
novo peptide sequencing

maas spectrometrylo, dii novo peptide sequencing anedi peptide amaino assid sequencenu tandum maas spectrometry nundi nirnayinche paddhati.
protein digest nundi peptides yokka amaino assid kramaanni telusukovadam anedi protein yokka jeevasambandhamaina paniteerunu adhyayanam cheyadaaniki chaalaa avasaram. paatha rojullo, idhi edman ksheenata prakriya dwara saadhinchabadindi. nedu, peptidela kramam parishkarinchadaaniki tandum maas spectrometer dwara vislaeshanha anedi marinta saadhaarana paddhati. saadhaaranamgaa, rendu vidhanalu unnaih database shodhana mariyu noothana kramam. database shodhana anedi oka saadhaarana version, endukante teliyani peptide yokka maas spectra dayta samarpinchabadutundi mariyu telisina peptide kramaanni kanugonadaaniki amalu cheyabadutundi, atyadhika saripolika skorutho peptide empika cheyabadutundi. eee vidhanam kotta peptidelanu gurtinchadamlo viphalamavutundi, endukante idhi database loe unna shrenulatho matrame saripolutundi. dii novo sequencing anedi maas spectrum nundi sakala ayanla ketayimpu. vividha algorithamlu
ivi vivarana kosam upayoginchabadataayi mariyu chaalaa parikaraalu kotta kramam kaaryakramaalato vastaayi.
peptide sakalam.
peptidelu saanukuula-ayan reetilo protonite cheyabadataayi. protan praarambhamlo enn-terminus ledhaa praathamika avasheshaala vaipu golusu vadda untundi, conny antargata draavanam kaaranamgaa, idhi vennemuka vichchinnam venta vividha pradaesaalaloo kadulutundi, dheeni phalitamgaa vividha sakalaalu erpadataayi. vicchinna niyamaalu konni prachuranala dwara baga vivarinchabaddaayi.
peptide sakalaalanu roopondinchadaaniki moodu ververu rakaala vennemuka bandhaalanu vichchinnam cheyavachuhu alkyl carbonyl (chr-co), peptide amide baand (co-nh), mariyu amaino alkyl baand (nh-chr).
vividha rakaala sakala ayanlu.
vennemuka bandhaalu cheelipoyinappudu, anjeerilo chuupina vidhamgaa aaru ververu rakaala sequence ayanlu erpadataayi. 1. n-terminal chaarj cheyabadina sakalam ayanlu a, b ledhaa c gaa vargeekarinchabadataayi, ayithe c-terminal chaarj cheyabadinavi x, y ledhaa z gaa vargeekarinchabadataayi. subscript n anedi amaino aamlam avasheshaala sankhya. ropestarff mariyu fohlmann modata eee naamakaranaanni pratipaadinchaaru, taruvaata baiman daanini savarinchaaru mariyu idhi atyanta vistrutamgaa aamodinchabadina samskaranagaa maarindi.
eee shrenilo ayanlu, a, b mariyu y-ayanlu atyanta saadhaarana ayan rakalu, mukhyamgaa takkuva-shakti gharshana-prerita viyojana (cid) maas spectrometerlalo, peptide amide baand (co-nh) atyanta haani kaliginchedi mariyu b-ayanla nundi koo nashtam.
b-ayanla dravyarashi = σ (avashesha dravyarashi) + 1 (h +)
y-ayanla dravyarashi = σ (avashesha dravyarashi) + 19 (h2o + h +)
a-ayanla dravyarashi = b-ayanla dravyarashi-28 (koo)
double bennemuka cheelika antargata ayaanlanu utpatti chestundi, esilium-rakam h2n-chr2-co-nh-chr3-co + ledhaa immonium-rakam h2n-chr2-co-nh + = chr3. eee ayanlu saadhaaranamgaa varnapatamlo bhangam kaligistaayi.
sii-terminal avasheshaala side chain vadda adhika-shakti sid kinda marinta cheelika jarugutundi, idhi dn, vn, doubluen-ayaanlanu yerparustundi.
vicchinna niyamaala saaraamsam.
chaalaa bhaaga ayanlu b-ledhaa y-ayanlu. bii-ayanla nundi koo nashtam kooda tarachugaa a-ayaanlanu chustundi.
