Proteomics

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Analytical guidelines for co-fractionation mass spectrometry obtained through global profiling of gold standard Saccharomyces cerevisiae protein complexes


ABSTRACT: Co-fractionation mass spectrometry (CF-MS) is a technique with potential to characterise endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study exploits very high proteome coverage libraries of gold standard Saccharomyces cerevisiae complexes to thoroughly evaluate novel and published yeast CF-MS datasets. A new method for identifying gold standard complexes in CF-MS data, Reference Complex Profiling, and the Extending ‘Guilt-by-Association’ by Degree (EGAD) R package are used for these evaluations, which are reinforced with concurrent analyses of published human data. By evaluating data collection designs, which involve fractionation of cell lysates, it is found that near-maximum recall of complexes can be achieved with fewer samples than published studies. Distributing sample collection across orthogonal fractionation methods, rather than a single high resolution dataset, leads to particularly efficient recall. By evaluating 17 different similarity scoring metrics, which are central to CF-MS data analysis, it is found that two metrics rarely used in past CF-MS studies – Spearman and Kendall correlations – and the recently introduced Co-apex metric frequently maximise recall, while a popular metric – Euclidean distance – delivers poor recall. The common practice of integrating external genomic data into CF-MS data analysis is also evaluated, revealing that this practice may improve the precision and recall of known complexes but is generally unsuitable for predicting novel complexes in model organisms. If studying non-model organisms using orthologous genomic data, it is found that particular subsets of fractionation profiles (e.g. the lowest abundance quartile) should be excluded to minimise false discovery. Together these guidelines identify avenues for precise, sensitive and efficient CF-MS studies of known complexes, and effective predictions of novel complexes for orthogonal experimental validation.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Bartonella henselae str. Houston-1   Brachypodium distachyon   Trypanosoma brucei brucei TREU927   wastewater metagenome   Cancer irroratus   Modiolus kurilensis   Apis mellifera   Saccharomyces cerevisiae   Ophiophagus hannah   Mucidula mucida   Thermochaetoides thermophila   Shewanella baltica   Methermicoccus shengliensis DSM 18856   Microcystis aeruginosa PCC 7806   Conus striatus   Prochlorococcus marinus str. MIT 9313   Musa ABB Group   Oncorhynchus tshawytscha   Bemisia cf. tabaci Middle East-Asia Minor 1   Mycoplasmopsis agalactiae   Geodermatophilus obscurus DSM 43160   Saimiri boliviensis boliviensis   Herpes simplex virus unknown type   Epstein-barr virus strain p3hr-1   Moraxella catarrhalis   Diploria labyrinthiformis   Cyprinodon variegatus   Clostridioides difficile 050-P50-2011   Microbacterium sp.   Pseudodiploria strigosa   Neisseria meningitidis FAM18   Hepatitis E virus type 1   Streptococcus dysgalactiae subsp. equisimilis SK1249   Salmonella bongori   Aspergillus carbonarius ITEM 5010   H1N1 subtype   Pachycladon cheesemanii   Rupicapra rupicapra   Clostridioides difficile ATCC 43255   Trichodesmium   Nitrososphaera viennensis   Tetrahymena thermophila CU428   Candidatus Protochlamydia amoebophila UWE25   Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759   Olavius algarvensis Gamma 1 endosymbiont   Peromyscus leucopus   HIV-1 M:B_HXB2R   Scophthalmus maximus   Rattus norvegicus   Mycobacterium tuberculosis SP7   Lactococcus lactis subsp. cremoris MG1363   Solenopsis invicta   Chitinophaga pinensis   Cupriavidus basilensis   Bison   Afrohybanthus enneaspermus   Neisseria gonorrhoeae   Legionella pneumophila   Xanthomonas oryzae pv. oryzae PXO99A   Solidesulfovibrio magneticus RS-1   Delonix regia   Chlorocebus aethiops   Mytilus edulis   Boiga irregularis   Botrytis cinerea   Bacillus thuringiensis serovar berliner ATCC 10792   Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150   Herbaspirillum seropedicae   Toxoplasma gondii CtCo5   Lactiplantibacillus plantarum subsp. plantarum   Thermococcus gammatolerans EJ3   Campylobacter jejuni   Rhipicephalus microplus   Tritrichomonas foetus   Gallus gallus   Bombus terrestris audax   Coprococcus eutactus   Komagataella pastoris   Paracoccus denitrificans   Musa acuminata subsp. acuminata   Synechocystis sp. PCC 6803   Viola tricolor   Manica rubida   Strix varia   Geobacillus kaustophilus   Renibacterium salmoninarum ATCC 33209   Mayaro virus (strain Brazil)   Mentha spicata   Fraxinus nigra   environmental samples   Madurella mycetomatis   Haemaphysalis longicornis   Tursiops truncatus   Klebsiella pneumoniae JH1   Tuber albidum   Prevotella ruminicola 23   Histomonas meleagridis   Rhodopseudomonas palustris   Yersinia ruckeri   Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841   Synechocystis sp. PCC 6803 substr. GT-S   Rhizoctonia solani AG-8 WAC10335   Tuber indicum   Tetranychus urticae   Clostridioides difficile 630   [Ruminococcus] gnavus   Desulfoluna spongiiphila   Komagataella pastoris DSMZ 70382   Levilactobacillus brevis   Pseudomonas stutzeri   Oreochromis niloticus niloticus   Akkermansia muciniphila ATCC BAA-835   Craterostigma plantagineum   freshwater sediment metagenome   Spondylus gaederopus   Penicillium sp. B12   Ophrys garganica   Acanthaster planci   Amblyomma americanum   Vipera berus berus   Blumeria graminis f. sp. tritici   Naja mandalayensis   Bacillus toyonensis BCT-7112   Saiga tatarica   Rousettus aegyptiacus   Bacillus pumilus   Azospirillum brasilense FP2   Actinomycetia   Brucella abortus 2308   Burkholderia cenocepacia H111   Nicotiana forgetiana   Exidia glandulosa HHB12029   Escherichia coli O157:H7   Plasmodium sp. pBT9   Escherichia coli HT115   Blumeria hordei DH14   Thermoclostridium stercorarium   Burkholderia thailandensis   Phaeobacter sp. MED193   Haptophyta   Paradendryphiella salina   Ehrlichia ruminantium str. Gardel   Vitis   Lilium   Parasynechococcus marenigrum WH 8102   Neisseria meningitidis MC58   Leishmania major strain Friedlin   Mrakia psychrophila   Acheta domesticus   environmental samples   Tomato spotted wilt orthotospovirus   Russula atropurpurea   Aspergillus terreus   Salmonella enterica subsp. enterica serovar Typhi str. CT18   Petunia   Naja ashei   Crocuta crocuta   Agrostis stolonifera   Mycoplasma gallisepticum S6   Viola odorata   Pristhesancus sp. 00004635   Streptococcus suis   Aspergillus niger ATCC 13496   Rathayibacter toxicus   Spirochaeta sp. ELBA   Human alphaherpesvirus 1 strain KOS   Gammarus pulex   Aiptasia   Mycoplasma pneumoniae M129   Artemisia annua   Fasciola hepatica   Human betaherpesvirus 5   Sepia officinalis   Ictalurid herpesvirus 1   Ruegeria pomeroyi   Yersinia pestis CO92   Schizosaccharomyces pombe 927   Marseillevirus   Pituophis melanoleucus   Mycoplasma suis KI3806   Toxoplasma gondii GT1   Steinernema carpocapsae   uncultured Phormidium sp.   