Line 27: | Line 27: | ||
==Data from publications== | ==Data from publications== | ||
- | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of | + | The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Jan. 22, 2018. |
#Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | #Lipton MS, Pasa-Tolic' L, Anderson GA, Anderson DJ, Auberry DL, Battista JR, Daly MJ, Fredrickson J, Hixson KK, Kostandarithes H, Masselon C, Markillie LM, Moore RJ, Romine MF, Shen Y, Stritmatter E, Tolic' N, Udseth HR, Venkateswaran A, Wong KK, Zhao R, Smith RD, (2002) "Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags." <i>Proc Natl Acad Sci U S A</i> <b>99</b>(17):11049–54; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/12177431 12177431]; doi: [https://dx.doi.org/10.1073/pnas.172170199 10.1073/pnas.172170199]; GPMDB: [http://gpmdb.org/data/keyword/12177431 498]. | ||
Line 1,253: | Line 1,253: | ||
#Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | #Mertins P, Mani DR, Ruggles KV, Gillette MA, Clauser KR, Wang P, Wang X, Qiao JW, Cao S, Petralia F, Kawaler E, Mundt F, Krug K, Tu Z, Lei JT, Gatza ML, Wilkerson M, Perou CM, Yellapantula V, Huang KL, Lin C, McLellan MD, Yan P, Davies SR, Townsend RR, Skates SJ, Wang J, Zhang B, Kinsinger CR, Mesri M, Rodriguez H, Ding L, Paulovich AG, Fenyö D, Ellis MJ, Carr SA, NCI CPTAC., (2016) "Proteogenomics connects somatic mutations to signalling in breast cancer." <i>Nature</i> <b>534</b>(7605):55–62; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27251275 27251275]; doi: [https://dx.doi.org/10.1038/nature18003 10.1038/nature18003]; GPMDB: [http://gpmdb.org/data/keyword/27251275 1265]. | ||
#Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | #Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ, (2016) "Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling." <i>Mol Cell Proteomics</i> <b>15</b>(8):2671–85; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27259358 27259358]; doi: [https://dx.doi.org/10.1074/mcp.M116.058313 10.1074/mcp.M116.058313]; GPMDB: [http://gpmdb.org/data/keyword/27259358 112]. | ||
+ | #Hintermair C, Voß K, Forné I, Heidemann M, Flatley A, Kremmer E, Imhof A, Eick D, (2016) "Specific threonine-4 phosphorylation and function of RNA polymerase II CTD during M phase progression." <i>Sci Rep</i> <b>6</b>:27401; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27264542 27264542]; doi: [https://dx.doi.org/10.1038/srep27401 10.1038/srep27401]; GPMDB: [http://gpmdb.org/data/keyword/27264542 63]. | ||
#Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i> <b>7</b>(28):43868–43893; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | #Xu L, Gao Y, Chen Y, Xiao Y, He Q, Qiu H, Ge W, (2016) "Quantitative proteomics reveals that distant recurrence-associated protein R-Ras and Transgelin predict post-surgical survival in patients with Stage III colorectal cancer." <i>Oncotarget</i> <b>7</b>(28):43868–43893; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27270312 27270312]; doi: [https://dx.doi.org/10.18632/oncotarget.9701 10.18632/oncotarget.9701]; GPMDB: [http://gpmdb.org/data/keyword/27270312 2]. | ||
#Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | #Gnad F, Doll S, Song K, Stokes MP, Moffat J, Liu B, Arnott D, Wallin J, Friedman LS, Hatzivassiliou G, Belvin M, (2016) "Phosphoproteome analysis of the MAPK pathway reveals previously undetected feedback mechanisms." <i>Proteomics</i> <b>16</b>(14):1998–2004; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/27273156 27273156]; doi: [https://dx.doi.org/10.1002/pmic.201600119 10.1002/pmic.201600119]; GPMDB: [http://gpmdb.org/data/keyword/27273156 56]. | ||
Line 1,495: | Line 1,496: | ||
#Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | #Tahir A, Bileck A, Muqaku B, Niederstaetter L, Kreutz D, Mayer RL, Wolrab D, Meier SM, Slany A, Gerner C, (2017) "Combined Proteome and Eicosanoid Profiling Approach for Revealing Implications of Human Fibroblasts in Chronic Inflammation." <i>Anal Chem</i> <b>89</b>(3):1945–1954; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28208246 28208246]; doi: [https://dx.doi.org/10.1021/acs.analchem.6b04433 10.1021/acs.analchem.6b04433]; GPMDB: [http://gpmdb.org/data/keyword/28208246 32]. | ||
#Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A, (2017) "Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28210003 28210003]; doi: [https://dx.doi.org/10.1038/leu.2017.61 10.1038/leu.2017.61]; GPMDB: [http://gpmdb.org/data/keyword/28210003 20]. | #Cutler JA, Tahir R, Sreenivasamurthy SK, Mitchell C, Renuse S, Nirujogi RS, Patil AH, Heydarian M, Wong X, Wu X, Huang TC, Kim MS, Reddy KL, Pandey A, (2017) "Differential signaling through p190 and p210 BCR-ABL fusion proteins revealed by interactome and phosphoproteome analysis." <i>Leukemia</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28210003 28210003]; doi: [https://dx.doi.org/10.1038/leu.2017.61 10.1038/leu.2017.61]; GPMDB: [http://gpmdb.org/data/keyword/28210003 20]. | ||
+ | #Hartwig T, Montinaro A, von Karstedt S, Sevko A, Surinova S, Chakravarthy A, Taraborrelli L, Draber P, Lafont E, Arce Vargas F, El-Bahrawy MA, Quezada SA, Walczak H, (2017) "The TRAIL-Induced Cancer Secretome Promotes a Tumor-Supportive Immune Microenvironment via CCR2." <i>Mol Cell</i> <b>65</b>(4):730–742.e5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28212753 28212753]; doi: [https://dx.doi.org/10.1016/j.molcel.2017.01.021 10.1016/j.molcel.2017.01.021]; GPMDB: [http://gpmdb.org/data/keyword/28212753 6]. | ||
#Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, (2017) "Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28217993 28217993]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00645 10.1021/acs.jproteome.6b00645]; GPMDB: [http://gpmdb.org/data/keyword/28217993 54]. | #Al Shweiki MR, Mönchgesang S, Majovsky P, Thieme D, Trutschel D, Hoehenwarter W, (2017) "Assessment of Label-Free Quantification in Discovery Proteomics and Impact of Technological Factors and Natural Variability of Protein Abundance." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28217993 28217993]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00645 10.1021/acs.jproteome.6b00645]; GPMDB: [http://gpmdb.org/data/keyword/28217993 54]. | ||
#Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | #Swertfeger DK, Li H, Rebholz S, Zhu X, Shah AS, Davidson WS, Lu LJ, (2017) "Mapping atheroprotective functions and related proteins/lipoproteins in size fractionated human plasma." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28223350 28223350]; doi: [https://dx.doi.org/10.1074/mcp.M116.066290 10.1074/mcp.M116.066290]; GPMDB: [http://gpmdb.org/data/keyword/28223350 180]. | ||
Line 1,577: | Line 1,579: | ||
#Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL, (2017) "Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors." <i>Endocrinology</i> <b>158</b>(8):2470–2485; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28591806 28591806]; doi: [https://dx.doi.org/10.1210/en.2017-00194 10.1210/en.2017-00194]; GPMDB: [http://gpmdb.org/data/keyword/28591806 10]. | #Jensen SR, Schoof EM, Wheeler SE, Hvid H, Ahnfelt-Rønne J, Hansen BF, Nishimura E, Olsen GS, Kislinger T, Brubaker PL, (2017) "Quantitative Proteomics of Intestinal Mucosa From Male Mice Lacking Intestinal Epithelial Insulin Receptors." <i>Endocrinology</i> <b>158</b>(8):2470–2485; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28591806 28591806]; doi: [https://dx.doi.org/10.1210/en.2017-00194 10.1210/en.2017-00194]; GPMDB: [http://gpmdb.org/data/keyword/28591806 10]. | ||
#Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [http://gpmdb.org/data/keyword/28601559 93]. | #Bekker-Jensen DB, Kelstrup CD, Batth TS, Larsen SC, Haldrup C, Bramsen JB, Sørensen KD, Høyer S, Ørntoft TF, Andersen CL, Nielsen ML, Olsen JV, (2017) "An Optimized Shotgun Strategy for the Rapid Generation of Comprehensive Human Proteomes." <i>Cell Syst</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28601559 28601559]; doi: [https://dx.doi.org/10.1016/j.cels.2017.05.009 10.1016/j.cels.2017.05.009]; GPMDB: [http://gpmdb.org/data/keyword/28601559 93]. | ||
+ | #Haas TL, Sciuto MR, Brunetto L, Valvo C, Signore M, Fiori ME, di Martino S, Giannetti S, Morgante L, Boe A, Patrizii M, Warnken U, Schnölzer M, Ciolfi A, Di Stefano C, Biffoni M, Ricci-Vitiani L, Pallini R, De Maria R, (2017) "Integrin α7 Is a Functional Marker and Potential Therapeutic Target in Glioblastoma." <i>Cell Stem Cell</i> <b>21</b>(1):35–50.e9; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28602620 28602620]; doi: [https://dx.doi.org/10.1016/j.stem.2017.04.009 10.1016/j.stem.2017.04.009]; GPMDB: [http://gpmdb.org/data/keyword/28602620 3]. | ||
#Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ, (2017) "Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28606917 28606917]; doi: [https://dx.doi.org/10.1074/mcp.M116.066019 10.1074/mcp.M116.066019]; GPMDB: [http://gpmdb.org/data/keyword/28606917 4]. | #Lapek JD Jr, Lewinski MK, Wozniak JM, Guatelli J, Gonzalez DJ, (2017) "Quantitative Temporal Viromics of an Inducible HIV-1 Model Yields Insight to Global Host Targets and Phospho-Dynamics Associated with Vpr." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28606917 28606917]; doi: [https://dx.doi.org/10.1074/mcp.M116.066019 10.1074/mcp.M116.066019]; GPMDB: [http://gpmdb.org/data/keyword/28606917 4]. | ||
#Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Bréhélin C, (2017) "Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions." <i>Front Plant Sci</i> <b>8</b>:894; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28611809 28611809]; doi: [https://dx.doi.org/10.3389/fpls.2017.00894 10.3389/fpls.2017.00894]; GPMDB: [http://gpmdb.org/data/keyword/28611809 3]. | #Brocard L, Immel F, Coulon D, Esnay N, Tuphile K, Pascal S, Claverol S, Fouillen L, Bessoule JJ, Bréhélin C, (2017) "Proteomic Analysis of Lipid Droplets from Arabidopsis Aging Leaves Brings New Insight into Their Biogenesis and Functions." <i>Front Plant Sci</i> <b>8</b>:894; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28611809 28611809]; doi: [https://dx.doi.org/10.3389/fpls.2017.00894 10.3389/fpls.2017.00894]; GPMDB: [http://gpmdb.org/data/keyword/28611809 3]. | ||
Line 1,603: | Line 1,606: | ||
#Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J, (2017) "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome." <i>Sci Rep</i> <b>7</b>(1):4513; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28674419 28674419]; doi: [https://dx.doi.org/10.1038/s41598-017-04798-z 10.1038/s41598-017-04798-z]; GPMDB: [http://gpmdb.org/data/keyword/28674419 133]. | #Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J, (2017) "Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome." <i>Sci Rep</i> <b>7</b>(1):4513; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28674419 28674419]; doi: [https://dx.doi.org/10.1038/s41598-017-04798-z 10.1038/s41598-017-04798-z]; GPMDB: [http://gpmdb.org/data/keyword/28674419 133]. | ||
#Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS, (2017) "Genes essential for phototrophic growth by a purple alphaproteobacterium." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28677146 28677146]; doi: [https://dx.doi.org/10.1111/1462-2920.13852 10.1111/1462-2920.13852]; GPMDB: [http://gpmdb.org/data/keyword/28677146 6]. | #Yang J, Yin L, Lessner FH, Nakayasu ES, Payne SH, Fixen KR, Gallagher L, Harwood CS, (2017) "Genes essential for phototrophic growth by a purple alphaproteobacterium." <i>Environ Microbiol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28677146 28677146]; doi: [https://dx.doi.org/10.1111/1462-2920.13852 10.1111/1462-2920.13852]; GPMDB: [http://gpmdb.org/data/keyword/28677146 6]. | ||
+ | #Soman KV, Stafford SJ, Pazdrak K, Wu Z, Luo X, White WI, Wiktorowicz JE, Calhoun WJ, Kurosky A, (2017) "Activation of Human Peripheral Blood Eosinophils by Cytokines in a Comparative Time-Course Proteomic/Phosphoproteomic Study." <i>J Proteome Res</i> <b>16</b>(8):2663–2679; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28679203 28679203]; doi: [https://dx.doi.org/10.1021/acs.jproteome.6b00367 10.1021/acs.jproteome.6b00367]; GPMDB: [http://gpmdb.org/data/keyword/28679203 47]. | ||
#Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM, (2017) "HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma." <i>Cancer Metab</i> <b>5</b>:5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28680592 28680592]; doi: [https://dx.doi.org/10.1186/s40170-017-0167-y 10.1186/s40170-017-0167-y]; GPMDB: [http://gpmdb.org/data/keyword/28680592 12]. | #Miikkulainen P, Högel H, Rantanen K, Suomi T, Kouvonen P, Elo LL, Jaakkola PM, (2017) "HIF prolyl hydroxylase PHD3 regulates translational machinery and glucose metabolism in clear cell renal cell carcinoma." <i>Cancer Metab</i> <b>5</b>:5; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28680592 28680592]; doi: [https://dx.doi.org/10.1186/s40170-017-0167-y 10.1186/s40170-017-0167-y]; GPMDB: [http://gpmdb.org/data/keyword/28680592 12]. | ||
