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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. | 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. | ||
- | <b>CAUTION</b>: Many papers contain serious errors in their | + | <b>CAUTION</b>:Many datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript. |
==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 January 1, 2024. |
#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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#Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K, (2016) "It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana." <i>Plant Cell</i> <b>28</b>(1):6–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26744219 26744219]; doi: [https://dx.doi.org/10.1105/tpc.15.00878 10.1105/tpc.15.00878]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26744219 110]. | #Walton A, Stes E, Cybulski N, Van Bel M, Iñigo S, Durand AN, Timmerman E, Heyman J, Pauwels L, De Veylder L, Goossens A, De Smet I, Coppens F, Goormachtig S, Gevaert K, (2016) "It's Time for Some "Site"-Seeing: Novel Tools to Monitor the Ubiquitin Landscape in Arabidopsis thaliana." <i>Plant Cell</i> <b>28</b>(1):6–16; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26744219 26744219]; doi: [https://dx.doi.org/10.1105/tpc.15.00878 10.1105/tpc.15.00878]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26744219 110]. | ||
#Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745281 72]. | #Wandinger SK, Lahortiga I, Jacobs K, Klammer M, Jordan N, Elschenbroich S, Parade M, Jacoby E, Linders JT, Brehmer D, Cools J, Daub H, (2016) "Quantitative Phosphoproteomics Analysis of ERBB3/ERBB4 Signaling." <i>PLoS One</i> <b>11</b>(1):e0146100; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745281 26745281]; doi: [https://dx.doi.org/10.1371/journal.pone.0146100 10.1371/journal.pone.0146100]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745281 72]. | ||
+ | #Finne K, Marti HP, Leh S, Skogstrand T, Vethe H, Tenstad O, Berven FS, Scherer A, Vikse BE, (2016) "Proteomic Analysis of Minimally Damaged Renal Tubular Tissue from Two-Kidney-One-Clip Hypertensive Rats Demonstrates Extensive Changes Compared to Tissue from Controls." <i>Nephron</i> <b>132</b>(1):70–80; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26745798 26745798]; doi: [https://dx.doi.org/10.1159/000442825 10.1159/000442825]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26745798 10]. | ||
#Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:8992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26754106 2]. | #Christoforou A, Mulvey CM, Breckels LM, Geladaki A, Hurrell T, Hayward PC, Naake T, Gatto L, Viner R, Martinez Arias A, Lilley KS, (2016) "A draft map of the mouse pluripotent stem cell spatial proteome." <i>Nat Commun</i> <b>7</b>:8992; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26754106 26754106]; doi: [https://dx.doi.org/10.1038/ncomms9992 10.1038/ncomms9992]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26754106 2]. | ||
#Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26755559 17]. | #Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Pawson T, Colwill K, (2016) "Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90." <i>Mol Cell Biol</i> <b>36</b>(6):1007–18; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/26755559 26755559]; doi: [https://dx.doi.org/10.1128/MCB.01045-15 10.1128/MCB.01045-15]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/26755559 17]. | ||
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#Chymkowitch P, Nguéa P A, Aanes H, Robertson J, Klungland A, Enserink JM, (2017) "TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(5):1039–1044; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096404 28096404]; doi: [https://dx.doi.org/10.1073/pnas.1615093114 10.1073/pnas.1615093114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28096404 21]. | #Chymkowitch P, Nguéa P A, Aanes H, Robertson J, Klungland A, Enserink JM, (2017) "TORC1-dependent sumoylation of Rpc82 promotes RNA polymerase III assembly and activity." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(5):1039–1044; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28096404 28096404]; doi: [https://dx.doi.org/10.1073/pnas.1615093114 10.1073/pnas.1615093114]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28096404 21]. | ||
#Reckel S, Hamelin R, Georgeon S, Armand F, Jolliet Q, Chiappe D, Moniatte M, Hantschel O, (2017) "Differential signaling networks of Bcr-Abl p210 and p190 kinases in leukemia cells defined by functional proteomics." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111465 28111465]; doi: [https://dx.doi.org/10.1038/leu.2017.36 10.1038/leu.2017.36]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111465 10]. | #Reckel S, Hamelin R, Georgeon S, Armand F, Jolliet Q, Chiappe D, Moniatte M, Hantschel O, (2017) "Differential signaling networks of Bcr-Abl p210 and p190 kinases in leukemia cells defined by functional proteomics." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111465 28111465]; doi: [https://dx.doi.org/10.1038/leu.2017.36 10.1038/leu.2017.36]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111465 10]. | ||
