Line 27: | Line 27: | ||
==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 March 8, 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]. | ||
Line 2,050: | Line 2,050: | ||
#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 27]. | ||
#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]. | ||
Line 2,128: | Line 2,129: | ||
#Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M, (2020) "Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery." <i>J Proteome Res</i> <b>19</b>(1):129–143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31661273 31661273]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00441 10.1021/acs.jproteome.9b00441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31661273 4]. | #Arima N, Sasaki Y, Lee LH, Zhang H, Figueiredo JL, Mlynarchik AK, Qiao J, Yamada I, Higashi H, Ha AH, Halu A, Mizuno K, Singh SA, Yamazaki Y, Aikawa M, (2020) "Multiorgan Systems Study Reveals Igfbp7 as a Suppressor of Gluconeogenesis after Gastric Bypass Surgery." <i>J Proteome Res</i> <b>19</b>(1):129–143; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31661273 31661273]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00441 10.1021/acs.jproteome.9b00441]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31661273 4]. | ||
#Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | #Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K, (2019) "Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes." <i>Cell Rep</i> <b>29</b>(5):1351–1368.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31665645 31665645]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.09.060 10.1016/j.celrep.2019.09.060]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31665645 122]. | ||
- | #Sohier P, Sanson R, Leduc M, Audebourg A, Broussard C, Salnot V, Just PA, Pasmant E, Mayeux P, Guillonneau F, Romagnolo B, Perret C, Terris B, (2019) "Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas reveals the heterogeneous nature of traditional serrated adenomas compared to other colorectal adenomas." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31729028 31729028]; doi: [https://dx.doi.org/10.1002/path.5366 10.1002/path.5366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31729028 | + | #Alvarez Hayes J, Surmann K, Lamberti Y, Depke M, Dhople V, Blancá B, Ruiz E, Vecerek B, Schmidt F, Völker U, Rodriguez ME, (2020) "Hfq modulates global protein pattern and stress response in Bordetella pertussis." <i>J Proteomics</i> <b>211</b>:103559; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31669358 31669358]; doi: [https://dx.doi.org/10.1016/j.jprot.2019.103559 10.1016/j.jprot.2019.103559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31669358 16]. |
+ | #Sohier P, Sanson R, Leduc M, Audebourg A, Broussard C, Salnot V, Just PA, Pasmant E, Mayeux P, Guillonneau F, Romagnolo B, Perret C, Terris B, (2019) "Proteome analysis of formalin-fixed paraffin-embedded colorectal adenomas reveals the heterogeneous nature of traditional serrated adenomas compared to other colorectal adenomas." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31729028 31729028]; doi: [https://dx.doi.org/10.1002/path.5366 10.1002/path.5366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31729028 61]. | ||
#Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. | #Newey A, Griffiths B, Michaux J, Pak HS, Stevenson BJ, Woolston A, Semiannikova M, Spain G, Barber LJ, Matthews N, Rao S, Watkins D, Chau I, Coukos G, Racle J, Gfeller D, Starling N, Cunningham D, Bassani-Sternberg M, Gerlinger M, (2019) "Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment." <i>J Immunother Cancer</i> <b>7</b>(1):309; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31735170 31735170]; doi: [https://dx.doi.org/10.1186/s40425-019-0769-8 10.1186/s40425-019-0769-8]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31735170 193]. | ||
#Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | #Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I, (2019) "TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set." <i>Anal Chem</i> <b>91</b>(24):15941–15950; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31738517 31738517]; doi: [https://dx.doi.org/10.1021/acs.analchem.9b04474 10.1021/acs.analchem.9b04474]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31738517 20]. | ||
Line 2,145: | Line 2,147: | ||
#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]. | ||
+ | #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]. | ||
#Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31975592 31975592]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00800 10.1021/acs.jproteome.9b00800]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31975592 3]. | #Meng K, Lu S, Yan X, Sun Y, Gao J, Wang Y, Yin X, Sun Z, He QY, (2020) "Quantitative Mitochondrial Proteomics Reveals ANXA7 as a Crucial Factor in Mitophagy." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31975592 31975592]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00800 10.1021/acs.jproteome.9b00800]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31975592 3]. | ||
#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]. | ||
+ | #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]. | ||
+ | #Storey AJ, Hardman RE, Byrum SD, Mackintosh SG, Edmondson RD, Wahls WP, Tackett AJ, Lewis JA, (2020) "Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32027144 32027144]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00704 10.1021/acs.jproteome.9b00704]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32027144 2]. | ||