#Zwittink RD, van Zoeren-Grobben D, Martin R, van Lingen RA, Groot Jebbink LJ, Boeren S, Renes IB, van Elburg RM, Belzer C, Knol J, (2017) "Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28684633 28684633]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000102 10.1074/mcp.RA117.000102]; GPMDB: [http://gpmdb.org/data/keyword/28684633 65]. | #Zwittink RD, van Zoeren-Grobben D, Martin R, van Lingen RA, Groot Jebbink LJ, Boeren S, Renes IB, van Elburg RM, Belzer C, Knol J, (2017) "Metaproteomics reveals functional differences in intestinal microbiota development of preterm infants." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28684633 28684633]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000102 10.1074/mcp.RA117.000102]; GPMDB: [http://gpmdb.org/data/keyword/28684633 65]. | ||
Line 1,692: | Line 1,696: | ||
#Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28965414 28965414]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00352 10.1021/acs.jproteome.7b00352]; GPMDB: [http://gpmdb.org/data/keyword/28965414 4]. | #Zhang W, Chen X, Yan Z, Chen Y, Cui Y, Chen B, Huang C, Zhang W, Yin X, He QY, He F, Wang T, (2017) "Detergent-insoluble proteome analysis revealed aberrantly aggregated proteins in human preeclampsia placentas." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28965414 28965414]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00352 10.1021/acs.jproteome.7b00352]; GPMDB: [http://gpmdb.org/data/keyword/28965414 4]. | ||
#Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28972080 28972080]; doi: [https://dx.doi.org/10.1074/mcp.M117.067116 10.1074/mcp.M117.067116]; GPMDB: [http://gpmdb.org/data/keyword/28972080 164]. | #Reyes ED, Kulej K, Pancholi NJ, Akhtar LN, Avgousti DC, Kim ET, Bricker DK, Spruce LA, Koniski SA, Seeholzer SH, Isaacs SN, Garcia BA, Weitzman MD, (2017) "Identifying host factors associated with DNA replicated during virus infection." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28972080 28972080]; doi: [https://dx.doi.org/10.1074/mcp.M117.067116 10.1074/mcp.M117.067116]; GPMDB: [http://gpmdb.org/data/keyword/28972080 164]. | ||
- | #Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA, (2017) "Systems-level identification of PKA-dependent signaling in epithelial cells." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(42):E8875–E8884; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28973931 28973931]; doi: [https://dx.doi.org/10.1073/pnas.1709123114 10.1073/pnas.1709123114]; GPMDB: [http://gpmdb.org/data/keyword/28973931 | + | #Isobe K, Jung HJ, Yang CR, Claxton J, Sandoval P, Burg MB, Raghuram V, Knepper MA, (2017) "Systems-level identification of PKA-dependent signaling in epithelial cells." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(42):E8875–E8884; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28973931 28973931]; doi: [https://dx.doi.org/10.1073/pnas.1709123114 10.1073/pnas.1709123114]; GPMDB: [http://gpmdb.org/data/keyword/28973931 75]. |
#Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | #Kollipara L, Buchkremer S, Coraspe JAG, Hathazi D, Senderek J, Weis J, Zahedi RP, Roos A, (2017) "In-depth phenotyping of lymphoblastoid cells suggests selective cellular vulnerability in Marinesco-Sjögren syndrome." <i>Oncotarget</i> <b>8</b>(40):68493–68516; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28978133 28978133]; doi: [https://dx.doi.org/10.18632/oncotarget.19663 10.18632/oncotarget.19663]; GPMDB: [http://gpmdb.org/data/keyword/28978133 23]. | ||
#Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | #Opitz N, Schmitt K, Hofer-Pretz V, Neumann B, Krebber H, Braus GH, Valerius O, (2017) "Capturing the Asc1p/RACK1 microenvironment at the head region of the 40S ribosome with quantitative BioID in yeast." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982715 28982715]; doi: [https://dx.doi.org/10.1074/mcp.M116.066654 10.1074/mcp.M116.066654]; GPMDB: [http://gpmdb.org/data/keyword/28982715 268]. | ||
#Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982716 28982716]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000020 10.1074/mcp.RA117.000020]; GPMDB: [http://gpmdb.org/data/keyword/28982716 12]. | #Parker BL, Burchfield JG, Clayton D, Geddes TA, Payne RJ, Kiens B, Wojtaszewski J, Richter EA, James DE, (2017) "Multiplexed temporal quantification of the exercise-regulated plasma peptidome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28982716 28982716]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000020 10.1074/mcp.RA117.000020]; GPMDB: [http://gpmdb.org/data/keyword/28982716 12]. | ||