+ | #Tsiatsiani L, Giansanti P, Scheltema RA, van den Toorn H, Overall CM, Altelaar AF, Heck AJ, (2017) "Opposite Electron-Transfer Dissociation and Higher-Energy Collisional Dissociation Fragmentation Characteristics of Proteolytic K/R(X)<sub>n</sub> and (X)<sub>n</sub>K/R Peptides Provide Benefits for Peptide Sequencing in Proteomics and Phosphoproteomics." <i>J Proteome Res</i> <b>16</b>(2):852–861; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28111955 28111955]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00825 10.1021/acs.jproteome.6b00825]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28111955 28]. | ||
#Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28112733 311]. | #Hendriks IA, Lyon D, Young C, Jensen LJ, Vertegaal AC, Nielsen ML, (2017) "Site-specific mapping of the human SUMO proteome reveals co-modification with phosphorylation." <i>Nat Struct Mol Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28112733 28112733]; doi: [https://dx.doi.org/10.1038/nsmb.3366 10.1038/nsmb.3366]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28112733 311]. | ||
#Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A, (2017) "Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties." <i>PLoS One</i> <b>12</b>(1):e0170524; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28114419 28114419]; doi: [https://dx.doi.org/10.1371/journal.pone.0170524 10.1371/journal.pone.0170524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28114419 24]. | #Badalato N, Guillot A, Sabarly V, Dubois M, Pourette N, Pontoire B, Robert P, Bridier A, Monnet V, Sousa DZ, Durand S, Mazéas L, Buléon A, Bouchez T, Mortha G, Bize A, (2017) "Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties." <i>PLoS One</i> <b>12</b>(1):e0170524; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28114419 28114419]; doi: [https://dx.doi.org/10.1371/journal.pone.0170524 10.1371/journal.pone.0170524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28114419 24]. | ||
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#Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28387123 12]. | #Young C, Podtelejnikov AV, Nielsen ML, (2017) "Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28387123 28387123]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b01055 10.1021/acs.jproteome.6b01055]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28387123 12]. | ||
#Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388408 3]. | #Beach RR, Ricci-Tam C, Brennan CM, Moomau CA, Hsu PH, Hua B, Silberman RE, Springer M, Amon A, (2017) "Aneuploidy Causes Non-genetic Individuality." <i>Cell</i> <b>169</b>(2):229–242.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388408 28388408]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.021 10.1016/j.cell.2017.03.021]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388408 3]. | ||
+ | #Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ, (2017) "An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells." <i>Cell</i> <b>169</b>(2):350–360.e12; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28388416 28388416]; doi: [https://dx.doi.org/10.1016/j.cell.2017.03.022 10.1016/j.cell.2017.03.022]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28388416 45]. | ||
#Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28396511 17]. | #Worst TS, von Hardenberg J, Gross JC, Erben P, Schnoelzer M, Hausser I, Bugert P, Michel MS, Boutros M, (2017) "A database-augmented, exosome-based mass spectrometry approach exemplarily identifies circulating claudin 3 as biomarker in prostate cancer." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28396511 28396511]; doi: [https://dx.doi.org/10.1074/mcp.M117.068577 10.1074/mcp.M117.068577]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28396511 17]. | ||
#Mohr S, Doebele C, Comoglio F, Berg T, Beck J, Bohnenberger H, Alexe G, Corso J, Ströbel P, Wachter A, Beissbarth T, Schnütgen F, Cremer A, Haetscher N, Göllner S, Rouhi A, Palmqvist L, Rieger MA, Schroeder T, Bönig H, Müller-Tidow C, Kuchenbauer F, Schütz E, Green AR, Urlaub H, Stegmaier K, Humphries RK, Serve H, Oellerich T, (2017) "Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia." <i>Cancer Cell</i> <b>31</b>(4):549–562.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28399410 28399410]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.03.001 10.1016/j.ccell.2017.03.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28399410 30]. | #Mohr S, Doebele C, Comoglio F, Berg T, Beck J, Bohnenberger H, Alexe G, Corso J, Ströbel P, Wachter A, Beissbarth T, Schnütgen F, Cremer A, Haetscher N, Göllner S, Rouhi A, Palmqvist L, Rieger MA, Schroeder T, Bönig H, Müller-Tidow C, Kuchenbauer F, Schütz E, Green AR, Urlaub H, Stegmaier K, Humphries RK, Serve H, Oellerich T, (2017) "Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia." <i>Cancer Cell</i> <b>31</b>(4):549–562.e11; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28399410 28399410]; doi: [https://dx.doi.org/10.1016/j.ccell.2017.03.001 10.1016/j.ccell.2017.03.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/28399410 30]. | ||
