Wu Enhui, Qiao Liang*
Lefapha la Khemistri, Univesithi ea Fudan, Shanghai 200433, Chaena
Likokoana-hloko li amana haufi-ufi le mafu a batho le bophelo bo botle. Mokhoa oa ho utloisisa sebopeho sa lichaba tsa likokoana-hloko le mesebetsi ea tsona ke taba e kholo e lokelang ho ithutoa ka potlako. Lilemong tsa morao tjena, metaproteomics e fetohile mokhoa oa bohlokoa oa tekheniki oa ho ithuta sebopeho le tšebetso ea likokoana-hloko. Leha ho le joalo, ka lebaka la ho rarahana le ho fapana ho phahameng ha lisampole tsa sechaba sa likokoana-hloko, ts'ebetso ea sampole, ho fumanoa ha data ea mass spectrometry le tlhahlobo ea data li fetohile liqholotso tse tharo tse kholo tseo hona joale metaproteomics li tobaneng le tsona. Tlhahlobong ea metaproteomics, hangata hoa hlokahala ho ntlafatsa kalafo ea pele ea mefuta e fapaneng ea lisampole le ho amohela karohano ea likokoana-hloko tse fapaneng, merero ea ho ntlafatsa, ho hula le lysis. Ho tšoana le proteome ea mofuta o le mong, mekhoa ea ho fumana data ea mass spectrometry ho metaproteomics e kenyelletsa mokhoa oa ho fumana data-dependent (DDA) le mokhoa oa ho fumana data-independent (DIA). Mokhoa oa ho fumana data oa DIA o ka bokella ka botlalo tlhaiso-leseling ea peptide ea sampole mme e na le menyetla e meholo ea nts'etsopele. Leha ho le joalo, ka lebaka la ho rarahana ha lisampole tsa metaproteome, tlhahlobo ea data ea DIA e fetohile bothata bo boholo bo sitisang ho koaheloa ho tebileng ha metaproteomics. Mabapi le tlhahlobo ea data, mohato oa bohlokoa ka ho fetisisa ke kaho ea polokelo ea tatellano ea protheine. Boholo le botlalo ba database ha bo na phello e kholo feela palo ea boitsebahatso, empa hape bo ama tlhahlobo ea mefuta le maemo a ts'ebetso. Hajoale, maemo a khauta a kaho ea polokelo ea metaproteome ke polokelo ea tatellano ea protheine e thehiloeng ho metagenome. Ka nako e ts'oanang, mokhoa oa ho sefa oa polokelong ea litaba oa sechaba o ipapisitseng le patlisiso e pheta-phetoang le ona o netefalitsoe hore o na le boleng bo matla bo sebetsang. Ho latela pono ea maano a ikhethileng a tlhahlobo ea data, mekhoa ea tlhahlobo ea data ea DIA e shebaneng le peptide e nkile karolo e kholo ka ho fetesisa. Ka nts'etsopele ea thuto e tebileng le bohlale ba maiketsetso, e tla khothaletsa haholo ho nepahala, ho koaheloa le lebelo la tlhahlobo ea tlhahlobo ea data ea macroproteomic. Mabapi le tlhahlobo ea bioinformatics e tlase, letoto la lisebelisoa tsa litlhaloso li entsoe lilemong tsa morao tjena, tse ka etsang tlhaloso ea mefuta maemong a protheine, boemo ba peptide le liphatsa tsa lefutso ho fumana sebopeho sa lichaba tsa likokoana-hloko. Ha ho bapisoa le mekhoa e meng ea omics, tlhahlobo ea ts'ebetso ea lichaba tsa likokoana-hloko ke tšobotsi e ikhethang ea macroproteomics. Macroproteomics e fetohile karolo ea bohlokoa ea tlhahlobo ea li-multi-omics tsa lichaba tsa likokoana-hloko, 'me e ntse e e-na le matla a maholo a nts'etsopele ho latela botebo ba ho fana ka boitsebiso, kutloisiso ea ho lemoha, le ho phethahala ha tlhahlobo ea data.