+ | #Berger CN, Crepin VF, Roumeliotis TI, Wright JC, Carson D, Pevsner-Fischer M, Furniss RCD, Dougan G, Dori-Bachash M, Yu L, Clements A, Collins JW, Elinav E, Larrouy-Maumus GJ, Choudhary JS, Frankel G, (2017) "Citrobacter rodentium Subverts ATP Flux and Cholesterol Homeostasis in Intestinal Epithelial Cells In Vivo." <i>Cell Metab</i> <b>26</b>(5):738–752.e6; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/28988824 28988824]; doi: [https://dx.doi.org/10.1016/j.cmet.2017.09.003 10.1016/j.cmet.2017.09.003]; GPMDB: [http://gpmdb.org/data/keyword/28988824 24]. | ||
#Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | #Novikova SE, Tikhonova OV, Kurbatov LK, Farafonova TE, Vakhrushev IV, Zgoda VG, (2017) "Application of selected reaction monitoring and parallel reaction monitoring for investigation of HL-60 cell line differentiation." <i>Eur J Mass Spectrom (Chichester)</i> <b>23</b>(4):202–208; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29028392 29028392]; doi: [https://dx.doi.org/10.1177/1469066717719848 10.1177/1469066717719848]; GPMDB: [http://gpmdb.org/data/keyword/29028392 25]. | ||
#Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | #Saravanan R, Adav SS, Choong YK, van der Plas MJA, Petrlova J, Kjellström S, Sze SK, Schmidtchen A, (2017) "Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo." <i>Sci Rep</i> <b>7</b>(1):13136; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29030565 29030565]; doi: [https://dx.doi.org/10.1038/s41598-017-13197-3 10.1038/s41598-017-13197-3]; GPMDB: [http://gpmdb.org/data/keyword/29030565 43]. | ||
Line 1,724: | Line 1,729: | ||
#Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [http://gpmdb.org/data/keyword/29145658 4]. | #Cherry JD, Zeineddin A, Dammer EB, Webster JA, Duong D, Seyfried NT, Levey AI, Alvarez VE, Huber BR, Stein TD, Kiernan PT, McKee AC, Lah JJ, Hales CM, (2017) "Characterization of Detergent Insoluble Proteome in Chronic Traumatic Encephalopathy." <i>J Neuropathol Exp Neurol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29145658 29145658]; doi: [https://dx.doi.org/10.1093/jnen/nlx100 10.1093/jnen/nlx100]; GPMDB: [http://gpmdb.org/data/keyword/29145658 4]. | ||
#Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS, (2017) "Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29155090 29155090]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.008 10.1016/j.jprot.2017.11.008]; GPMDB: [http://gpmdb.org/data/keyword/29155090 21]. | #Korkmaz AG, Popov T, Peisl L, Codrea MC, Nahnsen S, Steimle A, Velic A, Macek B, von Bergen M, Bernhardt J, Frick JS, (2017) "Proteome and phosphoproteome analysis of commensally induced dendritic cell maturation states." <i>J Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29155090 29155090]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.008 10.1016/j.jprot.2017.11.008]; GPMDB: [http://gpmdb.org/data/keyword/29155090 21]. | ||
+ | #Föll MC, Fahrner M, Gretzmeier C, Thoma K, Biniossek ML, Kiritsi D, Meiss F, Schilling O, Nyström A, Kern JS, (2017) "Identification of tissue damage, extracellular matrix remodeling and bacterial challenge as common mechanisms associated with high-risk cutaneous squamous cell carcinomas." <i>Matrix Biol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29158163 29158163]; doi: [https://dx.doi.org/10.1016/j.matbio.2017.11.004 10.1016/j.matbio.2017.11.004]; GPMDB: [http://gpmdb.org/data/keyword/29158163 24]. | ||
+ | #Hoffman MA, Fang B, Haura EB, Rix U, Koomen JM, (2017) "Comparison of Quantitative Mass Spectrometry Platforms for Monitoring Kinase ATP Probe Uptake in Lung Cancer." <i>J Proteome Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29164889 29164889]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00329 10.1021/acs.jproteome.7b00329]; GPMDB: [http://gpmdb.org/data/keyword/29164889 18]. | ||
#Hosp F, Gutiérrez-Ángel S, Schaefer MH, Cox J, Meissner F, Hipp MS, Hartl FU, Klein R, Dudanova I, Mann M, (2017) "Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function." <i>Cell Rep</i> <b>21</b>(8):2291–2303; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29166617 29166617]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.10.097 10.1016/j.celrep.2017.10.097]; GPMDB: [http://gpmdb.org/data/keyword/29166617 196]. | #Hosp F, Gutiérrez-Ángel S, Schaefer MH, Cox J, Meissner F, Hipp MS, Hartl FU, Klein R, Dudanova I, Mann M, (2017) "Spatiotemporal Proteomic Profiling of Huntington's Disease Inclusions Reveals Widespread Loss of Protein Function." <i>Cell Rep</i> <b>21</b>(8):2291–2303; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29166617 29166617]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.10.097 10.1016/j.celrep.2017.10.097]; GPMDB: [http://gpmdb.org/data/keyword/29166617 196]. | ||
#Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A, (2017) "Global landscape of cell envelope protein complexes in Escherichia coli." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29176613 29176613]; doi: [https://dx.doi.org/10.1038/nbt.4024 10.1038/nbt.4024]; GPMDB: [http://gpmdb.org/data/keyword/29176613 2972]. | #Babu M, Bundalovic-Torma C, Calmettes C, Phanse S, Zhang Q, Jiang Y, Minic Z, Kim S, Mehla J, Gagarinova A, Rodionova I, Kumar A, Guo H, Kagan O, Pogoutse O, Aoki H, Deineko V, Caufield JH, Holtzapple E, Zhang Z, Vastermark A, Pandya Y, Lai CC, El Bakkouri M, Hooda Y, Shah M, Burnside D, Hooshyar M, Vlasblom J, Rajagopala SV, Golshani A, Wuchty S, F Greenblatt J, Saier M, Uetz P, F Moraes T, Parkinson J, Emili A, (2017) "Global landscape of cell envelope protein complexes in Escherichia coli." <i>Nat Biotechnol</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29176613 29176613]; doi: [https://dx.doi.org/10.1038/nbt.4024 10.1038/nbt.4024]; GPMDB: [http://gpmdb.org/data/keyword/29176613 2972]. | ||
+ | #Kelstrup CD, Bekker-Jensen DB, Arrey TN, Hogrebe A, Harder A, Olsen JV, (2018) "Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics." <i>J Proteome Res</i> <b>17</b>(1):727–738; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183128 29183128]; doi: [https://dx.doi.org/10.1021/acs.jproteome.7b00602 10.1021/acs.jproteome.7b00602]; GPMDB: [http://gpmdb.org/data/keyword/29183128 107]. | ||
+ | #Winter DL, Hart-Smith G, Wilkins MR, (2018) "Characterization of Protein Methyltransferases Rkm1, Rkm4, Efm4, Efm7, Set5 and Hmt1 Reveals Extensive Post-Translational Modification." <i>J Mol Biol</i> <b>430</b>(1):102–118; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29183786 29183786]; doi: [https://dx.doi.org/10.1016/j.jmb.2017.11.009 10.1016/j.jmb.2017.11.009]; GPMDB: [http://gpmdb.org/data/keyword/29183786 18]. | ||
#Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | #Lacombe M, Marie-Desvergne C, Combes F, Kraut A, Bruley C, Vandenbrouck Y, Chamel Mossuz V, Couté Y, Brun V, (2017) "Proteomic characterization of human exhaled breath condensate." <i>J Breath Res</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29189203 29189203]; doi: [https://dx.doi.org/10.1088/1752-7163/aa9e71 10.1088/1752-7163/aa9e71]; GPMDB: [http://gpmdb.org/data/keyword/29189203 4]. | ||
#Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | #Klaeger S, Heinzlmeir S, Wilhelm M, Polzer H, Vick B, Koenig PA, Reinecke M, Ruprecht B, Petzoldt S, Meng C, Zecha J, Reiter K, Qiao H, Helm D, Koch H, Schoof M, Canevari G, Casale E, Depaolini SR, Feuchtinger A, Wu Z, Schmidt T, Rueckert L, Becker W, Huenges J, Garz AK, Gohlke BO, Zolg DP, Kayser G, Vooder T, Preissner R, Hahne H, Tõnisson N, Kramer K, Götze K, Bassermann F, Schlegl J, Ehrlich HC, Aiche S, Walch A, Greif PA, Schneider S, Felder ER, Ruland J, Médard G, Jeremias I, Spiekermann K, Kuster B, (2017) "The target landscape of clinical kinase drugs." <i>Science</i> <b>358</b>(6367):; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29191878 29191878]; doi: [https://dx.doi.org/10.1126/science.aan4368 10.1126/science.aan4368]; GPMDB: [http://gpmdb.org/data/keyword/29191878 3032]. | ||
#Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | #Smith MC, Timmins-Schiffman E, Coton M, Coton E, Hymery N, Nunn BL, Madec S, (2017) "Differential impacts of individual and combined exposures of deoxynivalenol and zearalenone on the HepaRG human hepatic cell proteome." <i>J Proteomics</i> <b>173</b>:89–98; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208510 29208510]; doi: [https://dx.doi.org/10.1016/j.jprot.2017.11.025 10.1016/j.jprot.2017.11.025]; GPMDB: [http://gpmdb.org/data/keyword/29208510 72]. | ||
+ | #Herzog R, Boehm M, Unterwurzacher M, Wagner A, Parapatics K, Majek P, Mueller AC, Lichtenauer A, Bennett KL, Alper SL, Vychytil A, Aufricht C, Kratochwill K, (2017) "Effects of alanyl-glutamine treatment on the peritoneal dialysis effluent proteome reveal pathomechanism-associated molecular signatures." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208752 29208752]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000186 10.1074/mcp.RA117.000186]; GPMDB: [http://gpmdb.org/data/keyword/29208752 10]. | ||