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#Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K, (2018) "Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling." <i>Cell</i> <b>172</b>(1-2):106–120.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29249356 29249356]; doi: [https://dx.doi.org/10.1016/j.cell.2017.11.023 10.1016/j.cell.2017.11.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29249356 24]. | #Brumbaugh J, Di Stefano B, Wang X, Borkent M, Forouzmand E, Clowers KJ, Ji F, Schwarz BA, Kalocsay M, Elledge SJ, Chen Y, Sadreyev RI, Gygi SP, Hu G, Shi Y, Hochedlinger K, (2018) "Nudt21 Controls Cell Fate by Connecting Alternative Polyadenylation to Chromatin Signaling." <i>Cell</i> <b>172</b>(1-2):106–120.e21; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29249356 29249356]; doi: [https://dx.doi.org/10.1016/j.cell.2017.11.023 10.1016/j.cell.2017.11.023]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29249356 24]. | ||
#Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29251727 33]. | #Krogager TP, Ernst RJ, Elliott TS, Calo L, Beránek V, Ciabatti E, Spillantini MG, Tripodi M, Hastings MH, Chin JW, (2017) "Labeling and identifying cell-specific proteomes in the mouse brain." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29251727 29251727]; doi: [https://dx.doi.org/10.1038/nbt.4056 10.1038/nbt.4056]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29251727 33]. | ||
+ | #Mackmull MT, Klaus B, Heinze I, Chokkalingam M, Beyer A, Russell RB, Ori A, Beck M, (2017) "Landscape of nuclear transport receptor cargo specificity." <i>Mol Syst Biol</i> <b>13</b>(12):962; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29254951 29254951]; doi: [https://dx.doi.org/10.15252/msb.20177608 10.15252/msb.20177608]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29254951 315]. | ||
#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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.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: [https://gpmdb.thegpm.org/data/keyword/29281840 2]. | ||
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#Drabikowski K, Ferralli J, Kistowski M, Oledzki J, Dadlez M, Chiquet-Ehrismann R, (2018) "Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling." <i>Sci Rep</i> <b>8</b>(1):1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348603 29348603]; doi: [https://dx.doi.org/10.1038/s41598-018-19424-9 10.1038/s41598-018-19424-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348603 37]. | #Drabikowski K, Ferralli J, Kistowski M, Oledzki J, Dadlez M, Chiquet-Ehrismann R, (2018) "Comprehensive list of SUMO targets in Caenorhabditis elegans and its implication for evolutionary conservation of SUMO signaling." <i>Sci Rep</i> <b>8</b>(1):1139; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348603 29348603]; doi: [https://dx.doi.org/10.1038/s41598-018-19424-9 10.1038/s41598-018-19424-9]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348603 37]. | ||
#Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348610 2]. | #Gao Y, Ge W, (2018) "The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis." <i>Cell Death Dis</i> <b>9</b>(2):33; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29348610 29348610]; doi: [https://dx.doi.org/10.1038/s41419-017-0040-5 10.1038/s41419-017-0040-5]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29348610 2]. | ||
+ | #Phuyal S, Kasem M, Knittelfelder O, Sharma A, Fonseca DM, Vebraite V, Shaposhnikov S, Slupphaug G, Skaug V, Zienolddiny S, (2018) "Characterization of the proteome and lipidome profiles of human lung cells after low dose and chronic exposure to multiwalled carbon nanotubes." <i>Nanotoxicology</i> <b>12</b>(2):138–152; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350075 29350075]; doi: [https://dx.doi.org/10.1080/17435390.2018.1425500 10.1080/17435390.2018.1425500]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350075 24]. | ||
#Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350274 6]. | #Mustafa DAM, Pedrosa RMSM, Smid M, van der Weiden M, de Weerd V, Nigg AL, Berrevoets C, Zeneyedpour L, Priego N, Valiente M, Luider TM, Debets R, Martens JWM, Foekens JA, Sieuwerts AM, Kros JM, (2018) "T lymphocytes facilitate brain metastasis of breast cancer by inducing Guanylate-Binding Protein 1 expression." <i>Acta Neuropathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350274 29350274]; doi: [https://dx.doi.org/10.1007/s00401-018-1806-2 10.1007/s00401-018-1806-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350274 6]. | ||
#Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS, (2018) "Proteomics Analysis of Skeletal Muscle from Leptin-Deficient Ob/Ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350465 29350465]; doi: [https://dx.doi.org/10.1002/pmic.201700375 10.1002/pmic.201700375]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350465 22]. | #Schönke M, Björnholm M, Chibalin AV, Zierath JR, Deshmukh AS, (2018) "Proteomics Analysis of Skeletal Muscle from Leptin-Deficient Ob/Ob Mice Reveals Adaptive Remodeling of Metabolic Characteristics and Fiber Type Composition." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29350465 29350465]; doi: [https://dx.doi.org/10.1002/pmic.201700375 10.1002/pmic.201700375]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/29350465 22]. | ||