01Mohlala oa kalafo ea pele
Hajoale, theknoloji ea metaproteomics e sebelisitsoe haholo lipatlisisong tsa microbiome ea motho, mobu, lijo, leoatle, seretse se sebetsang le masimo a mang. Ha ho bapisoa le tlhahlobo ea proteome ea mofuta o le mong, mohlala oa phekolo ea pele ea metaproteome ea lisampole tse rarahaneng o tobana le mathata a mangata. Sebopeho sa likokoana-hloko ka lisampole tsa sebele se rarahane, mefuta e mengata e matla ea bongata e kholo, sebopeho sa lerako la lisele tsa mefuta e sa tšoaneng ea likokoana-hloko li fapane haholo, 'me hangata lisampole li na le palo e kholo ea liprotheine tse amohelehang le litšila tse ling. Ka hona, tlhahlobong ea metaproteome, hangata hoa hlokahala ho ntlafatsa mefuta e fapaneng ea lisampole le ho amohela karohano e fapaneng ea likokoana-hloko, merero ea ho ruisa, ea ho hula le ea lysis.
Ho ntšoa ha metaproteome ea likokoana-hloko ho tsoa lisampoleng tse fapaneng ho na le ho tšoana ho itseng hammoho le liphapang tse itseng, empa hajoale ho na le khaello ea ts'ebetso e kopaneng ea pele ho ts'ebetso ea mefuta e fapaneng ea lisampole tsa metaproteome.
02 Khokahano ea data ea spectrometry ka bongata
Ha ho hlahlojoa lithunya tsa proteome, motsoako oa peptide ka mor'a ho phekoloa pele o qala ho aroloa ka har'a kholomo ea chromatographic, ebe o kena ho spectrometer ea boima bakeng sa ho fumana data ka mor'a ionization. Ho tšoana le tlhahlobo ea proteome ea mofuta o le mong, mekhoa ea ho fumana data ea mass spectrometry tlhahlobo ea macroproteome e kenyelletsa mokhoa oa DDA le mokhoa oa DIA.
Ka ho pheta-pheta le ho ntlafatsa lisebelisoa tsa "mass spectrometry", lisebelisoa tsa "mass spectrometry" tse nang le kutloisiso e phahameng le tharollo li sebelisoa ho metaproteome, 'me botebo ba tšireletso ea metaproteome le bona bo tsoela pele ho ntlafatsoa. Ka nako e telele, letoto la lisebelisoa tsa "high-resolution mass spectrometry" tse etelletsoeng pele ke Orbitrap li 'nile tsa sebelisoa haholo metaproteome.
Letlapa la 1 la sengoloa sa mantlha le bonts'a lithuto tse ling tse emelang metaproteomics ho tloha 2011 ho fihlela hajoale ho latela mofuta oa sampole, leano la tlhahlobo, sesebelisoa sa spectrometry, mokhoa oa ho fumana, software ea tlhahlobo, le palo ea boitsebahatso.
03 Tlhahlobo ea lintlha tsa spectrometry ea boima
3.1 Leano la ho hlahloba lintlha tsa DDA
3.1.1 Patlisiso ea Database
3.1.2de novoleano la tatellano
3.2 Leano la ho hlahloba lintlha tsa DIA
04Sehlopha sa mefuta le tlhaloso ea ts'ebetso
Sebopeho sa lichaba tsa likokoana-hloko maemong a fapaneng a taxonomic ke se seng sa libaka tsa bohlokoa tsa lipatlisiso lipatlisisong tsa microbiome. Lilemong tsa morao tjena, ho entsoe letoto la lisebelisoa tsa litlhaloso ho hlakisa mefuta e maemong a protheine, boemo ba peptide, le liphatsa tsa lefutso ho fumana sebopeho sa lichaba tsa likokoana-hloko.