Homo sapiens subsp. 'Denisova'   Triticum turgidum subsp. durum   Pseudomonas aeruginosa PA14   Boehmeria nivea   Pseudotsuga menziesii var. menziesii   Sepioloidea lineolata   HIV-1 vector pNL4-3   Pinctada maxima   Bacillus cereus   Viruses   Platichthys flesus   Chlorella sp. FC2 IITG   Mycoplasma hyopneumoniae 232   Human herpesvirus 5 strain AD169   Lactobacillus johnsonii N6.2   Anopheles gambiae   Chlorella vulgaris   Cavia porcellus   Dendroaspis polylepis polylepis   Streptococcus equi subsp. equi   Papio hamadryas   Aspergillus flavus NRRL3357   Pseudodiploria clivosa   Cryptococcus neoformans var. grubii H99W   Biomphalaria glabrata   Thymallus thymallus   Algoriphagus marincola HL-49   Leuconostoc gelidum subsp. gelidum   Oryza sativa   Phikzvirus phiKZ   Pseudomonas phage EL   Neospora caninum   Aepyceros melampus   Schizosaccharomyces pombe OY26   Hominidae   Mycobacterium avium subsp. paratuberculosis   Escherichia coli O157:H7 str. EDL933   Lichtheimia corymbifera JMRC:FSU:9682   Mycobacterium marinum   Streptomyces lincolnensis   Penicillium verrucosum   Ferroplasma   Salmonella enterica subsp. enterica serovar Typhimurium   Sulfolobus islandicus LAL14/1   Hydra vulgaris   Dasypogon diadema   Nostoc sp. FB71   Myxococcus xanthus DK 1622   Thermoanaerobacter pseudethanolicus   Sinorhizobium meliloti BL225C   Citrus sinensis   Sciuridae   Ascoidea rubescens   Microcystis aeruginosa   Toxoplasma gondii   Penaeus vannamei   Cuon alpinus   Stegodyphus mimosarum   Mycobacterium tuberculosis variant bovis BCG   Bithynia siamensis goniomphalos   Pyrus x bretschneideri   Chlamydomonas reinhardtii   Firmicutes   Martes martes   Human herpesvirus 2 strain 186   Komagataella phaffii   Trypanosoma cruzi strain CL Brener   Salmonella enterica subsp. enterica serovar Typhimurium str. A130   Gammarus fossarum   Zea mays   Fusarium oxysporum f. sp. lycopersici 4287   Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821   Roseobacter denitrificans OCh 114   Notamacropus eugenii   Salmonella enterica subsp. enterica serovar Typhimurium str. D23580   Human immunodeficiency virus   Pisolithus tinctorius Marx 270   Cryptococcus neoformans var. grubii H99S   Leucoraja erinacea   Naja sagittifera   Lasius niger   Podospora anserina S mat+   Crotalus adamanteus   gut metagenome   Homo sapiens/Mus musculus xenograft   Entamoeba histolytica HM-1:IMSS-A   Erythrobacter sp. HL-111   Heloderma suspectum suspectum   Taeniopygia guttata   Campylobacter concisus UNSWCD   Streptomyces sp.   Roseburia hominis A2-183   Leishmania infantum   Plasmodium falciparum Dd2   Aspergillus terreus NIH2624   Wolbachia endosymbiont of Diaphorina citri   Schizosaccharomyces pombe DM3650   Crustacea   Brucella abortus S19   Methanosarcina acetivorans   Sordaria macrospora   Armoracia rusticana   Saccharomyces mikatae IFO 1815   Pachycladon novaezelandiae   Deinococcus radiodurans ATCC 13939   Metarhizium robertsii   Gorilla gorilla   Rickettsia slovaca 13-B   Homo sapiens   Bombus terrestris   Rhodococcus jostii RHA1   Tilletia indica   Bacillus amyloliquefaciens   Pichia kudriavzevii   Pseudotsuga menziesii   Lutra lutra   Granulicella sp.   Lactobacillus johnsonii   Datura stramonium   Rangifer tarandus   Anas platyrhynchos   Thermus thermophilus   Populus tremula x Populus tremuloides   Colobanthus quitensis   Yarrowia lipolytica   Spirometra erinaceieuropaei   Staphylococcus aureus subsp. aureus MRSA252   Alces alces   Crotalus durissus terrificus   Staphylococcus epidermidis   Leishmania major   Laxus oneistus   Muvirus mu   Pseudomonas sp. 'Pseudom. M1'   Listeria monocytogenes EGD-e   Pinus radiata   Pichia fermentans   Paramoeba perurans   Rosaceae   Mastigamoeba balamuthi ATTC 30984   Human immunodeficiency virus type 1 3916-CRO   Saccharomycopsis capsularis   Anaerostipes caccae L1-92   Lentibacter algarum   Chlorella sp. SAG 211-18   [Candida] glabrata   Bacillus cytotoxicus NVH 391-98   Acinetobacter nosocomialis   Halobacterium salinarum R1   Helicobacter pylori J99   Nicotiana repanda   Nicotiana longiflora   Klebsiella pneumoniae LCT-KP289   Drosophila   Pseudomonas aeruginosa LESlike1   Oenothera glazioviana   Ovis canadensis mexicana   Tapirus terrestris   Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344   Andreprevotia sp. IGB-42   Aplysia californica   Trypanosoma cruzi Dm28c   Enterococcus mundtii CRL35   Prototheca zopfii   Cynodon dactylon   Formosa sp. Hel3_A1_48   Staphylococcus aureus subsp. aureus   Bacillus thuringiensis   Amphibalanus amphitrite   Streptococcus agalactiae   Citrullus lanatus   Brucella abortus   Betaproteobacteria bacterium RIFCSPLOWO2_02_64_14   Cyanidioschyzon merolae   Fragaria x ananassa   Lagomorpha   Sulfolobus acidocaldarius   Triaenophorus crassus   Bacillus cereus ATCC 14579   Mycoplasma feriruminatoris   Morchella importuna   Saccharopolyspora erythraea   Mycobacterium tuberculosis LAM7   Secale cereale   Latilactobacillus curvatus   Xenopsylla cheopis   Toxoplasma gondii PRU   Zymomonas mobilis   Dokdonia sp. MED134   Vitis riparia x Vitis rupestris   Schmidtea mediterranea   Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130   Pleuromamma xiphias   Cellulophaga baltica 18   Thelohanellus kitauei   Physalis angulata   Acinetobacter calcoaceticus/baumannii complex   Brugia malayi   Paucilactobacillus suebicus   Orthomyxoviridae   Canis lupus x Canis lupus familiaris   Mustela sp.   unclassified Candidatus Omnitrophica   biofilm metagenome   Ficus carica   Calvadosia cruxmelitensis   Tannerella forsythia   Corynebacterium diphtheriae NCTC 13129   Legionella pneumophila str. Paris   Bacillus thuringiensis Bt407   Ursus arctos arctos   Montastraea cavernosa   Paracoccus denitrificans PD1222   Vibrio parahaemolyticus   Aspergillus flavus   Harmonia axyridis   Neurospora crassa   Clostridium autoethanogenum   Nicotiana benthamiana   