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#Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | #Nilsen BW, Simon-Santamaria J, Örtengren U, Jensen E, Bruun JA, Michelsen VB, Sørensen KK, (2018) "Dose- and time-dependent effects of triethylene glycol dimethacrylate on the proteome of human THP-1 monocytes." <i>Eur J Oral Sci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30051916 30051916]; doi: [https://dx.doi.org/10.1111/eos.12559 10.1111/eos.12559]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30051916 92]. | ||
#Stokman MF, Bijnsdorp IV, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Giles RH, Bongers EMHF, Knoers NVAM, Lilien MR, Jiménez CR, Renkema KY, (2018) "Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30071318 30071318]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.07.008 10.1016/j.jprot.2018.07.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30071318 120]. | #Stokman MF, Bijnsdorp IV, Schelfhorst T, Pham TV, Piersma SR, Knol JC, Giles RH, Bongers EMHF, Knoers NVAM, Lilien MR, Jiménez CR, Renkema KY, (2018) "Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30071318 30071318]; doi: [https://dx.doi.org/10.1016/j.jprot.2018.07.008 10.1016/j.jprot.2018.07.008]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30071318 120]. | ||
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#Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | #Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D, (2018) "A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells." <i>Exp Mol Med</i> <b>50</b>(8):93; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076294 30076294]; doi: [https://dx.doi.org/10.1038/s12276-018-0120-3 10.1038/s12276-018-0120-3]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076294 24]. | ||
#de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ, (2018) "A widespread alternate form of cap-dependent mRNA translation initiation." <i>Nat Commun</i> <b>9</b>(1):3068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076308 30076308]; doi: [https://dx.doi.org/10.1038/s41467-018-05539-0 10.1038/s41467-018-05539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076308 21]. | #de la Parra C, Ernlund A, Alard A, Ruggles K, Ueberheide B, Schneider RJ, (2018) "A widespread alternate form of cap-dependent mRNA translation initiation." <i>Nat Commun</i> <b>9</b>(1):3068; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30076308 30076308]; doi: [https://dx.doi.org/10.1038/s41467-018-05539-0 10.1038/s41467-018-05539-0]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30076308 21]. | ||
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#Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 30]. | #Yanovich G, Agmon H, Harel M, Sonnenblick A, Peretz T, Geiger T, (2018) "Clinical Proteomics of Breast Cancer Reveals a Novel Layer of Breast Cancer Classification." <i>Cancer Res</i> <b>78</b>(20):6001–6010; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30154156 30154156]; doi: [https://dx.doi.org/10.1158/0008-5472.CAN-18-1079 10.1158/0008-5472.CAN-18-1079]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30154156 30]. | ||
#Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | #Ten-Doménech I, Simó-Alfonso EF, Herrero-Martínez JM, (2018) "Improving Fractionation of Human Milk Proteins through Calcium Phosphate Coprecipitation and Their Rapid Characterization by Capillary Electrophoresis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30156851 30156851]; doi: [https://dx.doi.org/10.1021/acs.jproteome.8b00526 10.1021/acs.jproteome.8b00526]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30156851 26]. | ||
+ | #Guneykaya D, Ivanov A, Hernandez DP, Haage V, Wojtas B, Meyer N, Maricos M, Jordan P, Buonfiglioli A, Gielniewski B, Ochocka N, Cömert C, Friedrich C, Artiles LS, Kaminska B, Mertins P, Beule D, Kettenmann H, Wolf SA, (2018) "Transcriptional and Translational Differences of Microglia from Male and Female Brains." <i>Cell Rep</i> <b>24</b>(10):2773–2783.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30184509 30184509]; doi: [https://dx.doi.org/10.1016/j.celrep.2018.08.001 10.1016/j.celrep.2018.08.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30184509 8]. | ||
#Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | #Carnielli CM, Macedo CCS, De Rossi T, Granato DC, Rivera C, Domingues RR, Pauletti BA, Yokoo S, Heberle H, Busso-Lopes AF, Cervigne NK, Sawazaki-Calone I, Meirelles GV, Marchi FA, Telles GP, Minghim R, Ribeiro ACP, Brandão TB, de Castro G Jr, González-Arriagada WA, Gomes A, Penteado F, Santos-Silva AR, Lopes MA, Rodrigues PC, Sundquist E, Salo T, da Silva SD, Alaoui-Jamali MA, Graner E, Fox JW, Coletta RD, Paes Leme AF, (2018) "Combining discovery and targeted proteomics reveals a prognostic signature in oral cancer." <i>Nat Commun</i> <b>9</b>(1):3598; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30185791 30185791]; doi: [https://dx.doi.org/10.1038/s41467-018-05696-2 10.1038/s41467-018-05696-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30185791 122]. | ||
