMDB: [http://gpmdb.org/data/keyword/28988824 24]. | ||
+ | #Kuenzi BM, Remsing Rix LL, Stewart PA, Fang B, Kinose F, Bryant AT, Boyle TA, Koomen JM, Haura EB, Rix U, (2017) "Polypharmacology-based ceritinib repurposing using integrated functional proteomics." <i>Nat Chem Biol</i> <b>13</b>(12):1222–1231; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28991240 28991240]; doi: [https://dx.doi.org/10.1038/nchembio.2489 10.1038/nchembio.2489]; GPMDB: [http://gpmdb.org/data/keyword/28991240 73]. | ||
#Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | #Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | ||
#Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | #Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | ||
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#Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | #Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | ||
#Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | #Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | ||
+ | #Mayer RL, Schwarzmeier JD, Gerner MC, Bileck A, Mader JC, Meier-Menches SM, Gerner SM, Schmetterer KG, Pukrop T, Reichle A, Slany A, Gerner C, (2017) "Proteomics and metabolomics identify molecular mechanisms of aging potentially predisposing for chronic lymphocytic leukemia." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29196338 29196338]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000425 10.1074/mcp.RA117.000425]; GPMDB: [http://gpmdb.org/data/keyword/29196338 6]. | ||
#Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | #Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | ||
#Herzog R, Boehm M, Unterwurzacher M, Wagner A, Parapatics K, Majek P, Mueller AC, Lichtenauer A, Bennett KL, Alper SL, Vychytil A, Aufricht C, Kratochwill K, (2017) "Effects of alanyl-glutamine treatment on the peritoneal dialysis effluent proteome reveal pathomechanism-associated molecular signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208752 29208752]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000186 10.1074/mcp.RA117.000186]; GPMDB: [http://gpmdb.org/data/keyword/29208752 10]. | #Herzog R, Boehm M, Unterwurzacher M, Wagner A, Parapatics K, Majek P, Mueller AC, Lichtenauer A, Bennett KL, Alper SL, Vychytil A, Aufricht C, Kratochwill K, (2017) "Effects of alanyl-glutamine treatment on the peritoneal dialysis effluent proteome reveal pathomechanism-associated molecular signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208752 29208752]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000186 10.1074/mcp.RA117.000186]; GPMDB: [http://gpmdb.org/data/keyword/29208752 10]. | ||
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#Stachowicz A, Siudut J, Suski M, Olszanecki R, Korbut R, Undas A, Wiśniewski JR, (2017) "Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism." <i>Clin Proteomics</i> <b>14</b>:38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29209155 29209155]; doi: [https://dx.doi.org/10.1186/s12014-017-9173-x 10.1186/s12014-017-9173-x]; GPMDB: [http://gpmdb.org/data/keyword/29209155 36]. | #Stachowicz A, Siudut J, Suski M, Olszanecki R, Korbut R, Undas A, Wiśniewski JR, (2017) "Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism." <i>Clin Proteomics</i> <b>14</b>:38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29209155 29209155]; doi: [https://dx.doi.org/10.1186/s12014-017-9173-x 10.1186/s12014-017-9173-x]; GPMDB: [http://gpmdb.org/data/keyword/29209155 36]. | ||
#Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY, (2017) "MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29215871 29215871]; doi: [https://dx.doi.org/10.1021/acs.analchem.7b03544 10.1021/acs.analchem.7b03544]; GPMDB: [http://gpmdb.org/data/keyword/29215871 3]. | #Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY, (2017) "MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29215871 29215871]; doi: [https://dx.doi.org/10.1021/acs.analchem.7b03544 10.1021/acs.analchem.7b03544]; GPMDB: [http://gpmdb.org/data/keyword/29215871 3]. | ||