Paulownia fortunei   Ixodes ricinus   Ambystoma mexicanum   Schistocephalus solidus   Pseudomonas aeruginosa UCBPP-PA14   (Vitis vinifera x Vitis berlandieri) x Vitis berlandieri   Viola tricolor subsp. tricolor   Delftia acidovorans SPH-1   Helicobacter pylori 26695-1   Planococcus halocryophilus Or1   Citrobacter freundii   Toxoplasma   Phaeodactylum tricornutum   Clostridioides difficile R20291   Burkholderia pseudomallei K96243   Botryococcus braunii   Sarcoptes scabiei   Coronavirus PREDICT CoV-2   Anopheles stephensi   Sistrurus catenatus   Faecalibacterium prausnitzii   Botrytis cinerea B05.10   Avian infectious bronchitis virus (strain Beaudette CK)   Moringa oleifera   environmental samples   Scolopendra morsitans   Vertebrata   Prochlorococcus marinus str. MIT 9312   Selaginella moellendorffii   Archaea   Murine leukemia virus   Brucella anthropi ATCC 49188   Saccostrea glomerata   Acanthamoeba castellanii str. Neff   Axis axis   Acinetobacter baylyi ADP1   Camellia sinensis   Vaccinia virus   Cyprinus carpio   Coxiella burnetii RSA 493   Hippopotamus amphibius   Betacoronavirus sp.   Human coronavirus NL63   Physcomitrium patens   Entamoeba histolytica   Staphylococcus lugdunensis   Cyanophora paradoxa   Streptococcus thermophilus LMD-9   Oryctolagus cuniculus algirus   Pseudomonas aeruginosa str. E2UoS   Thermococcus eurythermalis   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu   Candida dubliniensis CD36   Actinomycetospora chiangmaiensis DSM 45062   Dialister   Mus musculus x Rattus norvegicus   Tamias striatus   Brassica oleracea var. gemmifera   Lactococcus phage   Corucia zebrata   Plasmodium yoelii   Coprococcus comes ATCC 27758   Streptomyces griseorubens   Leptospira interrogans   Campylobacter concisus 13826   Geobacter sulfurreducens   Anopheles culicifacies A   Schistosoma mansoni   Hadronyche infensa   Craterostigmus tasmanianus   Influenza B virus (B/Memphis/13/2003)   Mycobacterium avium subsp. paratuberculosis K-10   'Phaseolus vulgaris' phytoplasma   Dryopteris affinis subsp. affinis   Camelidae   Heterosigma akashiwo   Bothrops jararaca   Staphylococcus aureus subsp. aureus USA300   Pinus nigra   Mycobacterium tuberculosis KZN 1435   Saccharomyces cerevisiae BY4741   Streptococcus equi subsp. equi 4047   Pogostemon cablin   Schizosaccharomyces pombe 972h-   Aspergillus niger CBS 513.88   Riptortus pedestris   Cajanus cajan   Tilletia laevis   Ogataea polymorpha   Tilletia caries   Legionella pneumophila subsp. pneumophila   Leishmania infantum JPCM5   Staphylococcus aureus   Arcobacter   Phaeodactylum tricornutum CCAP 1055/1   Hypsiglena jani   Megoura viciae   Olavius algarvensis spirochete endosymbiont   Klebsiella variicola At-22   Ciona intestinalis   Eukaryota   Carnobacterium divergens   Streptococcus pneumoniae TIGR4   Streptomyces sp. EF-93   Soa   Nicotiana clevelandii   Roseobacter sp. MED193   Human immunodeficiency virus 1   Anoplocephala perfoliata   Pseudovibrio sp. FO-BEG1   Dorea longicatena DSM 13814   Hepatitis B virus   Cellvibrio japonicus Ueda107   Clostridia   Lathyrus sativus   Lactiplantibacillus plantarum JDM1   Pseudomonas aeruginosa PAK   anaerobic digester metagenome   Saccharomyces cerevisiae YJM789   Synechococcus sp. BL107   Listeria monocytogenes serotype 4b str. F2365   Streptococcus pyogenes STAB901   Flavobacterium sp. 316   Clostridium tetani E88   Alternaria tomato   Toxoplasma gondii type III   Human herpesvirus 5 strain Merlin   Methanothrix   Lolium perenne subsp. perenne   Crassostrea gigas   Pseudoliparis swirei   Brevibacterium casei   Sorghum bicolor x Saccharum hybrid cultivar   Sinorhizobium meliloti   Brucella   Mycoplasmopsis bovis HB0801   Pseudomonas sp. UK4   Nitrospirillum amazonense CBAmc   Pongo sp.   Dioscorea oppositifolia   Desulfovibrio sp. G11   Nicotiana paniculata   Candidatus Thiosymbion oneisti   Catenibacterium   Streptococcus agalactiae FSL S3-026   Roseibaca calidilacus   Pseudomonas putida   Tortispora caseinolytica   Rhodopseudomonas palustris CGA009   Streptomyces sp. MBT84   Mycobacterium avium 100   Sulfobacillus thermosulfidooxidans   Rhizobium sp. Leaf68   Chromatiales bacterium OalgGamma1   Bradyrhizobium japonicum   Bacillus anthracis str. Sterne   Ursus maritimus   Xanthomonas translucens   Bifidobacterium longum NCC2705   Ovis aries   Roseburia intestinalis L1-82   Mammalia   Acidiphilium cryptum JF-5   Klebsiella pneumoniae   Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S   Manihot esculenta   Desulfovibrio ferrophilus   Mycobacterium tuberculosis str. Beijing/W BT1   Modestobacter marinus BC501   Hebomoia glaucippe   Clostridium butyricum E4 str. BoNT E BL5262   Nelumbo nucifera   Brochothrix thermosphacta   Eulimnogammarus cyaneus   Arachis hypogaea   microbial mat metagenome   Escherichia coli O157:H7 str. TW14359   Mariprofundus ferrooxydans   Enhydra lutris nereis   Dictyostelium discoideum AX4   Populus trichocarpa   Francisella tularensis subsp. holarctica FSC200   Neisseria gonorrhoeae FA 1090   Sanghuangporus   Myxobilatus gasterostei   Vitis vinifera   Ceratopteris richardii   Aspergillus tubingensis   Bungarus   Cowpox virus (Brighton Red)   Fusarium fujikuroi IMI 58289   Aspergillus aff. niger A2   Staphylococcus sp. 1   Ruminiclostridium papyrosolvens DSM 2782   Felis catus   Mollivirus sibericum   Bos grunniens   Trichoderma harzianum CBS 226.95   Arabidopsis   Aedes aegypti aegypti   Lingulodinium polyedra   Tarenaya hassleriana   Piaractus mesopotamicus   Xylocopa violacea   Vibrio cholerae   Aeromonas sp. enrichment culture clone AM2   Onchocerca volvulus   Lactococcus lactis subsp. cremoris UC509.9   Dehalococcoides mccartyi   Brassica oleracea var. capitata   Picea abies   Vairimorpha necatrix   Vibrio alginolyticus   Nitrospinae   Ascaris suum   Laodelphax striatellus   Staphylococcus aureus subsp. aureus NN50   Xanthomonas retroflexus   Tubastraea coccinea   Eubacterium limosum   Ebolavirus   Sepiadarium austrinum   Arachis hypogaea var. vulgaris   Mycobacterium tuberculosis SP10   Vitis hybrid cultivar   Octopus vulgaris   Fusarium graminearum PH-1   Trichinella pseudospiralis   Macaca fascicularis   Daphnia magna   Amycolatopsis mediterranei S699   Nicotiana tabacum   Pseudomonas aeruginosa LESB58   Methylorubrum extorquens PA1   Acinetobacter baumannii 1656-2   Apis mellifera pomonella   Tremella   Escherichia coli str. K-12 substr. MG1655   Olavius algarvensis Delta 1 endosymbiont   Avicennia officinalis   Aeropyrum pernix   Macaca nemestrina   Nanger dama mhorr   Neptuniibacter caesariensis   Candida parapsilosis CDC317   soil bacterium TS1114R   Oenococcus oeni   Acanthamoeba polyphaga   Gadus morhua   Ceuthophilus sp. Ceu_104_TX_San_Rattlesnake   Acholeplasma laidlawii PG-8A   Caenorhabditis elegans   Aspergillus brasiliensis   Klebsiella pneumoniae BIDMC 40   Synechococcus elongatus PCC 7942 = FACHB-805   Cladocopium goreaui   Nostoc sp.   