{"id":241,"date":"2018-07-05T11:03:24","date_gmt":"2018-07-05T15:03:24","guid":{"rendered":"https:\/\/wpdev.whoi.edu\/lab-migration8\/datasets\/"},"modified":"2021-11-03T16:17:17","modified_gmt":"2021-11-03T20:17:17","slug":"datasets","status":"publish","type":"page","link":"https:\/\/www2.whoi.edu\/site\/saito-lab\/datasets\/","title":{"rendered":"Datasets"},"content":{"rendered":"\n\n\t

Datasets<\/h1>\n

Trace Metal Datasets<\/h3>\n\n\n

 <\/p>\n

Experimental Microbial Proteomic Datasets<\/h3>\n\n

Saito, MA, EM Bertrand, VV Bulygin, DM Moran, S Dutkiewicz, FM Monteiro, MJ Follows, FW Valois, JB Waterbury. 2011. Iron Conservation by Reduction of Metalloenzyme Inventories in the Marine Diazotroph Crocosphaera watsonii<\/a>. Proc. Natl. Acad. Sci. doi:10.1073\/pnas.1006943108.<\/p>\n

Supplemental Proteomics dataset with spectral counting results and identified tryptic peptides from diel cycle and iron limitation of Crocosphaera watsonii<\/em>: PNAS2011Supplemental<\/a> (also available on PNAS site as an open access document<\/a>).<\/p>\n\n\nSpectral Counting results and identified peptides under B12 and iron colimitation: Supplemental Proteomics Dataset
\n<\/em><\/a>\n\n

ST Dyhrman, BD Jenkins, TA Rynearson, MA Saito, ML Mercier, H Alexander, LP. Whitney, A Drzewianowski, VV Bulygin, EM Bertrand, Z Wu, C Benitez-Nelson, A Heithoff. 2012 Coordination in the transcriptome and proteome of the diatom Thalassiosira pseudonana reveals a diverse phosphorus stress response.<\/a> PLoS One<\/a>.<\/p>\nSupplemental datasets<\/em>
\nPeptides from Thalassiosira pseudonana under phosphorus-limited and replete conditions: Dyhrman_PLOSONE2012_Table4Peptides<\/a>
\nSpectral count and corresponding transcriptome data from phosphorus-limited and replete Thalassiosira pseudonana: Dyhrman_PLOSONE_Table5SupplementalSpectralCounts<\/a>\n\n

Louie L. Wurch, Erin M. Bertrand, Mak A. Saito, Benjamin A.S. Van Mooy and Sonya T. Dyhrman. 2011. Proteome changes driven by phosphorus stress and recovery in the brown tide-forming alga, Aureococcus anophagefferens<\/a>. PLoS One<\/a>.<\/p>\nSupplemental Proteomics Datasets<\/em>
\nIdentified peptides: Wurch_TableS1Peptides<\/a>
\nProtein spectral count data and corresponding transcriptome results: Wurch_TableS2SpectralCounts<\/a>\n

 <\/p>\n\t\t\t\t\n\t\t\t\t\"METZYME\n\t\t\t\t<\/a>\n\t\tMETZYME Cruise Track R\/V Kilo Moana 2011\n\t\t\t\t\n\t\t\t\t\"BIG\n\t\t\t\t<\/a>\n\t\tBIG RAPA R\/V Melville 2010\n\t