+ | #Sciuto MR, Warnken U, Schnölzer M, Valvo C, Brunetto L, Boe A, Biffoni M, Krammer PH, De Maria R, Haas TL, (2017) "Two-Step Co-Immunoprecipitation (TIP) Enables Efficient and Highly Selective Isolation of Native Protein-Complexes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29217617 29217617]; doi: [https://dx.doi.org/10.1074/mcp.O116.065920 10.1074/mcp.O116.065920]; GPMDB: [http://gpmdb.org/data/keyword/29217617 36]. | ||
#Sobocińska J, Roszczenko-Jasińska P, Zaręba-Kozioł M, Hromada-Judycka A, Matveichuk OV, Traczyk G, Łukasiuk K, Kwiatkowska K, (2017) "LPS upregulates palmitoylated enzymes of the phosphatidylinositol cycle. An insight from proteomic studies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29217618 29217618]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000050 10.1074/mcp.RA117.000050]; GPMDB: [http://gpmdb.org/data/keyword/29217618 12]. | #Sobocińska J, Roszczenko-Jasińska P, Zaręba-Kozioł M, Hromada-Judycka A, Matveichuk OV, Traczyk G, Łukasiuk K, Kwiatkowska K, (2017) "LPS upregulates palmitoylated enzymes of the phosphatidylinositol cycle. An insight from proteomic studies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29217618 29217618]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000050 10.1074/mcp.RA117.000050]; GPMDB: [http://gpmdb.org/data/keyword/29217618 12]. | ||
#Holthoff ER, Byrum SD, Mackintosh SG, Kelly T, Tackett AJ, Quick CM, Post SR, (2017) "Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1." <i>Clin Proteomics</i> <b>14</b>:40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29225558 29225558]; doi: [https://dx.doi.org/10.1186/s12014-017-9175-8 10.1186/s12014-017-9175-8]; GPMDB: [http://gpmdb.org/data/keyword/29225558 414]. | #Holthoff ER, Byrum SD, Mackintosh SG, Kelly T, Tackett AJ, Quick CM, Post SR, (2017) "Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1." <i>Clin Proteomics</i> <b>14</b>:40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29225558 29225558]; doi: [https://dx.doi.org/10.1186/s12014-017-9175-8 10.1186/s12014-017-9175-8]; GPMDB: [http://gpmdb.org/data/keyword/29225558 414]. | ||
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#Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [http://gpmdb.org/data/keyword/29270287 12]. | #Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [http://gpmdb.org/data/keyword/29270287 12]. | ||
#Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | #Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | ||
- | #Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 5]. | + | #Abdelmegid S, Murugaiyan J, Abo-Ismail M, Caswell JL, Kelton D, Kirby GM, (2017) "Identification of Host Defense-Related Proteins Using Label-Free Quantitative Proteomic Analysis of Milk Whey from Cows with Staphylococcus aureus Subclinical Mastitis." <i>Int J Mol Sci</i> <b>19</b>(1):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29283389 29283389]; doi: [https://dx.doi.org/10.3390/ijms19010078 10.3390/ijms19010078]; GPMDB: [http://gpmdb.org/data/keyword/29283389 11]. |
+ | #Ritz D, Sani E, Debiec H, Ronco P, Neri D, Fugmann T, (2018) "Membranal and blood-soluble HLA class II peptidome analyses using data-dependent and independent acquisition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29314611 29314611]; doi: [https://dx.doi.org/10.1002/pmic.201700246 10.1002/pmic.201700246]; GPMDB: [http://gpmdb.org/data/keyword/29314611 27]. | ||
+ | #Nassa G, Giurato G, Cimmino G, Rizzo F, Ravo M, Salvati A, Nyman TA, Zhu Y, Vesterlund M, Lehtiö J, Golino P, Weisz A, Tarallo R, (2018) "Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications." <i>Sci Rep</i> <b>8</b>(1):498; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29323256 29323256]; doi: [https://dx.doi.org/10.1038/s41598-017-18985-5 10.1038/s41598-017-18985-5]; GPMDB: [http://gpmdb.org/data/keyword/29323256 1]. | ||
+ | #Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 14]. | ||
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GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Jan. 28, 2018.