Taenia hydatigena   Listeria monocytogenes EGD   Phormidium sp. OSCR   Streptococcus mutans UA159   Secale cereale x Triticum turgidum subsp. durum   Aliivibrio fischeri   Dictyostelia   Zymoseptoria tritici IPO323   Aspergillus nidulans TN02A3   Salmo salar   Tuber aestivum   Cyberlindnera jadinii   Eucalyptus   Acaryochloris marina MBIC11017   Teleogryllus oceanicus   Dickeya dadantii subsp. dadantii   Olavius algarvensis sulfate-reducing endosymbiont   Yersinia pestis   Bivalvia   Aspergillus niger NRRL3   Plasmodium berghei   Sinopodophyllum hexandrum   metagenomes   Spodoptera frugiperda   Glycine max x Glycine soja   Passer domesticus domesticus   Filifactor alocis   Burkholderia cenocepacia K56-2Valvano   Plasmodium falciparum 3D7   Xanthomonas citri pv. glycines str. 8ra   Bacillus cereus AH187   Palaemonetes sp. common grass shrimp associated circular virus   Lentinus crinitus   Malassezia furfur   cf. Chlorella sp.   Heliocidaris erythrogramma   Rickettsia conorii str. Malish 7   Helicobacter pylori 26695   Candidatus Endoriftia persephone   Avena strigosa   Rhynchocyon petersi   Candidatus Pelagibacter ubique   Bacillus weihenstephanensis   Cryptosporidium andersoni   Myxobolus honghuensis   Salmo sp.   Cryptosporidium parvum   Candidatus Methylomirabilis oxyfera   Paenibacillus amylolyticus   Ictidomys tridecemlineatus   Halomonas sp.   Francisella tularensis subsp. tularensis   Callinectes sapidus   Tribolium castaneum   Malassezia pachydermatis   Dirofilaria immitis   Merluccius bilinearis   Roseburia inulinivorans DSM 16841   Saturnispora dispora   Clostridium saccharoperbutylacetonicum   Alteromonas macleodii ATCC 27126   Rhodnius prolixus   Staphylococcus aureus subsp. aureus NCTC 8325   Gorilla   Brassica napus   Cellulomonas gilvus ATCC 13127   Manduca sexta   Agkistrodon piscivorus   Bacillus licheniformis   Oleidesulfovibrio alaskensis G20   Coelodonta antiquitatis   Bothrops leucurus   Haemonchus contortus   Caldanaerobacter subterraneus subsp. tengcongensis MB4   human metagenome   Frankliniella sp. BIOUG14947-G11   Dictyostelium discoideum   Entamoeba histolytica HM-1:IMSS   Daktulosphaira vitifoliae   Lipomyces starkeyi   Brucella melitensis   Equus hydruntinus   Trypanosoma brucei brucei   Mustela putorius furo   Xanthomonas campestris pv. campestris str. B100   Ophrys sphegodes   Thermoplasma acidophilum DSM 1728   Candidatus Accumulibacter phosphatis   Alligator mississippiensis   Paulownia   Agrobacterium tumefaciens   Syntrophus aciditrophicus   Bacteria   Ustilago maydis   Prochlorococcus marinus subsp. marinus str. CCMP1375   Physcomitrella   Quercus suber   Olea europaea   Pongo abelii   Odontotaenius disjunctus   Helicoverpa armigera   Juglans regia   Rattus rattus   Drosophila pseudoobscura   Chaetodon lunulatus   Architeuthis dux   Saccharomyces cerevisiae W303   Colinus virginianus   Sulfolobus islandicus REY15A   Nothobranchius furzeri   Thalassiosira pseudonana CCMP1335   Bothrops insularis   Erysipelatoclostridium ramosum DSM 1402   Bombyx mori   Scheffersomyces stipitis   Mus musculus wagneri   Allochromatium vinosum DSM 180   Leishmania tarentolae   Onchocerca ochengi   Acanthamoeba polyphaga mimivirus   Fungi   unidentified   Gynandropsis gynandra   Fusarium oxysporum Fo47   Oryza australiensis   Chelodina longicollis   Capra hircus   Bothrops moojeni   Citrus hybrid cultivar   Halorubrum lacusprofundi ATCC 49239   Alcaligenes faecalis   Vibrio cholerae O1 biovar El Tor str. N16961   Tuber melanosporum Mel28   Macaca mulatta   Leishmania chagasi   Legionella pneumophila subsp. pneumophila str. Philadelphia 1   Gallus   environmental samples   Danio rerio   Rhipicephalus sanguineus complex sp. ME-2011   Influenza A virus (A/New Caledonia/20-JY2/1999(H1N1))   Thermodesulfobium acidiphilum   Nostoc sp. PCC 7120 = FACHB-418   Fibrobacter succinogenes subsp. succinogenes S85   Leishmania tropica   Plasmodium berghei ANKA   Daphnia   Thermosynechococcus vestitus BP-1   Marthasterias glacialis   Bordetella pertussis Tohama I   Granulicatella adiacens ATCC 49175   Bubalus bubalis   Pseudomonas pseudoalcaligenes CECT 5344   Phytophthora sojae   Lachancea waltii NCYC 2644   Litoricola marina   Rhizobium sp. CIAT652   Vigna mungo   Vibrio cholerae O1 str. VC91   Ursus americanus   Shigella dysenteriae   Listeria monocytogenes   Saccharum sp.   Aerococcus urinae NBRC 15544 = CCUG 36881   Nicotiana bonariensis   Trichoderma reesei QM6a   Mycobacterium tuberculosis variant bovis AN5   Pygoscelis adeliae   Loxodonta africana   Malassezia sympodialis   Pachycladon enysii   Acetivibrio thermocellus   unidentified marine bacterioplankton   Dactylorhiza   mouse gut metagenome   Burkholderia sp. 2332   Shigella sonnei 53G   Yersinia enterocolitica   Nakazawaea wickerhamii   Oryza sativa Indica Group   Oryctolagus cuniculus   Spongospora subterranea   Rheum palmatum   Giardia intestinalis assemblage A   Bovine leukemia virus   Synechococcus elongatus   Nelumbo nucifera subsp. nucifera   Aspergillus nidulans   Prevotella bryantii B14   Meleagris gallopavo   Persicaria minor   Planctopirus limnophila DSM 3776   Venturia pyrina   Crassostrea hongkongensis   Aspergillus wentii   Heterorhabditis megidis   Mycobacterium tuberculosis H37RvAE   Dendrobium huoshanense   Streptomyces sp. MC1   Plutella xylostella   Aspergillus sydowii   Frankia coriariae   Acinetobacter sp.   Pseudomonas fluorescens SBW25   Acanthoscurria geniculata   Saccharum hybrid cultivar x Sorghum bicolor   Ornithodoros erraticus   Pomacea canaliculata   Phytophthora infestans   Enterococcus faecium   Capsaspora owczarzaki   [Candida] glabrata CBS 138   Mammuthus primigenius   Myodes glareolus   Rhizorhabdus wittichii   Mycoplasma pneumoniae M129-B7   Leishmania donovani BPK282A1   Rapana venosa   Capsicum annuum var. annuum   Drosophila melanogaster   Acipenser transmontanus   Polypodium hydriforme   environmental samples   Mycobacterium tuberculosis H37Rv   Serpentes   Thermochaetoides thermophila DSM 1495   Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10   Kluyveromyces lactis NRRL Y-1140   Streptococcus uberis   environmental samples   Veillonella parvula DSM 2008   Rhizobium leguminosarum bv. viciae   Magnaporthe sp. MG05   Acanthoscurria gomesiana   Priestia megaterium DSM 319   Perkinsus marinus   Rosa chinensis   Chara australis   Glycine max   Panopea generosa   Halomonas sp. HL-48   Leishmania donovani   Hevea brasiliensis   Paracentrotus lividus   Anopheles gambiae str. PEST   Myxobolus wulii   Musa AAB Group   Echinococcus granulosus   Euterpe oleracea   Staphylococcus aureus subsp. aureus USA300_FPR3757   Fusarium sp.   