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Targeted GC-MS detection of host and dietary metabolites and modifications by gut bacteria.
ORGANISM(S): Eggerthella Lenta (ncbitaxon:84112) Holdemania Filiformis (ncbitaxon:61171) Sutterella Wadsworthensis (ncbitaxon:40545)
The 15 strains of Gambierdiscus were cultivated in four separate laboratories. Each laboratory grew their available strains (see sample metadata) in addition to the G. australes strain AUS S080911_1 isolated from Pacific Ocean.
Irradiance (70-100 umol photons m-2 s-1) and light/dark cycle (12h:12h)...
ORGANISM(S): Gambierdiscus Silvae (ncbitaxon:1550089) Gambierdiscus Carolinianus (ncbitaxon:864182) Gambierdiscus Australes (ncbitaxon:439317) Gambierdiscus Belizeanus (ncbitaxon:439316) Gambierdiscus Excentricus (ncbitaxon:986170) Gambierdiscus Caribaeus (ncbitaxon:864185)
Gene expression profiling of the proximal, medial and distal parts of Amphiura filiformis arm explants.
ORGANISM(S): Amphiura filiformis
Human fecal communities were dosed with either choline, carnitine, butyrobetaine, or glycine betaine to measure the microbial response to quaternary amine addition. Samples were digested with trypsin, and analyzed by LC-MS/MS. Data was searched with MS-GF+ using PNNL's DMS Processing pipeline.
ORGANISM(S): Unclassified Bacteria (ncbitaxon:2323)
A collection of MS/MS data 112 microbial species. #BiodiversityLibrary
ORGANISM(S): Pseudonocardia Sp. (ncbitaxon:60912) Bacillus Anthracis Str. Ames (ncbitaxon:198094) Caulobacter Crescentus Cb15 (ncbitaxon:190650) Opitutaceae Bacterium Tav5 (ncbitaxon:794903) Enterobacter Cloacae Scf1 (ncbitaxon:701347) Heliobacterium Modesticaldum (ncbitaxon:35701) Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. 14028s (ncbitaxon:588858) Bacillus Subtilis Subsp. Subtilis Str. 168 (ncbitaxon:224308) Shewanella Sp. Ana-3 (ncbitaxon:94122) Sinorhizobium Meliloti 1021 (ncbitaxon:266834) Cyanothece Sp. Atcc 51142 (ncbitaxon:43989) Escherichia Coli Bl21 (ncbitaxon:511693) Diplosphaera Colitermitum Tav2 (ncbitaxon:278957) Anaplasma Phagocytophilum (ncbitaxon:948) Chloroflexus Aurantiacus (ncbitaxon:1108) Yersinia Pestis Co92 (ncbitaxon:214092) Yersinia Pseudotuberculosis Ip 32953 (ncbitaxon:273123) Syntrophobacter Fumaroxidans (ncbitaxon:119484) Saccharomonospora Viridis Dsm 43017 (ncbitaxon:471857) Brachybacterium Faecium Dsm 4810 (ncbitaxon:446465) Cenarchaeum Symbiosum (ncbitaxon:46770) Chloracidobacterium Thermophilum (ncbitaxon:458033) Acidiphilium Cryptum Jf-5 (ncbitaxon:349163) Geobacter Sulfurreducens Pca (ncbitaxon:243231) Nakamurella Multipartita Dsm 44233 (ncbitaxon:479431) Sulfolobus Acidocaldarius Dsm 639 (ncbitaxon:330779) Desulfovibrio Desulfuricans Nd132 (ncbitaxon:641491) Haloferax Volcanii (ncbitaxon:2246) Synechococcus Sp. Pcc 7002 (ncbitaxon:32049) Fibrobacter Succinogenes Subsp. Succinogenes S85 (ncbitaxon:59374) Sinorhizobium Medicae (ncbitaxon:110321) Deinococcus Radiodurans R1 (ncbitaxon:243230) Shewanella Sp. Mr-7 (ncbitaxon:60481) Cellulomonas Flavigena Dsm 20109 (ncbitaxon:446466) Mycobacterium Tuberculosis H37rv (ncbitaxon:83332) Chlorobaculum Tepidum (ncbitaxon:1097) Kosmotoga Olearia Tbf 19.5.1 (ncbitaxon:521045) Shewanella Frigidimarina Ncimb 400 (ncbitaxon:318167) Shewanella Putrefaciens 200 (ncbitaxon:399804) Prochlorococcus Marinus Subsp. Pastoris Str. Ccmp1986 (ncbitaxon:59919) Shewanella Baltica Os185 (ncbitaxon:402882) Hungateiclostridium Thermocellum (ncbitaxon:1515) Thiocapsa Marina (ncbitaxon:244573) Burkholderia Mallei (ncbitaxon:13373) Thermotoga Maritima (ncbitaxon:2336) Novosphingobium Aromaticivorans (ncbitaxon:48935) Arthrobacter Sp. Fb24 (ncbitaxon:290399) Salmonella Enterica Subsp. Enterica Serovar Typhimurium Str. Lt2 (ncbitaxon:99287) Xylanimonas Cellulosilytica Dsm 15894 (ncbitaxon:446471) Halorhabdus Utahensis Dsm 12940 (ncbitaxon:519442) Yersinia Enterocolitica (ncbitaxon:630) Thermosynechococcus Elongatus Bp-1 (ncbitaxon:197221) Geobacter Bemidjiensis Bem (ncbitaxon:404380) Kineococcus Radiotolerans