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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 (1,245 publications) was current, as of September | + | 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 (1,245 publications) was current, as of September 18, 2016. |
#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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#Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL, (2013) "A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies." <i>J Proteome Res</i> <b>12</b>(9):4005–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23901793 23901793]; doi: [https://dx.doi.org/10.1021/pr400309p 10.1021/pr400309p]; GPMDB: [http://gpmdb.org/data/keyword/23901793 56]. | #Chamrád I, Rix U, Stukalov A, Gridling M, Parapatics K, Müller AC, Altiok S, Colinge J, Superti-Furga G, Haura EB, Bennett KL, (2013) "A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies." <i>J Proteome Res</i> <b>12</b>(9):4005–17; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23901793 23901793]; doi: [https://dx.doi.org/10.1021/pr400309p 10.1021/pr400309p]; GPMDB: [http://gpmdb.org/data/keyword/23901793 56]. | ||
#Oosterkamp MJ, Boeren S, Plugge CM, Schaap PJ, Stams AJ, (2013) "Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation." <i>Proteomics</i> <b>13</b>(18-19):2886–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23907812 23907812]; doi: [https://dx.doi.org/10.1002/pmic.201200571 10.1002/pmic.201200571]; GPMDB: [http://gpmdb.org/data/keyword/23907812 16]. | #Oosterkamp MJ, Boeren S, Plugge CM, Schaap PJ, Stams AJ, (2013) "Metabolic response of Alicycliphilus denitrificans strain BC toward electron acceptor variation." <i>Proteomics</i> <b>13</b>(18-19):2886–94; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23907812 23907812]; doi: [https://dx.doi.org/10.1002/pmic.201200571 10.1002/pmic.201200571]; GPMDB: [http://gpmdb.org/data/keyword/23907812 16]. | ||
- | # | + | #Gholami AM, Hahne H, Wu Z, Auer FJ, Meng C, Wilhelm M, Kuster B, (2013) "Global proteome analysis of the NCI-60 cell line panel." <i>Cell Rep</i> <b>4</b>(3):609–20; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23933261 23933261]; doi: [https://dx.doi.org/10.1016/j.celrep.2013.07.018 10.1016/j.celrep.2013.07.018]; GPMDB: [http://gpmdb.org/data/keyword/23933261 899]. |
#Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM, (2013) "Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis." <i>J Proteome Res</i> <b>12</b>(9):4101–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23937099 23937099]; doi: [https://dx.doi.org/10.1021/pr400433h 10.1021/pr400433h]; GPMDB: [http://gpmdb.org/data/keyword/23937099 112]. | #Krishnappa L, Dreisbach A, Otto A, Goosens VJ, Cranenburgh RM, Harwood CR, Becher D, van Dijl JM, (2013) "Extracytoplasmic proteases determining the cleavage and release of secreted proteins, lipoproteins, and membrane proteins in Bacillus subtilis." <i>J Proteome Res</i> <b>12</b>(9):4101–10; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23937099 23937099]; doi: [https://dx.doi.org/10.1021/pr400433h 10.1021/pr400433h]; GPMDB: [http://gpmdb.org/data/keyword/23937099 112]. | ||
#Han D, Moon S, Kim Y, Kim J, Jin J, Kim Y, (2013) "In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation." <i>Proteomics</i> <b>13</b>(20):2984–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23943505 23943505]; doi: [https://dx.doi.org/10.1002/pmic.201300091 10.1002/pmic.201300091]; GPMDB: [http://gpmdb.org/data/keyword/23943505 36]. | #Han D, Moon S, Kim Y, Kim J, Jin J, Kim Y, (2013) "In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation." <i>Proteomics</i> <b>13</b>(20):2984–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/23943505 23943505]; doi: [https://dx.doi.org/10.1002/pmic.201300091 10.1002/pmic.201300091]; GPMDB: [http://gpmdb.org/data/keyword/23943505 36]. | ||
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#Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ, (2014) "A global non-coding RNA system modulates fission yeast protein levels in response to stress." <i>Nat Commun</i> <b>5</b>:3947; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24853205 24853205]; doi: [https://dx.doi.org/10.1038/ncomms4947 10.1038/ncomms4947]; GPMDB: [http://gpmdb.org/data/keyword/24853205 60]. | #Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ, (2014) "A global non-coding RNA system modulates fission yeast protein levels in response to stress." <i>Nat Commun</i> <b>5</b>:3947; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24853205 24853205]; doi: [https://dx.doi.org/10.1038/ncomms4947 10.1038/ncomms4947]; GPMDB: [http://gpmdb.org/data/keyword/24853205 60]. | ||
#Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A, (2014) "A draft map of the human proteome." <i>Nature</i> <b>509</b>(7502):575–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24870542 24870542]; doi: [https://dx.doi.org/10.1038/nature13302 10.1038/nature13302]; GPMDB: [http://gpmdb.org/data/keyword/24870542 88]. | #Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A, (2014) "A draft map of the human proteome." <i>Nature</i> <b>509</b>(7502):575–81; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24870542 24870542]; doi: [https://dx.doi.org/10.1038/nature13302 10.1038/nature13302]; GPMDB: [http://gpmdb.org/data/keyword/24870542 88]. | ||
- | #Wilhelm M, Schlegl J, Hahne H, | + | #Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B, (2014) "Mass-spectrometry-based draft of the human proteome." <i>Nature</i> <b>509</b>(7502):582–7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24870543 24870543]; doi: [https://dx.doi.org/10.1038/nature13319 10.1038/nature13319]; GPMDB: [http://gpmdb.org/data/keyword/24870543 1257]. |
#van der Post S, Hansson GC, (2014) "Membrane protein profiling of human colon reveals distinct regional differences." <i>Mol Cell Proteomics</i> <b>13</b>(9):2277–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24889196 24889196]; doi: [https://dx.doi.org/10.1074/mcp.M114.040204 10.1074/mcp.M114.040204]; GPMDB: [http://gpmdb.org/data/keyword/24889196 16]. | #van der Post S, Hansson GC, (2014) "Membrane protein profiling of human colon reveals distinct regional differences." <i>Mol Cell Proteomics</i> <b>13</b>(9):2277–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24889196 24889196]; doi: [https://dx.doi.org/10.1074/mcp.M114.040204 10.1074/mcp.M114.040204]; GPMDB: [http://gpmdb.org/data/keyword/24889196 16]. | ||
#Kim MS, Zhong Y, Yachida S, Rajeshkumar NV, Abel ML, Marimuthu A, Mudgal K, Hruban RH, Poling JS, Tyner JW, Maitra A, Iacobuzio-Donahue CA, Pandey A, (2014) "Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics." <i>Mol Cell Proteomics</i> <b>13</b>(11):2803–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24895378 24895378]; doi: [https://dx.doi.org/10.1074/mcp.M114.038547 10.1074/mcp.M114.038547]; GPMDB: [http://gpmdb.org/data/keyword/24895378 24]. | #Kim MS, Zhong Y, Yachida S, Rajeshkumar NV, Abel ML, Marimuthu A, Mudgal K, Hruban RH, Poling JS, Tyner JW, Maitra A, Iacobuzio-Donahue CA, Pandey A, (2014) "Heterogeneity of pancreatic cancer metastases in a single patient revealed by quantitative proteomics." <i>Mol Cell Proteomics</i> <b>13</b>(11):2803–11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/24895378 24895378]; doi: [https://dx.doi.org/10.1074/mcp.M114.038547 10.1074/mcp.M114.038547]; GPMDB: [http://gpmdb.org/data/keyword/24895378 24]. | ||
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#Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | #Dobó J, Szakács D, Oroszlán G, Kortvely E, Kiss B, Boros E, Szász R, Závodszky P, Gál P, Pál G, (2016) "MASP-3 is the exclusive pro-factor D activator in resting blood: the lectin and the alternative complement pathways are fundamentally linked." <i>Sci Rep</i> <b>6</b>:31877; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27535802 27535802]; doi: [https://dx.doi.org/10.1038/srep31877 10.1038/srep31877]; GPMDB: [http://gpmdb.org/data/keyword/27535802 6]. | ||
#Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | #Zhang P, Karani R, Turner RL, Dufresne C, Ferri S, Van Eyk JE, Semba RD, (2016) "The proteome of normal human retrobulbar optic nerve and sclera." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27538499 27538499]; doi: [https://dx.doi.org/10.1002/pmic.201600229 10.1002/pmic.201600229]; GPMDB: [http://gpmdb.org/data/keyword/27538499 60]. | ||
+ | #Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP, (2016) "Integration of omic networks in a developmental atlas of maize." <i>Science</i> <b>353</b>(6301):814–8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27540173 27540173]; doi: [https://dx.doi.org/10.1126/science.aag1125 10.1126/science.aag1125]; GPMDB: [http://gpmdb.org/data/keyword/27540173 568]. | ||
#Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8<sup>+</sup> T Cells." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. | #Ross SH, Rollings C, Anderson KE, Hawkins PT, Stephens LR, Cantrell DA, (2016) "Phosphoproteomic Analyses of Interleukin 2 Signaling Reveal Integrated JAK Kinase-Dependent and -Independent Networks in CD8<sup>+</sup> T Cells." <i>Immunity</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27566939 27566939]; doi: [https://dx.doi.org/10.1016/j.immuni.2016.07.022 10.1016/j.immuni.2016.07.022]; GPMDB: [http://gpmdb.org/data/keyword/27566939 208]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list (1,245 publications) was current, as of September 18, 2016.