Shewanella oneidensis MR-1   Calicophoron daubneyi   Angiostrongylus vasorum   Rhizopus delemar   Blastococcus saxobsidens   Puccinellia tenuiflora   Culex pipiens pipiens   Coxsackievirus B3   Bothrops jararacussu   Capreolus capreolus   Crocosphaera subtropica ATCC 51142   Globicatella sanguinis   Caprinae   prokaryotic environmental samples   Dendroaspis angusticeps   Prevotella intermedia ATCC 25611 = DSM 20706   Amaranthus tricolor   Afipia carboxidovorans   Mycoplasma pneumoniae 19294   Marchantia polymorpha subsp. ruderalis   Rickettsia massiliae MTU5   Castor canadensis   Helicobacter pylori E48   Novosphingobium nitrogenifigens   Bartonella quintana   Doryteuthis pealeii   Plasmodium falciparum 58.1   Candidatus Kuenenia stuttgartiensis   Dehalococcoides mccartyi CG1   Ectocarpus siliculosus   Cupriavidus pinatubonensis JMP134   Klebsiella variicola   Chlamydomonas reinhardtii CC3269   Corynebacterium glutamicum K051   Bos indicus   Austrolebias   Metopolophium dirhodum   human gut metagenome   soil bacterium 10G-05   Thermococcus gammatolerans   Lacticaseibacillus rhamnosus GG   Carica papaya   Lactobacillus iners   Beauveria bassiana   Haloferax volcanii DS2   Acanthochromis polyacanthus   Human coronavirus HKU1   Citrus maxima   Macaca fascicularis fascicularis   Vespula vulgaris   Clostridium butyricum DSM 10702   Fomitopsis pinicola   Amycolatopsis   Enterobacter cloacae   Acetomicrobium mobile   Ianthella basta   Thermothelomyces heterothallicus   Bacteroides caccae   Pogonomyrmex rugosus   Sulfolobus islandicus   Elaeis guineensis   Rhizobium cf. leguminosarum   Synechococcus sp. YX04-3   Nicotiana langsdorffii   Megaloceros giganteus   Nephotettix cincticeps   unclassified Thermococcus   Triticum aestivum   Stylophora pistillata   Ictidomys tridecemlineatus arenicola   uncultured microorganism   Streptococcus pneumoniae SP14-BS69   Aspergillus fumigatus CEA10   Nephila clavipes   Dimocarpus longan   Rhodobacter capsulatus SB 1003   Citrobacter rodentium   Luteibacter   Nannochloropsis oceanica strain IMET1   Siphoviridae   Acidithiobacillus ferrooxidans ATCC 53993   Cyclotella cryptica   Mycobacterium tuberculosis variant bovis str. Ravenel   Viridiplantae   Methanohalophilus   Alteromonadales   Glycine soja   Amblyomma cajennense   Populus tremula x Populus alba   Mycoplasma hominis ATCC 23114   Mytilus galloprovincialis   Papaver somniferum   Neosciurus carolinensis   Trypanosoma brucei   Simulium damnosum s.l. Me1   Ipomoea batatas   Olavius algarvensis Gamma 3 endosymbiont   Mycobacterium tuberculosis C StG4006   Schistosoma haematobium   Strongyloides venezuelensis   Willaertia magna   Actinidia chinensis var. chinensis   Anser cygnoides   Buddenbrockia plumatellae   Brachyspiraceae   Methanothermobacter thermautotrophicus   Helianthus tuberosus   Alicycliphilus denitrificans BC   Bacillus cereus ATCC 10987   Desulforapulum autotrophicum HRM2   Acinetobacter baumannii AB307-0294   Candida albicans SC5314   Tetraponera aethiops   Tropilaelaps mercedesae   Amphora coffeiformis   Mycolicibacterium smegmatis   Aves   Chlamydia trachomatis   Leptopilina   Mengo virus   Cupriavidus necator N-1   Mammut americanum   Pseudomonas fluorescens   Tachaea chinensis   Human alphaherpesvirus 1   Roseburia   Trichomonas gallinae   Cairina moschata   Trifolium pratense subsp. pratense   uncultured marine microorganism   Rhinocerotidae   Treponema   Thermus thermophilus HB8   Bacillus mycoides DSM 2048   Aeropyrum pernix K1   Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2   Ornithodoros moubata   uncultured soil microorganism   Sparus aurata   Haemophilus haemolyticus   Staphylococcus aureus subsp. aureus COL   Octopodiformes   Nicotiana africana   Haemophilus influenzae Rd KW20   Quercus   Streptomyces lividans TK24   Pseudomonas taiwanensis   Morganella   Methanospirillum hungatei JF-1   Fusarium oxysporum f. sp. lycopersici   Microcystis aeruginosa NIES-843   Ovis   Aspergillus oryzae var. oryzae   Brassica oleracea var. botrytis   Mesocricetus auratus   Streptomyces sp. MBT42   Malassezia globosa   Glossina morsitans   Myzus persicae   Porphyromonas gingivalis ATCC 33277   Acesta excavata   Streptococcus pyogenes M1 GAS   Syntrophobacter fumaroxidans MPOB   Chlorocebus sabaeus   Deinococcus radiodurans R1   Macadamia   Clostridioides difficile   Bordetella parapertussis   Oryza sativa Japonica Group   Nicotiana alata   Apteronotus leptorhynchus   Emiliania   Cricetulus griseus   Streptococcus pyogenes MGAS5005   Pisum sativum   Coprococcus sp. ART55/1   Trichoderma sp. 1 YW-2011   Saccharomyces cerevisiae EC1118   Marchantia polymorpha   Plasmodium vivax   Medicago truncatula   Piscirickettsia salmonis AUSTRAL-005   Mycobacterium tuberculosis TKK-01-0032   Dinoroseobacter shibae DFL 12 = DSM 16493   Trichechus manatus   Mycobacterium tuberculosis M24   Staphylococcus xylosus   Castor   Tetrastichus   Acromyrmex echinatior   Strawberry leafy fruit phytoplasma   synthetic construct   Momordica cochinchinensis   Arbacia punctulata   Amblyrhynchus cristatus   Cervus elaphus elaphus   Acinetobacter sp. PM-14   Plasmodium knowlesi strain H   Xanthomonas campestris   Desulforamulus reducens MI-1   Mus musculus musculus x Mus musculus castaneus   Phytophthora capsici   Pyrococcus abyssi   Klebsiella pneumoniae MGH 78578   Drosophila mauritiana   Ganoderma lingzhi   Faecalibacterium prausnitzii SL3/3   Peterozyma xylosa   Malassezia sympodialis ATCC 42132   Chlorobaculum tepidum   Polaribacter marinivivus   Pseudomonas aeruginosa PAO1   Dentex dentex   Halomonas sp. TD01   Haloferax volcanii   Francisella orientalis FNO12   Escherichia coli   Toxoplasma gondii RH   Aspergillus fumigatus Af293   Vicia faba   Streptococcus thermophilus   Rickettsia rickettsii   Beta vulgaris   Escherichia phage vB_EcoP_SU10   Knufia petricola   Chlamydia trachomatis D/UW-3/CX   Crotalus horridus   Bacillus mycoides NBRC 101238 = DSM 11821   Photobacterium profundum SS9   Moorella thermoacetica ATCC 39073   Faustovirus   Cryptochiton stelleri   Mycoplasma pneumoniae M29   Asterias rubens   rhizosphere soil bacteria ensemble   Pseudomonas composti   Stephanorhinus   Synechococcus phage S-SSM7   Candidatus Glomeribacter   Syntrophomonas wolfei   Burkholderia ubonensis MSMB22   Glia   Emiliania huxleyi   Agaricus bisporus   Plasmodium falciparum FcB1/Columbia   Ostreococcus tauri   Geobacter sulfurreducens PCA   Equus asinus africanus   Mycolicibacterium smegmatis MC2 155   Leptospirillum   Burkholderia cenocepacia   Orthopoxvirus   Oryctolagus sp. 