#Abreha MH, Dammer EB, Ping L, Zhang T, Duong DM, Gearing M, Lah JJ, Levey AI, Seyfried NT, (2018) "Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease." <i>Proteomics</i> <b>18</b>(20):e1800108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30230243 30230243]; doi: [https://dx.doi.org/10.1002/pmic.201800108 10.1002/pmic.201800108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30230243 29]. | #Abreha MH, Dammer EB, Ping L, Zhang T, Duong DM, Gearing M, Lah JJ, Levey AI, Seyfried NT, (2018) "Quantitative Analysis of the Brain Ubiquitylome in Alzheimer's Disease." <i>Proteomics</i> <b>18</b>(20):e1800108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30230243 30230243]; doi: [https://dx.doi.org/10.1002/pmic.201800108 10.1002/pmic.201800108]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30230243 29]. | ||
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#Fornecker LM, Muller L, Bertrand F, Paul N, Pichot A, Herbrecht R, Chenard MP, Mauvieux L, Vallat L, Bahram S, Cianférani S, Carapito R, Carapito C, (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." <i>Sci Rep</i> <b>9</b>(1):895; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30696890 30696890]; doi: [https://dx.doi.org/10.1038/s41598-018-37273-4 10.1038/s41598-018-37273-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30696890 20]. | #Fornecker LM, Muller L, Bertrand F, Paul N, Pichot A, Herbrecht R, Chenard MP, Mauvieux L, Vallat L, Bahram S, Cianférani S, Carapito R, Carapito C, (2019) "Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma." <i>Sci Rep</i> <b>9</b>(1):895; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30696890 30696890]; doi: [https://dx.doi.org/10.1038/s41598-018-37273-4 10.1038/s41598-018-37273-4]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30696890 20]. | ||
#McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 22]. | #McKetney J, Runde RM, Hebert AS, Salamat S, Roy S, Coon JJ, (2019) "Proteomic Atlas of the Human Brain in Alzheimer's Disease." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30735395 30735395]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00004 10.1021/acs.jproteome.9b00004]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30735395 22]. | ||
+ | #West KL, Byrum SD, Mackintosh SG, Edmondson RD, Taverna SD, Tackett AJ, (2019) "Proteomic characterization of the arsenic response locus in S. cerevisiae." <i>Epigenetics</i> <b>14</b>(2):130–145; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30739529 30739529]; doi: [https://dx.doi.org/10.1080/15592294.2019.1580110 10.1080/15592294.2019.1580110]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30739529 9]. | ||
#Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG, (2019) "Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae." <i>FEMS Yeast Res</i> <b>19</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30753445 30753445]; doi: [https://dx.doi.org/10.1093/femsyr/foz014 10.1093/femsyr/foz014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30753445 48]. | #Dikicioglu D, Nightingale DJH, Wood V, Lilley KS, Oliver SG, (2019) "Transcriptional regulation of the genes involved in protein metabolism and processing in Saccharomyces cerevisiae." <i>FEMS Yeast Res</i> <b>19</b>(2):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30753445 30753445]; doi: [https://dx.doi.org/10.1093/femsyr/foz014 10.1093/femsyr/foz014]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30753445 48]. | ||
#Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D, (2019) "An immunoproteomic approach to characterize the CAR interactome and signalosome." <i>Sci Signal</i> <b>12</b>(568):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30755478 30755478]; doi: [https://dx.doi.org/10.1126/scisignal.aap9777 10.1126/scisignal.aap9777]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30755478 54]. | #Ramello MC, Benzaïd I, Kuenzi BM, Lienlaf-Moreno M, Kandell WM, Santiago DN, Pabón-Saldaña M, Darville L, Fang B, Rix U, Yoder S, Berglund A, Koomen JM, Haura EB, Abate-Daga D, (2019) "An immunoproteomic approach to characterize the CAR interactome and signalosome." <i>Sci Signal</i> <b>12</b>(568):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/30755478 30755478]; doi: [https://dx.doi.org/10.1126/scisignal.aap9777 10.1126/scisignal.aap9777]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/30755478 54]. | ||
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#Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 523]. | #Charitou T, Srihari S, Lynn MA, Jarboui MA, Fasterius E, Moldovan M, Shirasawa S, Tsunoda T, Ueffing M, Xie J, Xin J, Wang X, Proud CG, Boldt K, Al-Khalili Szigyarto C, Kolch W, Lynn DJ, (2019) "Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRAS<sup>G13D</sup> mutation." <i>Br J Cancer</i> <b>121</b>(1):37–50; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31133691 31133691]; doi: [https://dx.doi.org/10.1038/s41416-019-0477-7 10.1038/s41416-019-0477-7]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31133691 523]. | ||
#Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | #Sap KA, Guler AT, Bezstarosti K, Bury AE, Juenemann K, Demmers J, Reits E, (2019) "Global Proteome and Ubiquitinome Changes in the Soluble and Insoluble Fractions of Q175 Huntington Mice Brains." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31138642 31138642]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001486 10.1074/mcp.RA119.001486]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31138642 64]. | ||