Moko-taba oa tlhaloso e sebetsang ke ho bapisa tatellano ea protheine e lebeletsoeng le database ea tatellano ea protheine e sebetsang. Ho sebelisoa li-database tsa ts'ebetso ea liphatsa tsa lefutso tse kang GO, COG, KEGG, eggNOG, joalo-joalo, litlhahlobo tse fapaneng tsa ts'ebetso li ka etsoa ho liprotheine tse khethiloeng ke li-macroproteomes. Lisebelisoa tsa litlhaloso li kenyelletsa Blast2GO, DAVID, KOBAS, joalo-joalo.
05Kakaretso le Pono
Likokoana-hloko li phetha karolo ea bohlokoa bophelong ba batho le maloetseng. Lilemong tsa morao tjena, metaproteomics e fetohile mokhoa oa bohlokoa oa tekheniki oa ho ithuta mosebetsi oa lichaba tsa likokoana-hloko. Ts'ebetso ea tlhahlobo ea metaproteomics e ts'oana le ea mofuta o le mong oa proteomics, empa ka lebaka la ho rarahana ha ntho ea lipatlisiso ea metaproteomics, maano a khethehileng a lipatlisiso a hloka ho amoheloa mohatong o mong le o mong oa tlhahlobo, ho tloha ho sampuli ea pele ho kalafo, ho fumana data ho isa tlhahlobong ea data. Hajoale, ka lebaka la ntlafatso ea mekhoa ea ho phekola pele, ntlafatso e tsoelang pele ea mahlale a spectrometry le nts'etsopele e potlakileng ea bioinformatics, metaproteomics e hatetse pele haholo botebong ba boitsebahatso le boholo ba ts'ebeliso.
Ts'ebetsong ea kalafo ea pele ho lisampole tsa macroproteome, mofuta oa sampole o tlameha ho nahanoa pele. Mokhoa oa ho arola likokoana-hloko le lisele tsa tikoloho le liprotheine ke e 'ngoe ea liphephetso tse ka sehloohong tse tobaneng le li-macroproteome,' me ho leka-lekana pakeng tsa katleho ea karohano le tahlehelo ea likokoana-hloko ke bothata bo potlakileng bo lokelang ho rarolloa. Taba ea bobeli, ho ntšoa ha protheine ea likokoana-hloko ho tlameha ho ela hloko liphapang tse bakoang ke ho fapana ha sebopeho sa libaktheria tse fapaneng. Mehlala ea macroproteome ka har'a marang-rang e boetse e hloka mekhoa e khethehileng ea kalafo pele ho kalafo.
Mabapi le lisebelisoa tsa "mass spectrometry", lisebelisoa tse kholo tsa "mass spectrometry" li bile le phetoho ho tloha ho "mass spectrometer" tse ipapisitseng le bahlahlobi ba boima ba Orbitrap joalo ka LTQ-Orbitrap le Q Exactive ho li-spectrometer tse ngata tse ipapisitseng le motsamao oa ion hammoho le litlhahlobo tsa nako ea sefofane joalo ka timsTOF Pro. . Letoto la lisebelisoa tsa timsTOF tse nang le tlhaiso-leseling ea ion mobility li na le ho nepahala ho holimo, moeli oa ho lemoha o tlase, le ho pheta-pheta hantle. Butle-butle li fetohile lisebelisoa tsa bohlokoa mafapheng a sa tšoaneng a lipatlisiso a hlokang ho lemoha spectrometry, tse kang proteome, metaproteome, le metabolome ea mofuta o le mong. Ke habohlokoa ho hlokomela hore ka nako e telele, mefuta e mengata ea lisebelisoa tsa "mass spectrometry" e fokolitse botebo ba tšireletso ea protheine ea lipatlisiso tsa metaproteome. Nakong e tlang, lisebelisoa tsa "mass spectrometry" tse nang le mefuta e mengata e matla li ka ntlafatsa kutloisiso le ho nepahala ha protheine e khethollang metaproteomes.