Metaproteomic Datasets<\/h3>\n\n

Samples analyzed by LC-MS (Thermo LTQ) for initial proteomic discovery work followed by analysis in X!!Tandem. Currently identified peptides dataset on station links below (Version July 10, 2013). These samples contain filtered material between 0.2 microns to 3.0 microns in size. Further high resolution and quantitative LC-MS analyses are underway. Funded by the Gordon and Betty Moore Foundation and Chemical Oceanography National Science Foundation.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\nMETZYME\n<\/td>\n\n<\/td>\n\nKM1128\n<\/td>\n\n<\/td>\n\n<\/td>\n<\/tr>\n
\nKM1128\n<\/td>\n\nOCTOBER -NOVEMBER 2011\n<\/td>\n\n<\/td>\n\n<\/td>\n\n<\/td>\n<\/tr>\n
\nStation\n<\/td>\n\nStation Start Date\n<\/td>\n\nLong E\n<\/td>\n\nLat N\n<\/td>\n\nDepth (M)\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n50\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n90\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n120\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n200\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n300\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n400\n<\/td>\n<\/tr>\n
\n1<\/a>\n<\/td>\n\n10\/3\/2011\n<\/td>\n\n205.60\n<\/td>\n\n17.00\n<\/td>\n\n600\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n40\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n60\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n120\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n150\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n200\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n250\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n300\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n500\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n550\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n600\n<\/td>\n<\/tr>\n
\n3<\/a>\n<\/td>\n\n10\/8\/2011\n<\/td>\n\n204.00\n<\/td>\n\n8.00\n<\/td>\n\n800\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n20\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n50\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n80\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n120\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n200\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n300\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n400\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n500\n<\/td>\n<\/tr>\n
\n5<\/a>\n<\/td>\n\n10\/13\/2011\n<\/td>\n\n202.01\n<\/td>\n\n0.00\n<\/td>\n\n600\n<\/td>\n<\/tr>\n
\n6<\/a>\n<\/td>\n\n10\/17\/2011\n<\/td>\n\n199.23\n<\/td>\n\n-3.50\n<\/td>\n\n40\n<\/td>\n<\/tr>\n
\n6<\/a>\n<\/td>\n\n10\/17\/2011\n<\/td>\n\n199.23\n<\/td>\n\n-3.50\n<\/td>\n\n80\n<\/td>\n<\/tr>\n
\n6<\/a>\n<\/td>\n\n10\/17\/2011\n<\/td>\n\n199.23\n<\/td>\n\n-3.50\n<\/td>\n\n200\n<\/td>\n<\/tr>\n
\n8<\/a>\n<\/td>\n\n10\/19\/2011\n<\/td>\n\n194.64\n<\/td>\n\n-9.25\n<\/td>\n\n40\n<\/td>\n<\/tr>\n
\n8<\/a>\n<\/td>\n\n10\/19\/2011\n<\/td>\n\n194.64\n<\/td>\n\n-9.25\n<\/td>\n\n70\n<\/td>\n<\/tr>\n
\n8<\/a>\n<\/td>\n\n10\/19\/2011\n<\/td>\n\n194.64\n<\/td>\n\n-9.25\n<\/td>\n\n200\n<\/td>\n<\/tr>\n
\n9<\/a>\n<\/td>\n\n10\/20\/2011\n<\/td>\n\n192.44\n<\/td>\n\n-12.00\n<\/td>\n\n40\n<\/td>\n<\/tr>\n
\n9<\/a>\n<\/td>\n\n10\/20\/2011\n<\/td>\n\n192.44\n<\/td>\n\n-12.00\n<\/td>\n\n70\n<\/td>\n<\/tr>\n
\n9<\/a>\n<\/td>\n\n10\/20\/2011\n<\/td>\n\n192.44\n<\/td>\n\n-12.00\n<\/td>\n\n380\n<\/td>\n<\/tr>\n
\n12<\/a>\n<\/td>\n\n10\/23\/2011\n<\/td>\n\n186.90\n<\/td>\n\n-15.00\n<\/td>\n\n40\n<\/td>\n<\/tr>\n
\n12<\/a>\n<\/td>\n\n10\/23\/2011\n<\/td>\n\n186.90\n<\/td>\n\n-15.00\n<\/td>\n\n120\n<\/td>\n<\/tr>\n
\n12<\/a>\n<\/td>\n\n10\/23\/2011\n<\/td>\n\n186.90\n<\/td>\n\n-15.00\n<\/td>\n\n300\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n\t