'Rabbit_OD'   Escherichia coli str. K-12 substr. W3110   Hyalella azteca   Medicago sativa   Triatoma sordida   Klebsiella pneumoniae ATCC BAA-2146   Oryctolagus cuniculus cuniculus   Synechocystis sp. PCC 6803 substr. GT-I   Micrococcus luteus   Salmonella enterica subsp. enterica serovar Typhimurium str. SDT1291   Gnathostoma spinigerum   Eimeria acervulina   Liquorilactobacillus nagelii   artificial sequences   Cyclopes didactylus   Sophora alopecuroides   Dengue virus   Staphylococcus haemolyticus   Leuconostoc gelidum subsp. gasicomitatum   Streptococcus pneumoniae   Giardia intestinalis   Ruminiclostridium cellulolyticum H10   Geobacillus kaustophilus HTA426   Giardia sp.   Haliotis discus hannai   Bos taurus   Theobroma cacao   Loxosceles intermedia   Halobacterium salinarum   Aggregatibacter actinomycetemcomitans   Listeria monocytogenes HCC23   Linnemannia elongata AG-77   Volvariella volvacea V23   Serpentes sp. WLS21042014   Coffea canephora   Lobaria pulmonaria   Aspergillus   Cereibacter sphaeroides 2.4.1   Plasmodium yoelii yoelii   Pachysolen tannophilus   Mycobacterium tuberculosis SP13   Myxococcus xanthus DZ2   Camelus dromedarius   Gasterosteus aculeatus   Coxiella burnetii   Aspergillus fumigatus   Haberlea rhodopensis   Piper nigrum   Candidatus Thioglobus autotrophicus   Sus scrofa domesticus   Gorilla gorilla gorilla   Paenibacillus sp.   Enterococcus faecalis   Aspergillus versicolor   Panthera leo   Colpophyllia natans   Tilletia controversa   Diplazium maximum   Eucalyptus spp. mixed library   Tepidanaerobacter acetatoxydans   Staphylococcus aureus subsp. aureus str. Newman   Toxoplasma gondii GAB3-2007-GAL-DOM9   Bacteroides thetaiotaomicron VPI-5482   Helianthus annuus   mixed sample   Jatropha curcas   Aedes aegypti densovirus   Borreliella burgdorferi B31   Liberibacter endosymbiont of Diaphorina citri   Stappia stellulata DSM 5886   Cucumber mosaic virus   Plasmodium falciparum   Desmodesmus subspicatus   Gulo gulo   unidentified chimeric sequence   Clostridium phage c-st   Rickettsia akari   Aggregatibacter actinomycetemcomitans D7S-1   Lactobacillus   Leishmania braziliensis   Bordetella pertussis   Bienertia sinuspersici   Leishmania mexicana   Sarcophilus harrisii   Oncorhynchus mykiss   Mycobacterium tuberculosis H37Rv_2009   Spiroplasma melliferum   Picea likiangensis var. rubescens   Paracoccidioides lutzii Pb01   Rhizobium leguminosarum bv. phaseoli CCGM1   Peniophora incarnata   Hordeum vulgare   Staphylococcus sp. KDM4   Bifidobacterium kashiwanohense PV20-2   Mycobacterium tuberculosis SP1   Gardnerella vaginalis   Fraxinus mandshurica   Ensifer adhaerens   Nicotiana noctiflora   Ophrys x arachnitiformis subsp. archipelagi   Anacardium occidentale   Andrias davidianus   Corynebacterium glutamicum ATCC 13032   Euglena gracilis   Aspergillus giganteus   Ictalurus punctatus   Nicotiana quadrivalvis   Conus betulinus   Acyrthosiphon pisum   Arabidopsis thaliana   Dolichospermum circinale AWQC131C   Mycobacterium tuberculosis variant bovis   Enchytraeus crypticus   sediment metagenome   Phaseolus vulgaris   Frankia alni ACN14a   Coprothermobacter proteolyticus   Mycobacterium marinum ATCC BAA-535   Acinetobacter baumannii ACICU   Cricetulus barabensis   Cucumis sativus   Corynebacterium diphtheriae   Candidatus Nitrospira inopinata   Daphnia pulex   Serratia phage JS26   Conus caracteristicus   Ustilaginoidea virens   marine plankton environmental sample   Diaphorina citri   Labeo rohita   [Candida] boidinii   Castor fiber   Pseudomonas ogarae   Strigomonas culicis   Shigella flexneri 2a str. 2457T   Influenza A virus (A/Viet Nam/1203/2004(H5N1))   HIV-1 M:G_PT919   Rhodospirillum rubrum ATCC 11170   Lactococcus lactis   Porphyromonas gingivalis   Bursaphelenchus xylophilus   Saccharina japonica   Beta vulgaris subsp. vulgaris   Ustilago maydis virus P4   Naegleria fowleri   Bacillus altitudinis   Thermococcus kodakarensis KOD1   Escherichia coli O157:NM   Fusobacterium nucleatum subsp. nucleatum ATCC 25586   Solanum lycopersicum   Tetrahymena thermophila   Helicobacter pylori A45   Clostridium cellulovorans 743B   Coxiella-like endosymbiont of Rhipicephalus sanguineus complex   Bacteria incertae sedis   Escherichia coli K-12   Pseudoalteromonas flavipulchra NCIMB 2033 = ATCC BAA-314   Hippoglossus hippoglossus   Norovirus   Nicotiana gossei   Bodo saltans   Populus tremula   Salmonella enterica subsp. enterica serovar Typhimurium str. 5579   Synechococcus phage syn9   Sturnus vulgaris   Zalophus californianus   Tetrahymena thermophila SB210   Strongylocentrotus purpuratus   Musa   Buchnera aphidicola (Acyrthosiphon pisum)   Naja oxiana   Lingula anatina   Lactococcus lactis subsp. lactis Il1403   Bacillus sp. 142311   Bartonella quintana JK 31   Panine betaherpesvirus 2   Acanthamoeba castellanii   Galloanserae   Cutibacterium acnes SK137   Bemisia tabaci   Sphingobium chlorophenolicum   Vulpes lagopus   Cupriavidus metallidurans   Limosilactobacillus mucosae LM1   Pyrococcus furiosus   Gammarus roeselii   Quercus robur   Wolbachia endosymbiont of Onchocerca volvulus str. Cameroon   Pseudomonas syringae   Camponotus floridanus   Butyrivibrio fibrisolvens   Anguilla anguilla   Noccaea caerulescens   Chaetoceros sp.   