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==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January | + | 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 22, 2017. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
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#Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | #Müller S, Balaz M, Stefanicka P, Varga L, Amri EZ, Ukropec J, Wollscheid B, Wolfrum C, (2016) "Proteomic Analysis of Human Brown Adipose Tissue Reveals Utilization of Coupled and Uncoupled Energy Expenditure Pathways." <i>Sci Rep</i> <b>6</b>:30030; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418403 27418403]; doi: [https://dx.doi.org/10.1038/srep30030 10.1038/srep30030]; GPMDB: [http://gpmdb.org/data/keyword/27418403 32]. | ||
#Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke DM, Roop DR, (2016) "Proteomic Analysis of Loricrin Knockout Mouse Epidermis." <i>J Proteome Res</i> <b>15</b>(8):2560–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418529 27418529]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00108 10.1021/acs.jproteome.6b00108]; GPMDB: [http://gpmdb.org/data/keyword/27418529 42]. | #Rice RH, Durbin-Johnson BP, Ishitsuka Y, Salemi M, Phinney BS, Rocke DM, Roop DR, (2016) "Proteomic Analysis of Loricrin Knockout Mouse Epidermis." <i>J Proteome Res</i> <b>15</b>(8):2560–6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27418529 27418529]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00108 10.1021/acs.jproteome.6b00108]; GPMDB: [http://gpmdb.org/data/keyword/27418529 42]. | ||
+ | #Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G, (2016) "Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors." <i>Cell Stem Cell</i> <b>19</b>(3):383–96; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27424784 27424784]; doi: [https://dx.doi.org/10.1016/j.stem.2016.06.008 10.1016/j.stem.2016.06.008]; GPMDB: [http://gpmdb.org/data/keyword/27424784 36]. | ||
#Petrera A, Kern U, Linz D, Gomez-Auli A, Hohl M, Gassenhuber J, Sadowski T, Schilling O, (2016) "Proteomic Profiling of Cardiomyocyte-Specific Cathepsin A Overexpression Links Cathepsin A to the Oxidative Stress Response." <i>J Proteome Res</i> <b>15</b>(9):3188–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432266 27432266]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00413 10.1021/acs.jproteome.6b00413]; GPMDB: [http://gpmdb.org/data/keyword/27432266 3]. | #Petrera A, Kern U, Linz D, Gomez-Auli A, Hohl M, Gassenhuber J, Sadowski T, Schilling O, (2016) "Proteomic Profiling of Cardiomyocyte-Specific Cathepsin A Overexpression Links Cathepsin A to the Oxidative Stress Response." <i>J Proteome Res</i> <b>15</b>(9):3188–95; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432266 27432266]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00413 10.1021/acs.jproteome.6b00413]; GPMDB: [http://gpmdb.org/data/keyword/27432266 3]. | ||
#Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | #Zhou Y, Xiong L, Zhang Y, Yu R, Jiang X, Xu G, (2016) "Quantitative proteomics identifies myoferlin as a novel regulator of A Disintegrin and Metalloproteinase 12 in HeLa cells." <i>J Proteomics</i> <b>148</b>:94–104; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27432471 27432471]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.07.015 10.1016/j.jprot.2016.07.015]; GPMDB: [http://gpmdb.org/data/keyword/27432471 14]. | ||
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#Duteil D, Tosic M, Lausecker F, Nenseth HZ, Müller JM, Urban S, Willmann D, Petroll K, Messaddeq N, Arrigoni L, Manke T, Kornfeld JW, Brüning JC, Zagoriy V, Meret M, Dengjel J, Kanouni T, Schüle R, (2016) "Lsd1 Ablation Triggers Metabolic Reprogramming of Brown Adipose Tissue." <i>Cell Rep</i> <b>17</b>(4):1008–1021; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27760309 27760309]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.09.053 10.1016/j.celrep.2016.09.053]; GPMDB: [http://gpmdb.org/data/keyword/27760309 142]. | #Duteil D, Tosic M, Lausecker F, Nenseth HZ, Müller JM, Urban S, Willmann D, Petroll K, Messaddeq N, Arrigoni L, Manke T, Kornfeld JW, Brüning JC, Zagoriy V, Meret M, Dengjel J, Kanouni T, Schüle R, (2016) "Lsd1 Ablation Triggers Metabolic Reprogramming of Brown Adipose Tissue." <i>Cell Rep</i> <b>17</b>(4):1008–1021; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27760309 27760309]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.09.053 10.1016/j.celrep.2016.09.053]; GPMDB: [http://gpmdb.org/data/keyword/27760309 142]. | ||
#Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | #Sarvaiya HA, Lazar IM, (2016) "Insulin stimulated MCF7 breast cancer cells: Proteome dataset." <i>Data Brief</i> <b>9</b>:579–584; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27761513 27761513]; doi: [https://dx.doi.org/10.1016/j.dib.2016.09.025 10.1016/j.dib.2016.09.025]; GPMDB: [http://gpmdb.org/data/keyword/27761513 1]. | ||
- | #Richter E, Harms M, Ventz K, Nölker R, Fraunholz MJ, Mostertz J, Hochgräfe F, (2016) "Quantitative Proteomics Reveals the Dynamics of Protein Phosphorylation in Human Bronchial Epithelial Cells during Internalization, Phagosomal Escape, and Intracellular Replication of Staphylococcus aureus." <i>J Proteome Res</i> <b>15</b>(12):4369–4386; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762562 27762562]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00421 10.1021/acs.jproteome.6b00421]; GPMDB: [http://gpmdb.org/data/keyword/27762562 | + | #Richter E, Harms M, Ventz K, Nölker R, Fraunholz MJ, Mostertz J, Hochgräfe F, (2016) "Quantitative Proteomics Reveals the Dynamics of Protein Phosphorylation in Human Bronchial Epithelial Cells during Internalization, Phagosomal Escape, and Intracellular Replication of Staphylococcus aureus." <i>J Proteome Res</i> <b>15</b>(12):4369–4386; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762562 27762562]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00421 10.1021/acs.jproteome.6b00421]; GPMDB: [http://gpmdb.org/data/keyword/27762562 75]. |
#Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | #Assoni A, Coatti G, Valadares MC, Beccari M, Gomes J, Pelatti M, Mitne-Neto M, Carvalho VM, Zatz M, (2016) "Different Donors Mesenchymal Stromal Cells Secretomes Reveal Heterogeneous Profile of Relevance for Therapeutic Use." <i>Stem Cells Dev</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27762666 27762666]; doi: [https://dx.doi.org/10.1089/scd.2016.0218 10.1089/scd.2016.0218]; GPMDB: [http://gpmdb.org/data/keyword/27762666 48]. | ||
+ | #Schanzenbächer CT, Sambandan S, Langer JD, Schuman EM, (2016) "Nascent Proteome Remodeling following Homeostatic Scaling at Hippocampal Synapses." <i>Neuron</i> <b>92</b>(2):358–371; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27764671 27764671]; doi: [https://dx.doi.org/10.1016/j.neuron.2016.09.058 10.1016/j.neuron.2016.09.058]; GPMDB: [http://gpmdb.org/data/keyword/27764671 80]. | ||
#Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | #Peng J, Cao J, Ng FM, Hill J, (2016) "Pseudomonas aeruginosa develops Ciprofloxacin resistance from low to high level with distinctive proteome changes." <i>J Proteomics</i> <b>152</b>:75–87; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27771372 27771372]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.10.005 10.1016/j.jprot.2016.10.005]; GPMDB: [http://gpmdb.org/data/keyword/27771372 25]. | ||
#Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | #Rafiee MR, Girardot C, Sigismondo G, Krijgsveld J, (2016) "Expanding the Circuitry of Pluripotency by Selective Isolation of Chromatin-Associated Proteins." <i>Mol Cell</i> <b>64</b>(3):624–635; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27773674 27773674]; doi: [https://dx.doi.org/10.1016/j.molcel.2016.09.019 10.1016/j.molcel.2016.09.019]; GPMDB: [http://gpmdb.org/data/keyword/27773674 13]. | ||
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#Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | #Lundquist PK, Mantegazza O, Stefanski A, Stühler K, Weber AP, (2016) "Surveying the Oligomeric State of Arabidopsis thaliana Chloroplasts." <i>Mol Plant</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27794502 27794502]; doi: [https://dx.doi.org/10.1016/j.molp.2016.10.011 10.1016/j.molp.2016.10.011]; GPMDB: [http://gpmdb.org/data/keyword/27794502 42]. | ||
#Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | #Fournier M, Orpinell M, Grauffel C, Scheer E, Garnier JM, Ye T, Chavant V, Joint M, Esashi F, Dejaegere A, Gönczy P, Tora L, (2016) "KAT2A/KAT2B-targeted acetylome reveals a role for PLK4 acetylation in preventing centrosome amplification." <i>Nat Commun</i> <b>7</b>:13227; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27796307 27796307]; doi: [https://dx.doi.org/10.1038/ncomms13227 10.1038/ncomms13227]; GPMDB: [http://gpmdb.org/data/keyword/27796307 114]. | ||
+ | #Kentache T, Ben Abdelkrim A, Jouenne T, Dé E, Hardouin J, (2017) "Global Dynamic Proteome Study of a Pellicle-forming Acinetobacter baumannii Strain." <i>Mol Cell Proteomics</i> <b>16</b>(1):100–112; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27799293 27799293]; doi: [https://dx.doi.org/10.1074/mcp.M116.061044 10.1074/mcp.M116.061044]; GPMDB: [http://gpmdb.org/data/keyword/27799293 35]. | ||
#Danda R, Ganapathy K, Sathe G, Madugundu AK, Ramachandran S, Krishnan UM, Khetan V, Rishi P, Keshava Prasad TS, Pandey A, Krishnakumar S, Gowda H, Elchuri SV, (2016) "Proteomic profiling of retinoblastoma by high resolution mass spectrometry." <i>Clin Proteomics</i> <b>13</b>:29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27799869 27799869]; doi: [https://dx.doi.org/10.1186/s12014-016-9128-7 10.1186/s12014-016-9128-7]; GPMDB: [http://gpmdb.org/data/keyword/27799869 1]. | #Danda R, Ganapathy K, Sathe G, Madugundu AK, Ramachandran S, Krishnan UM, Khetan V, Rishi P, Keshava Prasad TS, Pandey A, Krishnakumar S, Gowda H, Elchuri SV, (2016) "Proteomic profiling of retinoblastoma by high resolution mass spectrometry." <i>Clin Proteomics</i> <b>13</b>:29; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27799869 27799869]; doi: [https://dx.doi.org/10.1186/s12014-016-9128-7 10.1186/s12014-016-9128-7]; GPMDB: [http://gpmdb.org/data/keyword/27799869 1]. | ||
#Fahrmann JF, Grapov D, Phinney BS, Stroble C, DeFelice BC, Rom W, Gandara DR, Zhang Y, Fiehn O, Pass H, Miyamoto S, (2016) "Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival." <i>Clin Proteomics</i> <b>13</b>:31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27799870 27799870]; doi: [https://dx.doi.org/10.1186/s12014-016-9132-y 10.1186/s12014-016-9132-y]; GPMDB: [http://gpmdb.org/data/keyword/27799870 234]. | #Fahrmann JF, Grapov D, Phinney BS, Stroble C, DeFelice BC, Rom W, Gandara DR, Zhang Y, Fiehn O, Pass H, Miyamoto S, (2016) "Proteomic profiling of lung adenocarcinoma indicates heightened DNA repair, antioxidant mechanisms and identifies LASP1 as a potential negative predictor of survival." <i>Clin Proteomics</i> <b>13</b>:31; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27799870 27799870]; doi: [https://dx.doi.org/10.1186/s12014-016-9132-y 10.1186/s12014-016-9132-y]; GPMDB: [http://gpmdb.org/data/keyword/27799870 234]. | ||
+ | #Michalak M, Warnken U, André S, Schnölzer M, Gabius HJ, Kopitz J, (2016) "Detection of Proteome Changes in Human Colon Cancer Induced by Cell Surface Binding of Growth-Inhibitory Human Galectin-4 Using Quantitative SILAC-Based Proteomics." <i>J Proteome Res</i> <b>15</b>(12):4412–4422; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27801591 27801591]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00473 10.1021/acs.jproteome.6b00473]; GPMDB: [http://gpmdb.org/data/keyword/27801591 6]. | ||
#Karunakaran KP, Yu H, Jiang X, Chan Q, Goldberg MF, Jenkins MK, Foster LJ, Brunham RC, (2017) "Identification of MHC-Bound Peptides from Dendritic Cells Infected with Salmonella enterica Strain SL1344: Implications for a Nontyphoidal Salmonella Vaccine." <i>J Proteome Res</i> <b>16</b>(1):298–306; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27802388 27802388]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00926 10.1021/acs.jproteome.6b00926]; GPMDB: [http://gpmdb.org/data/keyword/27802388 3]. | #Karunakaran KP, Yu H, Jiang X, Chan Q, Goldberg MF, Jenkins MK, Foster LJ, Brunham RC, (2017) "Identification of MHC-Bound Peptides from Dendritic Cells Infected with Salmonella enterica Strain SL1344: Implications for a Nontyphoidal Salmonella Vaccine." <i>J Proteome Res</i> <b>16</b>(1):298–306; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27802388 27802388]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00926 10.1021/acs.jproteome.6b00926]; GPMDB: [http://gpmdb.org/data/keyword/27802388 3]. | ||