Bakeng sa phumano ea data ea mass spectrometry, leha mokhoa oa ho fumana data oa DIA o amohetsoe haholo proteome ea mofuta o le mong, litlhahlobo tse ngata tsa hajoale tsa macroproteome li ntse li sebelisa mokhoa oa ho fumana data oa DDA. Mokhoa oa ho fumana data oa DIA o ka fumana ka botlalo tlhaiso-leseling ea ion ea sampole, mme ha e bapisoa le mokhoa oa ho fumana data oa DDA, e na le monyetla oa ho fumana tlhaiso-leseling ea peptide ea sampole ea macroproteome ka botlalo. Leha ho le joalo, ka lebaka la ho rarahana ho hoholo ha data ea DIA, tlhahlobo ea data ea DIA macroproteome e ntse e tobana le mathata a maholo. Nts'etsopele ea bohlale ba maiketsetso le thuto e tebileng e lebelletsoe ho ntlafatsa ho nepahala le botlalo ba tlhahlobo ea data ea DIA.
Tlhahlobong ea data ea metaproteomics, e 'ngoe ea mehato ea bohlokoa ke kaho ea polokelo ea tatellano ea protheine. Bakeng sa libaka tse tsebahalang tsa lipatlisiso tse kang limela tsa mala, li-database tsa likokoana-hloko tsa mala tse kang IGC le HMP li ka sebelisoa, 'me ho fihletsoe liphello tse ntle tsa boitsebiso. Bakeng sa litlhahlobo tse ling tse ngata tsa metaproteomics, leano le sebetsang ka ho fetesisa la kaho ea polokelo ea polokelo e ntse e le ho theha sampole e khethehileng ea tatelano ea protheine e thehiloeng ho data ea tatellano ea metagenomic. Bakeng sa lisampole tsa sechaba sa likokoana-hloko tse rarahaneng haholo le mefuta e mengata e matla, hoa hlokahala ho eketsa botebo ba tatellano ho eketsa boitsebahatso ba mefuta e mengata e fokolang, ka hona ho ntlafatsa ts'ebetso ea polokelo ea tatellano ea liprotheine. Ha tatellano ea data e haella, mokhoa oa ho batla o pheta-phetoang o ka sebelisoa ho ntlafatsa database ea sechaba. Leha ho le joalo, ho batla khafetsa ho ka ama taolo ea boleng ba FDR, kahoo liphetho li hloka ho hlahlojoa ka hloko. Ho feta moo, ho sebetsa ha mekhoa ea khale ea taolo ea boleng ba FDR tlhahlobisong ea metaproteomics e ntse e lokela ho hlahlojoa. Mabapi le leano la ho batla, leano la laeborari ea hybrid spectral le ka ntlafatsa botebo ba tšireletso ea DIA metaproteomics. Lilemong tsa morao tjena, laeborari e boletsoeng esale pele ea spectral e hlahisitsoeng ho latela thuto e tebileng e bonts'itse ts'ebetso e phahameng ho DIA proteomics. Leha ho le joalo, li-database tsa metaproteome hangata li na le limilione tsa li-protein tse kenngoeng, e leng se etsang hore ho be le lilaebrari tse ngata tse boletsoeng esale pele, tse jang lisebelisoa tse ngata tsa k'homphieutha, 'me li fella ka sebaka se seholo sa ho batla. Ntle le moo, ho tšoana ho teng lipakeng tsa tatellano ea protheine ho metaproteomes ho fapana haholo, ho etsa hore ho be thata ho netefatsa ho nepahala ha mohlala oa ponelopele ea laeborari ea spectral, kahoo lilaebrari tse boletsoeng esale pele tsa spectral ha li so sebelisoe haholo metaproteomics. Ntle le moo, ho tlameha ho hlahisoe maano a macha a protheine le litlhaloso tsa likarolo ho sebetsa tlhahlobong ea metaproteomics ea liprotheine tse ts'oanang haholo.
Ka bokhutšoanyane, joalo ka theknoloji e ntseng e hlaha ea lipatlisiso tsa microbiome, theknoloji ea metaproteomics e fihletse liphetho tsa bohlokoa tsa lipatlisiso hape e na le menyetla e meholo ea nts'etsopele.
Nako ea poso: Aug-30-2024