Srs30216 (ncbitaxon:266940) Shewanella Oneidensis Mr-1 (ncbitaxon:211586) Delta Proteobacterium Naphs2 (ncbitaxon:88274) Desulfovibrio Vulgaris Str. Hildenborough (ncbitaxon:882) Ralstonia Pickettii (ncbitaxon:329) Ehrlichia Chaffeensis (ncbitaxon:945) Rhodobacter Capsulatus Sb 1003 (ncbitaxon:272942) Escherichia Coli Str. K-12 Substr. Mg1655 (ncbitaxon:511145) Rhodobacter Sphaeroides 2.4.1 (ncbitaxon:272943) Halogeometricum Borinquense Dsm 11551 (ncbitaxon:469382) Anabaena Variabilis (ncbitaxon:1172) Bartonella Henselae Str. Houston-1 (ncbitaxon:283166) Dethiosulfovibrio Peptidovorans Dsm 11002 (ncbitaxon:469381) Synechocystis Sp. Pcc 6803 (ncbitaxon:1148) Shewanella Loihica Pv-4 (ncbitaxon:323850) Geobacter Metallireducens Gs-15 (ncbitaxon:269799) Shewanella Baltica Os195 (ncbitaxon:399599) Roseiflexus Castenholzii (ncbitaxon:120962) Opitutaceae Bacterium Tav1 (ncbitaxon:278956) Borrelia Burgdorferi B31 (ncbitaxon:224326) Pseudomonas Aeruginosa Pao1 (ncbitaxon:208964) Sanguibacter Keddieii Dsm 10542 (ncbitaxon:446469) Methanosarcina Barkeri (ncbitaxon:2208) Thermosynechococcus Sp. Nk55a Slackia Heliotrinireducens Dsm 20476 (ncbitaxon:471855) Cyanothece Sp. Pcc 7822 (ncbitaxon:497965) Thermobispora Bispora Dsm 43833 (ncbitaxon:469371) Rhodopseudomonas Palustris (ncbitaxon:1076) Cyanothece Sp. Pcc 8801 (ncbitaxon:41431) Cyanothece Sp. Pcc 7424 (ncbitaxon:65393) Desulfovibrio Desulfuricans (ncbitaxon:876) Escherichia Coli Rk4353 Shewanella Putrefaciens Cn-32 (ncbitaxon:319224) Yersinia Pestis Kim10+ (ncbitaxon:187410) Candidatus Pelagibacter Ubique Htcc1062 (ncbitaxon:335992) Methanospirillum Hungatei Jf-1 (ncbitaxon:323259) Cyanothece Sp. Atcc 51472 (ncbitaxon:860575) Shewanella Sp. W3-18-1 (ncbitaxon:351745) Stackebrandtia Nassauensis Dsm 44728 (ncbitaxon:446470) Cyanothece Sp. Pcc 8802 (ncbitaxon:395962) Cryptobacterium Curtum Dsm 15641 (ncbitaxon:469378) Shewanella Amazonensis Sb2b (ncbitaxon:326297) Nocardiopsis Dassonvillei Subsp. Dassonvillei Dsm 43111 (ncbitaxon:446468) Dehalococcoides Ethenogenes 195 (ncbitaxon:243164) Shewanella Denitrificans Os217 (ncbitaxon:318161) Anaeromyxobacter Dehalogenans (ncbitaxon:161493) Actinosynnema Mirum Dsm 43827 (ncbitaxon:446462) Shewanella Baltica Os223 (ncbitaxon:407976) Geobacter Uraniireducens (ncbitaxon:351604) Pseudomonas Fluorescens Pf0-1 (ncbitaxon:205922) Pelobacter Carbinolicus Dsm 2380 (ncbitaxon:338963) Salmonella Enterica Subsp. Enterica Serovar Typhi Str. Ty2 (ncbitaxon:209261) Bacillus Anthracis Str. Sterne (ncbitaxon:260799) Yersinia Pseudotuberculosis Pb1/+ (ncbitaxon:502801) Methylophilales Bacterium Htcc2181 (ncbitaxon:383631) Shewanella Sp. Mr-4 (ncbitaxon:60480) Shewanella Baltica Os155 (ncbitaxon:325240) Cyanothece Sp. Pcc 7425 (ncbitaxon:395961)
We analysed data collected as part of the Biomarkers of Acute Serious Illness in Children (BASIC) study. BASIC was a prospective cohort study that enrolled critically ill children admitted to four PICUs in London and Eastern England, UK, during emergency transport by the Children’s Acute Transport S...
ORGANISM(S): Homo sapiens
Metabolic networks are interconnected and influence diverse cellular processes. The protein-metabolite interactions that mediate these networks are frequently low affinity and challenging to systematically discover. We developed mass spectrometry integrated with equilibrium dialysis for the disco...
FLAG immunoprecipitation of NUDT5 WT and Y74F, and Strep-FLAG sequential immunoprecipitation of PPAT-NUDT5 complexes from HEK293T cells lentivirally expressing tagged constructs
ORGANISM(S): Homo sapiens (Human)
The consistent and accurate quantification of proteins is a challenging task for mass spectrometry (MS)-based proteomics. SWATH-MS uses data-independent acquisition (DIA) for label-free quantification. Here we evaluated five software tools for processing SWATH-MS data: OpenSWATH, SWATH2.0, Skyline, ...
ORGANISM(S): Escherichia Coli (ncbitaxon:562) Homo Sapiens (ncbitaxon:9606) Saccharomyces Cerevisiae (ncbitaxon:4932)