upagraha ayanlu (doubluen, vn, dn-ayanlu) adhika-shakti sid dwara erpadataayi.
serr-, thurr-, asp-mariyu gloo-kaligina ayanlu tatastha paramaanu nashtam neetini (-18) utpatti chestaayi.
asn-, glun-, lies-, arg-kaligina ayanlu ammonia (-17) yokka tatastha paramaanu nashtanni utpatti chestaayi.
arg nundi ammonia tatastha nashtam sakala ayanlu (y-17) ledhaa (b-17) ayanlaku daariteestundi, vaati sambandhita ayanla kante ekkuva samruddhiga untundi.
sii-terminus praathamika avasheshaanni kaligi unnappudu, peptide (bn-1+18) ayaannu utpatti chestundi.
oka paripuurakaramaina b-y ayan jatanu gunakam aavesam kaligina ayanla varnapatamlo gamaninchavacchu. eee b-y ayan jatha kosam, vaati subscripts mottam teliyani peptideloni mottam amaino assid avasheshaalaku samanam.
sii-terminus arg ledhaa lies ayithe, daanini niroopinchadaaniki varnapatamlo y1-ayaannu kanugonavacchu.
peptide vichchinnam kosam paddhatulu.
takkuva shakti gharshanalo prerepita viyojana (sii. ii. dii) loe, bii-mariyu vai-ayanlu pradhana utpatti ayanlu. adanamgaa, ammonia (-17 daa) nashtam daanilo aarr. keey. enn. kyuu amaino aamlaalatoe mukkaluga gamaninchabadutundi. neeti nashtam (-18 daa) anedi stead amaino aamlaalatoe kuudina mukkalo gamaninchavacchu. spectraalo upagraha ayanlu chuupabadavu.
adhika shakti gala sid loe, anni rakaala sakala ayaanlanu gamaninchavacchu, conny ammonia ledhaa neeti nashtam undadu.
electron badilee viyojanam (eah. tii. dii) mariyu electron capture viyojanam (ii. sii. dii) loe, pradhana ayanlu c, y, z + 1, z + 2 mariyu konnisaarlu w ayanlu.
muldiiloo post soars dickay (psd) kosam, eah, bii, vai-ayanlu atyanta saadhaarana utpatti ayanlu.
vichchinnatanu prabhaavitam chese karakalu chaarj sthithi (adhika chaarj sthithi, vichchinnam kosam takkuva shakti avasaram), peptide dravyarashi (pedda dravyarashi, ekkuva shakti avasaram), prerita shakti (adhika shakti marinta vichchinnataku daariteestundi), praadhamika amaino aamlam kramam, viyojana mode mariyu gharshana vayuvu.
vivarana kosam maargadarsakaalu.
vivarana kosam, modata, oke amaino aamlam immonium ayanla kosam chudandi (h2n + = chr2). amaino aamlaala kosam sambandhita immonium ayanlu pattika 1loe jabita cheyabaddaayi. spectrum yokka adhika dravyarashi chivaralo konni sikharaalanu vismarinchandi. avi [m + h] + ayanla nundi tatastha anuvula nashtalaku (h2o, nh3, co2, hcoh) lonayye ayanlu. 28 daa vadda dravyarashi vyatyaasaalanu kanugonandi endukante bii-ayanlu koo nashtam dwara eah-ayaanlanu yerparustaayi. varnapatam yokka takkuva dravyarashi chivaralo b2-ayanla kosam chudandi, idhi yn-2-ayaanlanu gurtinchadaaniki kooda sahaayapadutundi. bii2-ayanla dravyarashi pattika 2loe jabita cheyabadindi, alaage bii2-ayanlaku samaana dravyaraasini kaligi unna oke amaino aamlalu. b2-ayan dravyarashi = rendu amaino aamlam avasheshaala dravyarashi + 1.