#Wierer M, Prestel M, Schiller H, Yan G, Schaab C, Azghandi S, Werner J, Kessler T, Malik R, Murgia M, Aherrahrou Z, Schunkert H, Dichgans M, Mann M, (2017) "Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208753 29208753]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000315 10.1074/mcp.RA117.000315]; GPMDB: [http://gpmdb.org/data/keyword/29208753 156]. | #Wierer M, Prestel M, Schiller H, Yan G, Schaab C, Azghandi S, Werner J, Kessler T, Malik R, Murgia M, Aherrahrou Z, Schunkert H, Dichgans M, Mann M, (2017) "Compartment-resolved Proteomic Analysis of Mouse Aorta during Atherosclerotic Plaque Formation Reveals Osteoclast-specific Protein Expression." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29208753 29208753]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000315 10.1074/mcp.RA117.000315]; GPMDB: [http://gpmdb.org/data/keyword/29208753 156]. | ||
+ | #Stachowicz A, Siudut J, Suski M, Olszanecki R, Korbut R, Undas A, Wiśniewski JR, (2017) "Optimization of quantitative proteomic analysis of clots generated from plasma of patients with venous thromboembolism." <i>Clin Proteomics</i> <b>14</b>:38; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29209155 29209155]; doi: [https://dx.doi.org/10.1186/s12014-017-9173-x 10.1186/s12014-017-9173-x]; GPMDB: [http://gpmdb.org/data/keyword/29209155 36]. | ||
+ | #Muth T, Kohrs F, Heyer R, Benndorf D, Rapp E, Reichl U, Martens L, Renard BY, (2017) "MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go." <i>Anal Chem</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29215871 29215871]; doi: [https://dx.doi.org/10.1021/acs.analchem.7b03544 10.1021/acs.analchem.7b03544]; GPMDB: [http://gpmdb.org/data/keyword/29215871 3]. | ||
+ | #Sobocińska J, Roszczenko-Jasińska P, Zaręba-Kozioł M, Hromada-Judycka A, Matveichuk OV, Traczyk G, Łukasiuk K, Kwiatkowska K, (2017) "LPS upregulates palmitoylated enzymes of the phosphatidylinositol cycle. An insight from proteomic studies." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29217618 29217618]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000050 10.1074/mcp.RA117.000050]; GPMDB: [http://gpmdb.org/data/keyword/29217618 12]. | ||
+ | #Holthoff ER, Byrum SD, Mackintosh SG, Kelly T, Tackett AJ, Quick CM, Post SR, (2017) "Vulvar squamous cell carcinoma aggressiveness is associated with differential expression of collagen and STAT1." <i>Clin Proteomics</i> <b>14</b>:40; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29225558 29225558]; doi: [https://dx.doi.org/10.1186/s12014-017-9175-8 10.1186/s12014-017-9175-8]; GPMDB: [http://gpmdb.org/data/keyword/29225558 414]. | ||
+ | #Stewart NA, Gerlach RF, Gowland RL, Gron KJ, Montgomery J, (2017) "Sex determination of human remains from peptides in tooth enamel." <i>Proc Natl Acad Sci U S A</i> <b>114</b>(52):13649–13654; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29229823 29229823]; doi: [https://dx.doi.org/10.1073/pnas.1714926115 10.1073/pnas.1714926115]; GPMDB: [http://gpmdb.org/data/keyword/29229823 13]. | ||
+ | #Bizzotto S, Uzquiano A, Dingli F, Ershov D, Houllier A, Arras G, Richards M, Loew D, Minc N, Croquelois A, Houdusse A, Francis F, (2017) "Eml1 loss impairs apical progenitor spindle length and soma shape in the developing cerebral cortex." <i>Sci Rep</i> <b>7</b>(1):17308; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29229923 29229923]; doi: [https://dx.doi.org/10.1038/s41598-017-15253-4 10.1038/s41598-017-15253-4]; GPMDB: [http://gpmdb.org/data/keyword/29229923 28]. | ||
+ | #Alli-Shaik A, Wee S, Lim LHK, Gunaratne J, (2017) "Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells." <i>Breast Cancer Res</i> <b>19</b>(1):132; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29233185 29233185]; doi: [https://dx.doi.org/10.1186/s13058-017-0924-4 10.1186/s13058-017-0924-4]; GPMDB: [http://gpmdb.org/data/keyword/29233185 263]. | ||
+ | #Chong C, Marino F, Pak HS, Racle J, Daniel RT, Müller M, Gfeller D, Coukos G, Bassani-Sternberg M, (2017) "High-throughput and sensitive immunopeptidomics platform reveals profound IFNγ-mediated remodeling of the HLA ligandome." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29242379 29242379]; doi: [https://dx.doi.org/10.1074/mcp.TIR117.000383 10.1074/mcp.TIR117.000383]; GPMDB: [http://gpmdb.org/data/keyword/29242379 121]. | ||