#Borziak K, Álvarez-Fernández A, L Karr T, Pizzari T, Dorus S, (2016) "The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication." <i>Sci Rep</i> <b>6</b>:35864; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27804984 27804984]; doi: [https://dx.doi.org/10.1038/srep35864 10.1038/srep35864]; GPMDB: [http://gpmdb.org/data/keyword/27804984 144]. | #Borziak K, Álvarez-Fernández A, L Karr T, Pizzari T, Dorus S, (2016) "The Seminal fluid proteome of the polyandrous Red junglefowl offers insights into the molecular basis of fertility, reproductive ageing and domestication." <i>Sci Rep</i> <b>6</b>:35864; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27804984 27804984]; doi: [https://dx.doi.org/10.1038/srep35864 10.1038/srep35864]; GPMDB: [http://gpmdb.org/data/keyword/27804984 144]. | ||
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#Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." <i>J Proteome Res</i> <b>15</b>(12):4476–4489; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27934295 27934295]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00613 10.1021/acs.jproteome.6b00613]; GPMDB: [http://gpmdb.org/data/keyword/27934295 18]. | #Sharma R, Fedorenko I, Spence PT, Sondak VK, Smalley KS, Koomen JM, (2016) "Activity-Based Protein Profiling Shows Heterogeneous Signaling Adaptations to BRAF Inhibition." <i>J Proteome Res</i> <b>15</b>(12):4476–4489; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27934295 27934295]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00613 10.1021/acs.jproteome.6b00613]; GPMDB: [http://gpmdb.org/data/keyword/27934295 18]. | ||
#Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 6]. | #Zhao H, Konzer A, Mi J, Chen M, Pettersson U, Lind SB, (2016) "Posttranscriptional Regulation in Adenovirus Infected Cells." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27959563 27959563]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00834 10.1021/acs.jproteome.6b00834]; GPMDB: [http://gpmdb.org/data/keyword/27959563 6]. | ||
+ | #Seidel G, Meierhofer D, Şen NE, Guenther A, Krobitsch S, Auburger G, (2016) "Quantitative Global Proteomics of Yeast PBP1 Deletion Mutants and Their Stress Responses Identifies Glucose Metabolism, Mitochondrial, and Stress Granule Changes." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27966978 27966978]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00647 10.1021/acs.jproteome.6b00647]; GPMDB: [http://gpmdb.org/data/keyword/27966978 27]. | ||
#Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW, (2016) "Architecture of the yeast Elongator complex." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27974378 27974378]; doi: [https://dx.doi.org/10.15252/embr.201643353 10.15252/embr.201643353]; GPMDB: [http://gpmdb.org/data/keyword/27974378 44]. | #Dauden MI, Kosinski J, Kolaj-Robin O, Desfosses A, Ori A, Faux C, Hoffmann NA, Onuma OF, Breunig KD, Beck M, Sachse C, Séraphin B, Glatt S, Müller CW, (2016) "Architecture of the yeast Elongator complex." <i>EMBO Rep</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27974378 27974378]; doi: [https://dx.doi.org/10.15252/embr.201643353 10.15252/embr.201643353]; GPMDB: [http://gpmdb.org/data/keyword/27974378 44]. | ||
#Herfs M, Longuespée R, Quick CM, Roncarati P, Suarez-Carmona M, Hubert P, Lebeau A, Bruyere D, Mazzucchelli G, Smargiasso N, Baiwir D, Lai K, Dunn A, Obregon F, Yang EJ, De Pauw E, Crum CP, Delvenne P, (2016) "Proteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27976366 27976366]; doi: [https://dx.doi.org/10.1002/path.4858 10.1002/path.4858]; GPMDB: [http://gpmdb.org/data/keyword/27976366 60]. | #Herfs M, Longuespée R, Quick CM, Roncarati P, Suarez-Carmona M, Hubert P, Lebeau A, Bruyere D, Mazzucchelli G, Smargiasso N, Baiwir D, Lai K, Dunn A, Obregon F, Yang EJ, De Pauw E, Crum CP, Delvenne P, (2016) "Proteomic signatures reveal a dualistic and clinically relevant classification of anal canal carcinoma." <i>J Pathol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27976366 27976366]; doi: [https://dx.doi.org/10.1002/path.4858 10.1002/path.4858]; GPMDB: [http://gpmdb.org/data/keyword/27976366 60]. | ||