Dioscorea alata   Acinetobacter baumannii ATCC 17978   Human alphaherpesvirus 1 strain 17   Pachycladon exile   Butyrivibrio proteoclasticus B316   Cenchrus americanus   Gossypium   Pseudomonas aeruginosa PAO1H2O   Fusarium oxysporum f. sp. cucumerinum   Legionella   Hendra virus horse/Australia/Hendra/1994   Quercus petraea   Tepidimicrobium xylanilyticum   Tyrannosaurus rex   Staphylococcus pseudintermedius   Plasmodium vivax Sal-1   Passer hispaniolensis   Microbiota   Micrurus tener   Mycobacterium tuberculosis SP22   Equisetum arvense   Lachancea kluyveri   Schistosoma japonicum   Pogona vitticeps   Toxoplasma gondii ME49   Sinorhizobium americanum CCGM7   Amphimedon   Palaemon carinicauda   Sus scrofa   Opsanus beta   Clavibacter michiganensis subsp. nebraskensis NCPPB 2581   Crithidia fasciculata   Anaerococcus hydrogenalis DSM 7454   Gossypium hirsutum   Breviatea   Lysiphlebus fabarum   Serratia inhibens PRI-2C   Pseudomonas aeruginosa   Oomycota   Sterolibacterium denitrificans   Staphylococcus cohnii   Leishmania mexicana MHOM/GT/2001/U1103   Myotis ricketti   Sphingomonas sp. Leaf257   Lymnaea stagnalis   Streptomyces avidinii   Cassiopea xamachana   Melioribacter roseus P3M-2   Pachysolen tannophilus NRRL Y-2460   Pomacea maculata   Ailuropoda melanoleuca   Lentinula edodes   Brachionus plicatilis   Saccharolobus solfataricus   Pyricularia oryzae B157   Lactobacillus crispatus   Venturia inaequalis   Ovis aries musimon   Nostoc punctiforme PCC 73102   Nicotiana glauca   Kuraishia capsulata   Brenneria nigrifluens   Bicyclus anynana   Dinosauria   Sistrurus miliarius barbouri   Candidatus Profftella armatura   Solanum tuberosum   Flavobacterium columnare   Brassica rapa   Methylorubrum extorquens DM4   Caulobacter vibrioides NA1000   Hypsizygus marmoreus   uncultured bacterium   Conus zonatus   Salmonella enterica subsp. enterica serovar Enteritidis str. P125109   Equus sp.   Influenza A virus (H1N1)   Methylocystis sp. SC2   Pseudomonas putida BIRD-1   Streptococcus pneumoniae R6   Nicotiana rustica   Streptomyces coelicolor A3(2)   Olavius algarvensis   West Nile virus   Francisella tularensis subsp. novicida U112   Bacillus amyloliquefaciens DSM 7 = ATCC 23350   Sinorhizobium americanum   Dreissena polymorpha   Actinoplanes sp. SE50/110   Nematostella vectensis   Brassica carinata   Capra ibex   Streptomyces coelicolor   Trypanosoma vivax Y486   Taenia solium   Pedobacter sp.   environmental samples   Lineus longissimus   Acinetobacter baumannii AB5075   Fusarium graminearum GZ3639   Beauveria bassiana CGMCC 7.34   Trypanosoma   Ctenopharyngodon idella   Eimeria tenella   Streptomyces venezuelae   unclassified Marseilleviridae   Bacteroides fragilis 638R   Hepatitis C virus genotype 1   Oreochromis mossambicus   Pasteurella multocida subsp. multocida str. Pm70   Arvicola   Chryseobacterium indologenes   Coffea eugenioides   Sitobion avenae   Agkistrodon contortrix   Musa acuminata AAA Group   Stylosanthes guianensis   Paramecium tetraurelia   Mycobacterium tuberculosis   Mycobacteroides abscessus ATCC 19977   Influenza A virus (A/Wilson-Smith/1933(H1N1))   Candidatus Midichloriaceae   Aspergillus aculeatus ATCC 16872   Listeria phage A118   Dichomitus squalens   Apostichopus japonicus   Severe acute respiratory syndrome coronavirus 2   Phytophthora capsici LT1534   Quercus ilex   Exiguobacterium sp. SH31   Argulus foliaceus   Rhizophagus irregularis   Thermothelomyces thermophilus ATCC 42464   Struthio camelus   Anopheles culicifacies B   Cecropia peltata   Synechococcus cyanophage syn   Japanese encephalitis virus   Spiroplasma melliferum KC3   Erysipelothrix rhusiopathiae   Sorghum bicolor   Crunoecia irrorata   Acinetobacter baumannii   Candidatus Paraburkholderia kirkii   Zygaena filipendulae   Litoditis marina   hybrid   Apis mellifera ligustica   Oryzias latipes   Lentimonas   Ursus deningeri   Vibrio anguillarum   Malus domestica   Fusarium cf. oxysporum   Lotus japonicus   Ixodes scapularis   Tuber magnatum   Candida tropicalis   Murine leukemia virus isolates   Tenebrio molitor   Bothrops asper   Breviolum minutum   Antidorcas marsupialis   Tequatrovirus T4   Clostridium perfringens   Larimichthys crocea   Paracoccidioides brasiliensis Pb18   phytoplankton environmental sample   Populus yunnanensis   Lacticaseibacillus rhamnosus   Fagus grandifolia   Corynebacterium glutamicum   albimanus section   Vitis labrusca x Vitis riparia   Frankia alni   Sedum plumbizincicola   Synechococcus sp. PCC 7002   Fusarium graminearum   Schizophyllum commune H4-8   uncultured Desulfobacterium sp.   Salmonella enterica subsp. enterica serovar Cerro   Nicotiana benavidesii   Heligmosomoides polygyrus bakeri   Shigella flexneri   Carnobacterium maltaromaticum   Tremarctos ornatus   Oryza longistaminata   Olavius algarvensis Delta 4 endosymbiont   Eucalyptus globulus   glacier metagenome   Mucilaginibacter   Bacillus subtilis subsp. subtilis str. 168   Plum pox virus   Trypanosoma cruzi cruzi   Pectobacterium carotovorum   Streptococcus suis SC84   Nilaparvata lugens   Sulfuritalea   Equus caballus   Drosophila simulans   rat gut metagenome   Helicobacter pylori H13-1   Cicer arietinum   Ralstonia solanacearum GMI1000   Myzus persicae persicae   Aeromonas salmonicida subsp. salmonicida   Cervus elaphus   Desulfofundulus kuznetsovii DSM 6115   Botrytis cinerea T4   Dunaliella salina   Oscillatoriaceae cyanobacterium   Cervus nippon nippon   Pyricularia oryzae P131   Xenopus laevis   Bothrops brazili   Trypanosoma cruzi   Cyanobacterium stanieri   Qipengyuania flava   Mammuthus sp.   Parasteatoda tepidariorum   Meandrina meandrites   Clostridioides difficile str. A-027   Streptococcus pyogenes ABC020006030   Synechocystis sp. PCC 6803 substr. Kazusa   Brucella abortus 104M   Aedes aegypti   Riftia pachyptila   Cancer   Liquorilactobacillus hordei   Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940   Trichodesmium erythraeum IMS101   Nicotiana sylvestris   Brachylophosaurus canadensis   Trichinella britovi   Saccharum hybrid cultivar   Pseudoalteromonas sp. D41   Chlamydia trachomatis 434/Bu   Orycteropus afer   Potentilla saundersiana   Yersinia pseudotuberculosis   Bactrocera dorsalis   Chlorocebus aethiops aethiops   Influenza A virus (A/California/07/2009(H1N1))   Paenibacillus polymyxa ATCC 842   Onchocerca lupi   Blautia producta ATCC 27340 = DSM 2950   Bacillus pseudomycoides DSM 12442   Wheat dwarf virus - [Taiyuan]   Pseudomonas putida KT2440   Pinus pinaster   Pseudomonas sp.   