+ | #Müller AK, Föll M, Heckelmann B, Kiefer S, Werner M, Schilling O, Biniossek ML, Jilg CA, Drendel V, (2017) "Proteomic Characterization of Prostate Cancer to Distinguish Nonmetastasizing and Metastasizing Primary Tumors and Lymph Node Metastases." <i>Neoplasia</i> <b>20</b>(2):140–151; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29248718 29248718]; doi: [https://dx.doi.org/10.1016/j.neo.2017.10.009 10.1016/j.neo.2017.10.009]; GPMDB: [http://gpmdb.org/data/keyword/29248718 15]. | ||
#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: [http://gpmdb.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: [http://gpmdb.org/data/keyword/29251727 33]. | ||
+ | #Bielecka ZF, Malinowska A, Brodaczewska KK, Klemba A, Kieda C, Krasowski P, Grzesiuk E, Piwowarski J, Czarnecka AM, Szczylik C, (2017) "Hypoxic 3D in vitro culture models reveal distinct resistance processes to TKIs in renal cancer cells." <i>Cell Biosci</i> <b>7</b>:71; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29270287 29270287]; doi: [https://dx.doi.org/10.1186/s13578-017-0197-8 10.1186/s13578-017-0197-8]; GPMDB: [http://gpmdb.org/data/keyword/29270287 12]. | ||
+ | #Gao Y, Liu X, Tang B, Li C, Kou Z, Li L, Liu W, Wu Y, Kou X, Li J, Zhao Y, Yin J, Wang H, Chen S, Liao L, Gao S, (2017) "Protein Expression Landscape of Mouse Embryos during Pre-implantation Development." <i>Cell Rep</i> <b>21</b>(13):3957–3969; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29281840 29281840]; doi: [https://dx.doi.org/10.1016/j.celrep.2017.11.111 10.1016/j.celrep.2017.11.111]; GPMDB: [http://gpmdb.org/data/keyword/29281840 2]. | ||
+ | #Thriene K, Grüning BA, Bornert O, Erxleben A, Leppert J, Athanasiou I, Weber E, Kiritsi D, Nyström A, Reinheckel T, Backofen R, Has C, Bruckner-Tuderman L, Dengjel J, (2018) "Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes." <i>Mol Cell Proteomics</i>; PMID: [http://www.ncbi.nlm.nih.gov/pubmed/29326176 29326176]; doi: [https://dx.doi.org/10.1074/mcp.RA117.000437 10.1074/mcp.RA117.000437]; GPMDB: [http://gpmdb.org/data/keyword/29326176 5]. |
GPMDB was originally constructed to serve as a reference work for all publicly available proteomics generated using tandem mass spectrometry. Public data is downloaded and reanalyzed using the current version of X! Tandem. The result files generated by the reanalysis and the relevant metadata are imported into the database and made available through the associated web site, ftp site and REST interfaces.
Contents |
The following public data repositories are checked daily for new suitable raw data for reanalysis:
Data made available from specific large projects, such as CPTAC or the Human Proteome Atlas, are also included when they are made available. Every effort is made so that reanalyzed results from all data sources are made available within 48 hours of their being released. In addition, data from lab web sites, ftp sites and direct contributions through the GPM sites made available to researchers are imported into GPMDB as part of a daily incremental update process.
GPMDB has been in operation since Jan. 1, 2004. Several large data source repositories have come into existence and ceased activity in the period since that time. All of the data from those repositories (e.g., TRANCHE, Peptidome) were reanalyzed and stored in GPMDB and they are still available even though the source repository sites are no longer active.
Simply because data is made available does not mean that it will be included in GPMDB. The data must be approved our quality control AI for its initial acceptance and it may be rejected subsequently because of either quality or originality concerns.
CAUTION: Many papers contain serious errors in their Methods sections. When using data from the literature, it is important to be skeptical of any experimental parameter (cell line, tissue type, modification reagents, quantitation methoods, etc.) that may impact on your use of the data. We have tried to correct any obvious errors, but there is no way to guarantee that we found them all. When attempting to analyze or reproduce results, keep in mind the likelyhood that even key parts of the experiment methods may have been recorded incorrectly in the associated manuscript, as methods are rarely reviewed properly in the current journal publication process.
The following is a list of data sets with associated PubMed IDs that have supplied data to the GPMDB Project through the data sources mentioned above. The list was current, as of Jan. 22, 2018.