- | #Schunter AJ, Yue X, Hummon AB, (2016) "Phosphoproteomics of colon cancer metastasis: comparative mass spectrometric analysis of the isogenic primary and metastatic cell lines SW480 and SW620." <i>Anal Bioanal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27987026 27987026]; doi: [https://dx.doi.org/10.1007/s00216-016-0125-5 10.1007/s00216-016-0125-5]; GPMDB: [http://gpmdb.org/data/keyword/27987026 | + | #Zhang S, Weng T, Cheruba E, Guo T, Chan H, Sze SK, Koh CG, (2016) "Phosphatase POPX2 Exhibits Dual Regulatory Functions in Cancer Metastasis." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27976581 27976581]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00748 10.1021/acs.jproteome.6b00748]; GPMDB: [http://gpmdb.org/data/keyword/27976581 60]. |
+ | #Schunter AJ, Yue X, Hummon AB, (2016) "Phosphoproteomics of colon cancer metastasis: comparative mass spectrometric analysis of the isogenic primary and metastatic cell lines SW480 and SW620." <i>Anal Bioanal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27987026 27987026]; doi: [https://dx.doi.org/10.1007/s00216-016-0125-5 10.1007/s00216-016-0125-5]; GPMDB: [http://gpmdb.org/data/keyword/27987026 35]. | ||
#Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27990823 27990823]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00881 10.1021/acs.jproteome.6b00881]; GPMDB: [http://gpmdb.org/data/keyword/27990823 12]. | #Choi M, Eren-Dogu ZF, Colangelo CM, Cottrell JS, Hoopmann MR, Kapp EA, Kim S, Lam H, Neubert TA, Palmblad M, Phinney BS, Weintraub ST, MacLean B, Vitek O, (2016) "ABRF Proteome Informatics Research Group (iPRG) 2015 Study: Detection of differentially abundant proteins in label-free quantitative LC-MS/MS experiments." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27990823 27990823]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00881 10.1021/acs.jproteome.6b00881]; GPMDB: [http://gpmdb.org/data/keyword/27990823 12]. | ||
#Bertile F, Fouillen L, Wasselin T, Maes P, Le Maho Y, Van Dorsselaer A, Raclot T, (2016) "The Safety Limits Of An Extended Fast: Lessons from a Non-Model Organism." <i>Sci Rep</i> <b>6</b>:39008; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27991520 27991520]; doi: [https://dx.doi.org/10.1038/srep39008 10.1038/srep39008]; GPMDB: [http://gpmdb.org/data/keyword/27991520 194]. | #Bertile F, Fouillen L, Wasselin T, Maes P, Le Maho Y, Van Dorsselaer A, Raclot T, (2016) "The Safety Limits Of An Extended Fast: Lessons from a Non-Model Organism." <i>Sci Rep</i> <b>6</b>:39008; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27991520 27991520]; doi: [https://dx.doi.org/10.1038/srep39008 10.1038/srep39008]; GPMDB: [http://gpmdb.org/data/keyword/27991520 194]. | ||
+ | #Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC, (2016) "VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007913 28007913]; doi: [https://dx.doi.org/10.1074/mcp.M116.064428 10.1074/mcp.M116.064428]; GPMDB: [http://gpmdb.org/data/keyword/28007913 89]. | ||
#Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW, Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M, (2016) "Proteomics reveals the effects of sustained weight loss on the human plasma proteome." <i>Mol Syst Biol</i> <b>12</b>(12):901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007936 28007936]; GPMDB: [http://gpmdb.org/data/keyword/28007936 1145]. | #Geyer PE, Wewer Albrechtsen NJ, Tyanova S, Grassl N, Iepsen EW, Lundgren J, Madsbad S, Holst JJ, Torekov SS, Mann M, (2016) "Proteomics reveals the effects of sustained weight loss on the human plasma proteome." <i>Mol Syst Biol</i> <b>12</b>(12):901; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28007936 28007936]; GPMDB: [http://gpmdb.org/data/keyword/28007936 1145]. | ||