+ | #Eldridge MJG, Pereira JM, Impens F, Hamon MA, (2020) "Active nuclear import of the deacetylase Sirtuin-2 is controlled by its C-terminus and importins." <i>Sci Rep</i> <b>10</b>(1):2034; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32042025 32042025]; doi: [https://dx.doi.org/10.1038/s41598-020-58397-6 10.1038/s41598-020-58397-6]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32042025 6]. | ||
+ | #Zhao Q, Laverdure JP, Lanoix J, Durette C, Coté C, Bonneil E, Laumont CM, Gendron P, Vincent K, Courcelles M, Lemieux S, Millar DG, Ohashi PS, Thibault P, Perreault C, (2020) "Proteogenomics uncovers a vast repertoire of shared tumor-specific antigens in ovarian cancer." <i>Cancer Immunol Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32047025 32047025]; doi: [https://dx.doi.org/10.1158/2326-6066.CIR-19-0541 10.1158/2326-6066.CIR-19-0541]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32047025 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]. | ||
+ | #Ray S, Valekunja UK, Stangherlin A, Howell SA, Snijders AP, Damodaran G, Reddy AB, (2020) "Circadian rhythms in the absence of the clock gene <i>Bmal1</i>." <i>Science</i> <b>367</b>(6479):800–806; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32054765 32054765]; doi: [https://dx.doi.org/10.1126/science.aaw7365 10.1126/science.aaw7365]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32054765 40]. | ||
+ | #Kosok M, Alli-Shaik A, Bay BH, Gunaratne J, (2020) "Comprehensive Proteomic Characterization Reveals Subclass-Specific Molecular Aberrations within Triple-negative Breast Cancer." <i>iScience</i> <b>23</b>(2):100868; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32058975 32058975]; doi: [https://dx.doi.org/10.1016/j.isci.2020.100868 10.1016/j.isci.2020.100868]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32058975 1]. | ||
+ | #Dou Y, Kawaler EA, Cui Zhou D, Gritsenko MA, Huang C, Blumenberg L, Karpova A, Petyuk VA, Savage SR, Satpathy S, Liu W, Wu Y, Tsai CF, Wen B, Li Z, Cao S, Moon J, Shi Z, Cornwell M, Wyczalkowski MA, Chu RK, Vasaikar S, Zhou H, Gao Q, Moore RJ, Li K, Sethuraman S, Monroe ME, Zhao R, Heiman D, Krug K, Clauser K, Kothadia R, Maruvka Y, Pico AR, Oliphant AE, Hoskins EL, Pugh SL, Beecroft SJI, Adams DW, Jarman JC, Kong A, Chang HY, Reva B, Liao Y, Rykunov D, Colaprico A, Chen XS, Czekański A, Jędryka M, Matkowski R, Wiznerowicz M, Hiltke T, Boja E, Kinsinger CR, Mesri M, Robles AI, Rodriguez H, Mutch D, Fuh K, Ellis MJ, DeLair D, Thiagarajan M, Mani DR, Getz G, Noble M, Nesvizhskii AI, Wang P, Anderson ML, Levine DA, Smith RD, Payne SH, Ruggles KV, Rodland KD, Ding L, Zhang B, Liu T, Fenyö D, Clinical Proteomic Tumor Analysis Consortium., (2020) "Proteogenomic Characterization of Endometrial Carcinoma." <i>Cell</i> <b>180</b>(4):729–748.e26; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32059776 32059776]; doi: [https://dx.doi.org/10.1016/j.cell.2020.01.026 10.1016/j.cell.2020.01.026]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32059776 208]. | ||
+ | #Kalaora S, Lee JS, Barnea E, Levy R, Greenberg P, Alon M, Yagel G, Bar Eli G, Oren R, Peri A, Patkar S, Bitton L, Rosenberg SA, Lotem M, Levin Y, Admon A, Ruppin E, Samuels Y, (2020) "Immunoproteasome expression is associated with better prognosis and response to checkpoint therapies in melanoma." <i>Nat Commun</i> <b>11</b>(1):896; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32060274 32060274]; doi: [https://dx.doi.org/10.1038/s41467-020-14639-9 10.1038/s41467-020-14639-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32060274 30]. | ||
+ | #Kurimchak AM, Herrera-Montávez C, Brown J, Johnson KJ, Sodi V, Srivastava N, Kumar V, Deihimi S, O'Brien S, Peri S, Mantia-Smaldone GM, Jain A, Winters RM, Cai KQ, Chernoff J, Connolly DC, Duncan JS, (2020) "Functional proteomics interrogation of the kinome identifies MRCKA as a therapeutic target in high-grade serous ovarian carcinoma." <i>Sci Signal</i> <b>13</b>(619):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32071169 32071169]; doi: [https://dx.doi.org/10.1126/scisignal.aax8238 10.1126/scisignal.aax8238]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32071169 51]. | ||
+ | #Touzelet O, Broadbent L, Armstrong SD, Aljabr W, Cloutman-Green E, Power UF, Hiscox JA, (2020) "The secretome profiling of a pediatric airway epithelium infected with hRSV identified aberrant apical/basolateral trafficking and novel immune modulating (CXCL6, CXCL16, CSF3) and antiviral (CEACAM1) proteins." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32075873 32075873]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001546 10.1074/mcp.RA119.001546]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32075873 15]. | ||
+ | #Peters F, Tellkamp F, Brodesser S, Wachsmuth E, Tosetti B, Karow U, Bloch W, Utermöhlen O, Krönke M, Niessen CM, (2020) "Murine Epidermal Ceramide Synthase 4 is a Key Regulator of Skin Barrier Homeostasis." <i>J Invest Dermatol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32092351 32092351]; doi: [https://dx.doi.org/10.1016/j.jid.2020.02.006 10.1016/j.jid.2020.02.006]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32092351 40]. | ||
+ | #Fan Y, Cheng Y, Li Y, Chen B, Wang Z, Wei T, Zhang H, Guo Y, Wang Q, Wei Y, Chen F, Sha J, Guo X, Wang L, (2020) "Phosphoproteomic Analysis of Neonatal Regenerative Myocardium Revealed Important Roles of CHK1 via Activating mTORC1/P70S6K Pathway." <i>Circulation</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32098494 32098494]; doi: [https://dx.doi.org/10.1161/CIRCULATIONAHA.119.040747 10.1161/CIRCULATIONAHA.119.040747]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32098494 31]. | ||
+ | #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]. |
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 March 8, 2020.