BIG RAPA Chile-Easter Island Expedition R\/V Melville 2010<\/h3>\n

Samples analyzed by LC-MS (Thermo LTQ) for initial proteomic discovery work followed by analysis in X!!Tandem. Currently identified peptides dataset (in preparation). These samples contain filtered material between 0.2 microns to 3.0 microns in size. Further high-resolution and quantitative LC-MS analyses are underway. Funded by the Gordon and Betty Moore Foundation and Center for Microbial Oceanography Research and Eduction (C-MORE, National Science Foundation).<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
BIG RAPA<\/td>\nMV1015<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
<\/td>\nNov-Dec 2010<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Station<\/td>\nStation Start Date<\/td>\nLong E<\/td>\nLat N<\/td>\nDepth (M)<\/td>\n<\/tr>\n
1<\/td>\n11\/22\/2010<\/td>\n289.20<\/td>\n-20.08<\/td>\n25<\/td>\n<\/tr>\n
2<\/td>\n11\/25\/2010<\/td>\n283.43<\/td>\n-21.18<\/td>\n48<\/td>\n<\/tr>\n
2<\/td>\n11\/25\/2010<\/td>\n283.43<\/td>\n-21.18<\/td>\n110<\/td>\n<\/tr>\n
2<\/td>\n11\/25\/2010<\/td>\n283.43<\/td>\n-21.18<\/td>\n800<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n20<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n100<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n200<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n375<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n500<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n650<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n800<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n1000<\/td>\n<\/tr>\n
4<\/td>\n11\/29\/2010<\/td>\n271.24<\/td>\n-23.46<\/td>\n1500<\/td>\n<\/tr>\n
6<\/td>\n12\/6\/2010<\/td>\n259.86<\/td>\n-25.55<\/td>\n10<\/td>\n<\/tr>\n
6<\/td>\n12\/6\/2010<\/td>\n259.86<\/td>\n-25.55<\/td>\n20<\/td>\n<\/tr>\n
6<\/td>\n12\/6\/2010<\/td>\n259.86<\/td>\n-25.55<\/td>\n60<\/td>\n<\/tr>\n
6<\/td>\n12\/6\/2010<\/td>\n259.86<\/td>\n-25.55<\/td>\n120<\/td>\n<\/tr>\n
6<\/td>\n12\/6\/2010<\/td>\n259.86<\/td>\n-25.55<\/td>\n250<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n20<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n75<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n175<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n250<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n400<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n500<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n800<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n1100<\/td>\n<\/tr>\n
7<\/td>\n12\/7\/2010<\/td>\n257.10<\/td>\n-26.05<\/td>\n1900<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Related Files\u00a0<\/strong>
\n\u00bb Metzyme_S1<\/a>
\n\u00bb Metzyme_S3<\/a>
\n\u00bb Metzyme_S5<\/a>
\n\u00bb Metzyme_S6<\/a>
\n\u00bb Metzyme_S8<\/a>
\n\u00bb Metzyme_S9<\/a>
\n\u00bb Metzyme_S12<\/a><\/h3>\n

Computational Proteomics Tools<\/h3>\n\n

These scripts provide tools and documentation for detecting redundant tryptic peptides between multiple genomes. These tools are intended to assist proteomics scientists understand the potential for identifying unique and shared tryptic peptides in metaproteomic data. Github repository link<\/a>.<\/p>\n\n","protected":false},"excerpt":{"rendered":"

Datasets Trace Metal Datasets   Experimental Microbial Proteomic Datasets Saito, MA, EM Bertrand, VV Bulygin, DM Moran, S Dutkiewicz, FM Monteiro, MJ Follows, FW Valois, JB Waterbury. 2011. Iron Conservation by Reduction of Metalloenzyme Inventories in the Marine Diazotroph Crocosphaera watsonii. Proc. Natl. Acad. Sci. doi:10.1073\/pnas.1006943108. Supplemental Proteomics dataset with spectral counting results and identified…<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":8,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/pages\/241"}],"collection":[{"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/comments?post=241"}],"version-history":[{"count":3,"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/pages\/241\/revisions"}],"predecessor-version":[{"id":494,"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/pages\/241\/revisions\/494"}],"wp:attachment":[{"href":"https:\/\/www2.whoi.edu\/site\/saito-lab\/wp-json\/wp\/v2\/media?parent=241"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}