+ | #Shraibman B, Barnea E, Kadosh DM, Haimovich Y, Slobodin G, Rosner I, López-Larrea C, Hilf N, Kuttruff S, Song C, Britten C, Castle J, Kreiter S, Frenzel K, Tatagiba M, Tabatabai G, Dietrich PY, Dutoit V, Wick W, Platten M, Winkler F, von Deimling A, Kroep J, Sahuquillo J, Martinez-Ricarte F, Rodon J, Lassen U, Ottensmeier C, van der Burg SH, Thor Straten P, Poulsen HS, Ponsati B, Okada H, Rammensee HG, Sahin U, Singh H, Admon A, (2019) "Identification of Tumor Antigens Among the HLA Peptidomes of Glioblastoma Tumors and Plasma." <i>Mol Cell Proteomics</i> <b>18</b>(6):1255–1268; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31154438 31154438]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001524 10.1074/mcp.RA119.001524]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31154438 75]. | ||
#Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | #Pladevall-Morera D, Munk S, Ingham A, Garribba L, Albers E, Liu Y, Olsen JV, Lopez-Contreras AJ, (2019) "Proteomic characterization of chromosomal common fragile site (CFS)-associated proteins uncovers ATRX as a regulator of CFS stability." <i>Nucleic Acids Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31180492 31180492]; doi: [https://dx.doi.org/10.1093/nar/gkz510 10.1093/nar/gkz510]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31180492 32]. | ||
#Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | #Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC, (2019) "Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation." <i>iScience</i> <b>16</b>:206–217; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31185456 31185456]; doi: [https://dx.doi.org/10.1016/j.isci.2019.05.028 10.1016/j.isci.2019.05.028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31185456 96]. | ||
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#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]. | ||
+ | #Deshmukh AS, Peijs L, Beaudry JL, Jespersen NZ, Nielsen CH, Ma T, Brunner AD, Larsen TJ, Bayarri-Olmos R, Prabhakar BS, Helgstrand C, Severinsen MCK, Holst B, Kjaer A, Tang-Christensen M, Sanfridson A, Garred P, Privé GG, Pedersen BK, Gerhart-Hines Z, Nielsen S, Drucker DJ, Mann M, Scheele C, (2019) "Proteomics-Based Comparative Mapping of the Secretomes of Human Brown and White Adipocytes Reveals EPDR1 as a Novel Batokine." <i>Cell Metab</i> <b>30</b>(5):963–975.e7; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31668873 31668873]; doi: [https://dx.doi.org/10.1016/j.cmet.2019.10.001 10.1016/j.cmet.2019.10.001]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31668873 28]. | ||
#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]. | #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]. | #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]. | ||
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#Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, (2019) "Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity." <i>Genes Dev</i> <b>33</b>(23-24):1751–1774; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31753913 31753913]; doi: [https://dx.doi.org/10.1101/gad.331231.119 10.1101/gad.331231.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31753913 66]. | #Kim JJ, Lee SY, Gong F, Battenhouse AM, Boutz DR, Bashyal A, Refvik ST, Chiang CM, Xhemalce B, Paull TT, Brodbelt JS, Marcotte EM, Miller KM, (2019) "Systematic bromodomain protein screens identify homologous recombination and R-loop suppression pathways involved in genome integrity." <i>Genes Dev</i> <b>33</b>(23-24):1751–1774; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31753913 31753913]; doi: [https://dx.doi.org/10.1101/gad.331231.119 10.1101/gad.331231.119]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31753913 66]. | ||
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#Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | #Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y, (2019) "Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31773964 31773964]; doi: [https://dx.doi.org/10.1021/acs.jproteome.9b00590 10.1021/acs.jproteome.9b00590]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31773964 16]. | ||
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#Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | #Szibor M, Gainutdinov T, Fernandez-Vizarra E, Dufour E, Gizatullina Z, Debska-Vielhaber G, Heidler J, Wittig I, Viscomi C, Gellerich F, Moore AL, (2020) "Bioenergetic consequences from xenotopic expression of a tunicate AOX in mouse mitochondria: Switch from RET and ROS to FET." <i>Biochim Biophys Acta Bioenerg</i> <b>1861</b>(2):148137; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31825809 31825809]; doi: [https://dx.doi.org/10.1016/j.bbabio.2019.148137 10.1016/j.bbabio.2019.148137]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31825809 96]. | ||
#Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | #Solleder M, Guillaume P, Racle J, Michaux J, Pak HS, Müller M, Coukos G, Bassani-Sternberg M, Gfeller D, (2019) "Mass spectrometry based immunopeptidomics leads to robust predictions of phosphorylated HLA class I ligands." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31848261 31848261]; doi: [https://dx.doi.org/10.1074/mcp.TIR119.001641 10.1074/mcp.TIR119.001641]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31848261 208]. | ||
#Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | #Nobre LV, Nightingale K, Ravenhill BJ, Antrobus R, Soday L, Nichols J, Davies JA, Seirafian S, Wang EC, Davison AJ, Wilkinson GW, Stanton RJ, Huttlin EL, Weekes MP, (2019) "Human cytomegalovirus interactome analysis identifies degradation hubs, domain associations and viral protein functions." <i>Elife</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31873071 31873071]; doi: [https://dx.doi.org/10.7554/eLife.49894 10.7554/eLife.49894]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31873071 354]. | ||
#Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | #Mühlhofer M, Berchtold E, Stratil CG, Csaba G, Kunold E, Bach NC, Sieber SA, Haslbeck M, Zimmer R, Buchner J, (2019) "The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins." <i>Cell Rep</i> <b>29</b>(13):4593–4607.e8; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31875563 31875563]; doi: [https://dx.doi.org/10.1016/j.celrep.2019.11.109 10.1016/j.celrep.2019.11.109]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31875563 15]. | ||
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#Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | #Van JAD, Clotet-Freixas S, Zhou J, Batruch I, Sun C, Glogauer M, Rampoldi L, Elia Y, Mahmud F, Sochett E, Diamandis EP, Scholey J, Konvalinka A, (2019) "Peptidomic analysis of urine from youths with early type 1 diabetes reveals novel bioactivity of uromodulin peptides <i>in vitro</i>." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879271 31879271]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001858 10.1074/mcp.RA119.001858]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879271 90]. | ||
#Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | #Nguyen AM, Zhou J, Sicairos B, Sonney S, Du Y, (2019) "Upregulation of CD73 Confers Acquired Radioresistance and is Required for Maintaining Irradiation-Selected Pancreatic Cancer Cells in a Mesenchymal State." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/31879272 31879272]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001779 10.1074/mcp.RA119.001779]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/31879272 20]. | ||
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#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 | + | #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 158]. |
#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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#Zhang J, Tang N, Zhao Y, Zhao R, Fu X, Zhao D, Zhao Y, Huang L, Li C, Qiu Y, Xue B, Fang L, (2020) "Global Phosphoproteomic Analysis Reveals Significant Metabolic Reprogramming in the Termination of Liver Regeneration in Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32105074 32105074]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00028 10.1021/acs.jproteome.0c00028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32105074 24]. | #Zhang J, Tang N, Zhao Y, Zhao R, Fu X, Zhao D, Zhao Y, Huang L, Li C, Qiu Y, Xue B, Fang L, (2020) "Global Phosphoproteomic Analysis Reveals Significant Metabolic Reprogramming in the Termination of Liver Regeneration in Mice." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32105074 32105074]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00028 10.1021/acs.jproteome.0c00028]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32105074 24]. | ||
#Kwon OK, Ha YS, Na AY, Chun SY, Kwon TG, Lee JN, Lee S, (2020) "Identification of Novel Prognosis and Prediction Markers in Advanced Prostate Cancer Tissues Based on Quantitative Proteomics." <i>Cancer Genomics Proteomics</i> <b>17</b>(2):195–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32108042 32108042]; doi: [https://dx.doi.org/10.21873/cgp.20180 10.21873/cgp.20180]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32108042 5]. | #Kwon OK, Ha YS, Na AY, Chun SY, Kwon TG, Lee JN, Lee S, (2020) "Identification of Novel Prognosis and Prediction Markers in Advanced Prostate Cancer Tissues Based on Quantitative Proteomics." <i>Cancer Genomics Proteomics</i> <b>17</b>(2):195–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32108042 32108042]; doi: [https://dx.doi.org/10.21873/cgp.20180 10.21873/cgp.20180]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32108042 5]. | ||
+ | #Villaseñor R, Pfaendler R, Ambrosi C, Butz S, Giuliani S, Bryan E, Sheahan TW, Gable AL, Schmolka N, Manzo M, Wirz J, Feller C, von Mering C, Aebersold R, Voigt P, Baubec T, (2020) "ChromID identifies the protein interactome at chromatin marks." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32123383 32123383]; doi: [https://dx.doi.org/10.1038/s41587-020-0434-2 10.1038/s41587-020-0434-2]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32123383 32]. | ||
#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]. | #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]. | #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]. | ||
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#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]. | #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]. | ||
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#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]. | #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]. | ||