- | #Reimann L, Wiese H, Leber Y, Schwäble AN, Fricke AL, Rohland A, Knapp B, Peikert CD, Drepper F, van der Ven PF, Radziwill G, Fürst DO, Warscheid B, (2016) "Myofibrillar Z-discs are a protein phosphorylation hot spot with PKC α modulating protein dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28028127 28028127]; doi: [https://dx.doi.org/10.1074/mcp.M116.065425 10.1074/mcp.M116.065425]; GPMDB: [http://gpmdb.org/data/keyword/28028127 | + | #Reimann L, Wiese H, Leber Y, Schwäble AN, Fricke AL, Rohland A, Knapp B, Peikert CD, Drepper F, van der Ven PF, Radziwill G, Fürst DO, Warscheid B, (2016) "Myofibrillar Z-discs are a protein phosphorylation hot spot with PKC α modulating protein dynamics." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28028127 28028127]; doi: [https://dx.doi.org/10.1074/mcp.M116.065425 10.1074/mcp.M116.065425]; GPMDB: [http://gpmdb.org/data/keyword/28028127 206]. |
+ | #Hickox AE, Wong AC, Pak K, Strojny C, Ramirez M, Yates JR Rd, Ryan AF, Savas JN, (2016) "Global Analysis of Protein Expression of Inner Ear Hair Cells." <i>J Neurosci</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28039372 28039372]; doi: [https://dx.doi.org/10.1523/JNEUROSCI.2267-16.2016 10.1523/JNEUROSCI.2267-16.2016]; GPMDB: [http://gpmdb.org/data/keyword/28039372 71]. | ||
#Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | #Chen J, Zheng Q, Hammers CM, Ellebrecht CT, Mukherjee EM, Tang HY, Lin C, Yuan H, Pan M, Langenhan J, Komorowski L, Siegel DL, Payne AS, Stanley JR, (2017) "Proteomic Analysis of Pemphigus Autoantibodies Indicates a Larger, More Diverse, and More Dynamic Repertoire than Determined by B Cell Genetics." <i>Cell Rep</i> <b>18</b>(1):237–247; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052253 28052253]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.013 10.1016/j.celrep.2016.12.013]; GPMDB: [http://gpmdb.org/data/keyword/28052253 128]. | ||
+ | #Cristobal A, van den Toorn HW, van de Wetering M, Clevers H, Heck AJ, Mohammed S, (2017) "Personalized Proteome Profiles of Healthy and Tumor Human Colon Organoids Reveal Both Individual Diversity and Basic Features of Colorectal Cancer." <i>Cell Rep</i> <b>18</b>(1):263–274; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28052255 28052255]; doi: [https://dx.doi.org/10.1016/j.celrep.2016.12.016 10.1016/j.celrep.2016.12.016]; GPMDB: [http://gpmdb.org/data/keyword/28052255 54]. | ||
#Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | #Degroote RL, Uhl PB, Amann B, Krackhardt AM, Ueffing M, Hauck SM, Deeg CA, (2017) "Formin like 1 expression is increased on CD4+ T lymphocytes in spontaneous autoimmune uveitis." <i>J Proteomics</i> <b>154</b>:102–108; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28057602 28057602]; doi: [https://dx.doi.org/10.1016/j.jprot.2016.12.015 10.1016/j.jprot.2016.12.015]; GPMDB: [http://gpmdb.org/data/keyword/28057602 6]. | ||
+ | #Braakman RB, Stingl C, Tilanus-Linthorst MM, Deurzen CH, Timmermans MA, Smid M, Foekens JA, Luider TM, Martens JW, Umar A, (2017) "Proteomic characterization of microdissected breast tissue environment provides a protein-level overview of malignant transformation." <i>Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28058811 28058811]; doi: [https://dx.doi.org/10.1002/pmic.201600213 10.1002/pmic.201600213]; GPMDB: [http://gpmdb.org/data/keyword/28058811 70]. | ||
+ | #Johnston HE, Carter MJ, Cox KL, Dunscombe M, Manousopoulou A, Townsend PA, Garbis SD, Cragg MS, (2017) "Integrated Cellular and Plasma Proteomics of Contrasting B-cell Cancers Reveals Common, Unique and Systemic Signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28062796 28062796]; doi: [https://dx.doi.org/10.1074/mcp.M116.063511 10.1074/mcp.M116.063511]; GPMDB: [http://gpmdb.org/data/keyword/28062796 166]. | ||
+ | #Scott NE, Rogers LD, Prudova A, Brown NF, Fortelny N, Overall CM, Foster LJ, (2017) "Interactome disassembly during apoptosis occurs independent of caspase cleavage." <i>Mol Syst Biol</i> <b>13</b>(1):906; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28082348 28082348]; GPMDB: [http://gpmdb.org/data/keyword/28082348 19]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must pass our internal automated quality control tests for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of January 22, 2017.