Catalpa fargesii   Malaclemys terrapin   Candidatus Carsonella ruddii DC   Methanosarcina mazei Go1   Cercopithecidae   Mylodon darwinii   Francisella tularensis subsp. holarctica LVS   Dugesia japonica   Tannerella forsythia 92A2   Morganella   Bothrops cotiara   Meles meles   Nicotiana maritima   Selenomonas sputigena ATCC 35185   Angiostrongylus cantonensis   Cellulophaga baltica NN016038   marine metagenome   bioreactor sludge metagenome   Syntrophus aciditrophicus SB   Mycobacteroides abscessus   Arion vulgaris   Thalassiosira pseudonana   Mahonia   [Ruminococcus] gnavus ATCC 29149   Parhyale hawaiensis   Camponotus fellah   Didelphis aurita   Acidipropionibacterium acidipropionici   Tetratrichomonas gallinarum   Euprymna scolopes   Ambrosiozyma philentoma   Trichomonas vaginalis   Rhodothermus marinus DSM 4252   Sulfurihydrogenibium   Panicum virgatum   Giardia lamblia ATCC 50803   Clostridium cellulovorans   Natronomonas pharaonis DSM 2160   Passiflora edulis   Aspergillus flavus partitivirus 1   Agrobacterium fabrum str. C58   Methanoculleus sp. 10   Mus musculus   Streptococcus mutans 19   Trypanosoma cruzi strain Esmeraldo   Latrodectus hesperus   Colobus guereza   Ricinus communis   Micrurus fulvius   Candida parapsilosis   Eryx colubrinus loveridgei   Halobacterium   Vibrio harveyi   Millerozyma acaciae   Tetronarce californica   Orbicella annularis   Hippophae rhamnoides   Citeromyces matritensis   Leishmania donovani Ld 2001   Petunia x hybrida   Conus geographus   Canis lupus familiaris   Trichoderma reesei RUT C-30   Escherichia coli BL21(DE3)   Wolbachia sp. wMelPop   Bothrops neuwiedi   Phascolarctos cinereus   Broussonetia papyrifera   Scutigera coleoptrata   Cryptococcus neoformans var. grubii H99   Pinus taeda   Bradyrhizobium   Human herpesvirus 4 type 1   Osphranter rufus   Pan troglodytes   Diplonema papillatum   Lecanicillium fungicola var. fungicola   Eremothecium gossypii   Francisella tularensis   Penicilliopsis zonata   Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088   Klebsiella pneumoniae ATCC 43816   Lithobius forficatus   Pteropus alecto   Aspergillus nidulans FGSC A4   Python molurus   Panthera tigris   Rupicapra pyrenaica   Sorangium cellulosum So ce56   Bacillus subtilis subsp. subtilis   Babjeviella inositovora   Candidatus Margulisbacteria   Cleome angustifolia   Eriocheir sinensis   [Candida] auris   Staphylococcus aureus subsp. aureus USA300_TCH1516   Mycobacterium tuberculosis CAS   Leishmania braziliensis MHOM/BR/75/M2904   Schizosaccharomyces pombe   Hydrolagus colliei   Cytomegalovirus   Francisella tularensis subsp. holarctica   Mycoplasma pneumoniae   Neoporphyra haitanensis   Lens culinaris   Epichloe festucae E2368   Nicotiana glutinosa   Moneuplotes crassus   Paenibacillus pabuli   Pyricularia oryzae   Aedes albopictus   Solanum lycopersicum x Solanum tuberosum   Strigamia maritima   Durusdinium trenchii   Aspergillus niger   Escherichia coli Nissle 1917   Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499   Capsicum annuum   Mytilus sp. CHGF4   Saccharomyces cerevisiae S288C   Stenotrophomonas maltophilia   Pandanus amaryllifolius   Porphyromonas gingivalis W83   Tradescantia spathacea   Avena sativa   Populus tomentosa   Coprothermobacter   Brassica oleracea   Capra pyrenaica   Populus cathayana   Burkholderia pseudomallei 1026b   Meyerozyma guilliermondii   Synechocystis sp.   Gossypium robinsonii   Dichocoenia stokesii   Orbicella faveolata   Streptococcus pneumoniae D39   Bradyrhizobium diazoefficiens   Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819   Naja naja   Colon   Candida albicans   Pseudo-nitzschia delicatissima   Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044   Deinococcus deserti VCD115   Cervus nippon hortulorum   Bacillus subtilis   Chenopodium quinoa   Euzebya tangerina   Phytophthora pisi   Kluyveromyces marxianus   Acinetobacter baumannii D1279779   Trichoplax sp. H2   Flavivirus   Thalassiosira cf. oceanica   Medicago truncatula var. truncatula   Caretta caretta x Chelonia mydas   Trichoderma reesei QM9414   Rhizobium favelukesii   Channa striata   Caryophyllales   Prochlorococcus marinus subsp. pastoris str. CCMP1986   Cuniculiplasma divulgatum   Corynebacterium diphtheriae bv. mitis str. ISS 3319   Brassica oleracea var. italica   Pseudomonas putida F1   Human papillomavirus type 16   Salmonella enterica subsp. enterica serovar Typhimurium str. LT2   Mus   Pongo pygmaeus   Dolichospermum circinale AWQC310F   fungal sp. 5OL6-6PL1   Telmatactis   Nerodia clarkii   Stigmatella aurantiaca DW4/3-1   Nicotiana x sanderae   Caballeronia mineralivorans   Deinococcus radiodurans   Haemophilus influenzae   Deltaproteobacteria bacterium RIFCSPLOWO2_12_FULL_50_11   Dionaea muscipula   Podospora   Vitis riparia   Neospora caninum Liverpool   Clavibacter michiganensis subsp. michiganensis NCPPB 382   Equus asinus   Saccharum hybrid cultivar SP80-3280   Ursus arctos   Influenza A virus   Dehalobacter restrictus   uncultured Clostridium sp.   Mytilus edulis/galloprovincialis MCLGV-2007   Polytomella parva   Pteropus rodricensis   Pachycladon fastigiatum   Beauveria bassiana ARSEF 2860   Lynx lynx   Campylobacter fetus subsp. fetus 82-40   Trametes versicolor   Streptococcus pyogenes   Rhodotorula toruloides   Coccinia grandis   Allexis   Leishmania guyanensis species complex   Bifidobacterium pseudolongum   Galleria mellonella   Nicotiana plumbaginifolia   Bradyrhizobium diazoefficiens USDA 110   Cloning vector pEGFP-C1   Vulpes vulpes   Coffea arabica   Minona ileanae   Pseudomonas sp. Lz4W   Bifidobacterium bifidum ATCC 29521 = JCM 1255 = DSM 20456   Nostoc flagelliforme   Rickettsia conorii subsp. raoultii   Dehalococcoides mccartyi CBDB1   Cupiennius salei   mixed culture metagenome   Candidatus Accumulibacter   Phlebotomus papatasi   Homo   Mycoplasma gallisepticum  

SUBMITTER: Gene Hart-Smith  

LAB HEAD: Gene Hart-Smith

PROVIDER: PXD019513 | Pride | 2020-08-24

REPOSITORIES: Pride

Dataset's files

Source:
Action DRS
Oxidation (M)Sites.txt Txt
Phospho (STY)Sites.txt Txt
SECPCP_zymo_lysate_1.raw Raw
SECPCP_zymo_lysate_10.raw Raw
SECPCP_zymo_lysate_11.raw Raw
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Publications

Analytical Guidelines for co-fractionation Mass Spectrometry Obtained through Global Profiling of Gold Standard <i>Saccharomyces cerevisiae</i> Protein Complexes.

Pang Chi Nam Ignatius CNI   Ballouz Sara S   Weissberger Daniel D   Thibaut Loïc M LM   Hamey Joshua J JJ   Gillis Jesse J   Wilkins Marc R MR   Hart-Smith Gene G  

Molecular & cellular proteomics : MCP 20200818 11


Co-fractionation MS (CF-MS) is a technique with potential to characterize endogenous and unmanipulated protein complexes on an unprecedented scale. However this potential has been offset by a lack of guidelines for best-practice CF-MS data collection and analysis. To obtain such guidelines, this study thoroughly evaluates novel and published <i>Saccharomyces cerevisiae</i> CF-MS data sets using very high proteome coverage libraries of yeast gold standard complexes. A new method for identifying g  ...[more]

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