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#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]. | #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]. | ||
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#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]. | #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]. | ||
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+ | #Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A, (2020) "BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain." <i>Cell Syst</i> <b>10</b>(4):333–350.e14; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32325033 32325033]; doi: [https://dx.doi.org/10.1016/j.cels.2020.03.003 10.1016/j.cels.2020.03.003]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32325033 578]. | ||
+ | #Ojalill M, Virtanen N, Rappu P, Siljamäki E, Taimen P, Heino J, (2020) "Interaction between prostate cancer cells and prostate fibroblasts promotes accumulation and proteolytic processing of basement membrane proteins." <i>Prostate</i> <b>80</b>(9):715–726; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32364250 32364250]; doi: [https://dx.doi.org/10.1002/pros.23985 10.1002/pros.23985]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32364250 18]. | ||
+ | #Bekes K, Mitulović G, Meißner N, Resch U, Gruber R, (2020) "Saliva proteomic patterns in patients with molar incisor hypomineralization." <i>Sci Rep</i> <b>10</b>(1):7560; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32371984 32371984]; doi: [https://dx.doi.org/10.1038/s41598-020-64614-z 10.1038/s41598-020-64614-z]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32371984 10]. | ||
+ | #Bansal P, Madlung J, Schaaf K, Macek B, Bono F, (2020) "An interaction network of RNA-binding proteins involved in Drosophila oogenesis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32554711 32554711]; doi: [https://dx.doi.org/10.1074/mcp.RA119.001912 10.1074/mcp.RA119.001912]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32554711 24]. | ||
+ | #Zecha J, Lee CY, Bayer FP, Meng C, Grass V, Zerweck J, Schnatbaum K, Michler T, Pichlmair A, Ludwig C, Kuster B, (2020) "Data, reagents, assays and merits of proteomics for SARS-CoV-2 research and testing." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32591346 32591346]; doi: [https://dx.doi.org/10.1074/mcp.RA120.002164 10.1074/mcp.RA120.002164]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32591346 96]. | ||
+ | #Chen Q, Samidurai A, Thompson J, Hu Y, Das A, Willard B, Lesnefsky EJ, (2020) "Endoplasmic reticulum stress-mediated mitochondrial dysfunction in aged hearts." <i>Biochim Biophys Acta Mol Basis Dis</i> <b>1866</b>(11):165899; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32698045 32698045]; doi: [https://dx.doi.org/10.1016/j.bbadis.2020.165899 10.1016/j.bbadis.2020.165899]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32698045 18]. | ||
+ | #Steiner G, Marban-Doran C, Langer J, Pimenova T, Duran-Pacheco G, Sauter D, Langenkamp A, Solier C, Singer T, Bray-French K, Ducret A, (2020) "Enabling Routine MHC-II-Associated Peptide Proteomics for Risk Assessment of Drug-Induced Immunogenicity." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/32786679 32786679]; doi: [https://dx.doi.org/10.1021/acs.jproteome.0c00309 10.1021/acs.jproteome.0c00309]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/32786679 162]. | ||
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+ | #Lobato-Gil S, Heidelberger JB, Maghames C, Bailly A, Brunello L, Rodriguez MS, Beli P, Xirodimas DP, (2021) "Proteome-wide identification of NEDD8 modification sites reveals distinct proteomes for canonical and atypical NEDDylation." <i>Cell Rep</i> <b>34</b>(3):108635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33472076 33472076]; doi: [https://dx.doi.org/10.1016/j.celrep.2020.108635 10.1016/j.celrep.2020.108635]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33472076 24]. | ||
+ | #Del Favero G, Janker L, Neuditschko B, Hohenbichler J, Kiss E, Woelflingseder L, Gerner C, Marko D, (2021) "Exploring the dermotoxicity of the mycotoxin deoxynivalenol: combined morphologic and proteomic profiling of human epidermal cells reveals alteration of lipid biosynthesis machinery and membrane structural integrity relevant for skin barrier function." <i>Arch Toxicol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/33890134 33890134]; doi: [https://dx.doi.org/10.1007/s00204-021-03042-y 10.1007/s00204-021-03042-y]; GPMDB: [https://gpmdb.thegpm.org/data/keyword/33890134 58]. |
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 datasets/papers contain serious errors in their metadata/methods sections. When using data from repositories, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methods, etc.) that may impact on your use of the data. We have corrected for as many of these errors as we could detect, but there is no way to be sure that we found them all. When attempting to analyze or reproduce results, keep in mind the likelihood that key parts of the experimental methods may have been recorded incorrectly in the associated metadata or manuscript.
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 January 1, 2024.