amaino aamlam avashesha dravyaraasilo okadaanitoe saripolina adhe dravyarashi vyatyaasam dwara oka shreni ayan shrenini gurtinchandi (pattika 1 chudandi). udaaharanaku, an mariyu an-1, bn mariyu bn-1, cn mariyu cn-1 madhya dravyarashi thedaalu okate. varnapatam yokka adhika dravyarashi chivaralo yn-1-ayaannu gurtinchandi. appudu yn-2, yn-3 nuu gurtinchadam konasaginchandi.. amaino aamlam avashesha dravyaraasitoe dravyarashi vyatyaasaalanu saripolchadam dwara ayanlu (pattika 1 chudandi). gurtinchina y-ayanla sambandhita b-ayanla kosam chudandi. b + y ayanla dravyarashi anedi peptide + 2 daa dravyarashi. vai-ayan shreni mariyu bii-ayan shrenini gurtinchina taruvaata, amaino aamlam kramaanni ketaayinchi dravyaraasini tanikhi cheyandi. itara paddhati emitante, modata b-ayaanlanu gurtinchadam, aapai sambandhita y-ayaanlanu kanugonadam.
algorithamlu mariyu software.
manueval dii novo sequencing sramatho kuudukunnadi mariyu samayam teesukuntundi. saadhaaranamgaa algorithamlu ledhaa prograamlu maas spectrometer parikaramtho vastaayi, ivi spectraanu ardham chesukovadaniki vartinchabadataayi.
noothana kramabaddheekarana algorithamla abhivruddhi.
maas spectrum loe puurvagaami ayan kosam saadhyamayye anni peptidelanu jabita cheyadam mariyu prati abhyardhiki maas spectramnu prayogaatmaka spectramtho saripolchadam anedi oka paatha paddhati. atyanta saaruupya varnapatam kaligina saadhyamayye peptide saraina kramamlo undataaniki atyadhika avakaasam untundi. ayithe, saadhyamayye peptidela sankhya peddadi kaavacchu. udaaharanaku, 774 paramaanu baruvutho puurvagaami peptide 21,909,046 saadhyamayye peptidelanu kaligi untundi. idhi computerlo chesinappatiki, dheeniki chaalaa samayam padutundi.
maroka paddhatini "sequencing" anie pilustaaru, idhi saadhyamayye peptidela yokka mottam kramaanni jabita cheyadaaniki badulugaa, puurti peptidelo oka bhaganni matrame soochinche peptidela yokka chinna kramaanni saripolchutundi. prayogaatmaka varnapatamlo sakala ayaanlatho baga saripoye shrenulu kanugonabadinappudu, uttama saripolikanu kanugonadaaniki avi avasheshaala dwara okkokatigaa vistarinchabadataayi.
moodava paddhatiloo, dayta yokka graphical display vartinchabadutundi, dheenilo oka amaino aamlam avasheshaala yokka oke dravyarashi vyatyaasaalanu kaligi unna sakala ayanlu panktula dwara anusandhaaninchabadi untaayi. eee vidhamgaa, adhe rakamaina ayan shreni yokka spashtamaina chitraanni pondadam sulabham. eee paddhati manueval dii novo peptide sequencingku sahaayapadavachhu, conny adhika-nirgamaamsa paristhitiki panicheyadu.
vijayavantamainadigaa pariganinchabade nalgava paddhati graph siddhaantam. graph siddhaantaanni novo peptide sequencinglo vartimpajeyadam gurinchi modata bartels prastaavinchaaru. varnapatamloni sikharaalu "varnapatam graph" anie piluvabade graphlo sheershaalugaa maarchabadataayi. rendu sheershaalu okati ledhaa aneka amaino aamlaala dravyarashi vyatyaasaanni kaligi unte, oka nirdesita anchu vartinchabadutundi. secms algorithm, lutefisk algorithm, sherenga algorithm eee rakaniki konni udaaharanalu.
lothaina abhyasam.
iteevala, dii novo peptide sequencing samasyanu parishkarinchadaaniki lothaina abhyasa paddhatulu vartimpajeyabaddaayi. modati purogati deepnovo, idhi convolutional neural network nirmaanaanni sweekarinchindi, sequence khachitatvamlo pradhana merugudalalanu saadhinchindi mariyu databaselaku sahayam cheyakunda puurti protein sequence assembleeni praarambhinchindi, taruvaata, pointnet (payintnovo) vanti adanapu network nirmaanaalu, mudi spectrum nundi lakshanaalanu velikiteese vidhamgaa sweekarinchabaddaayi. dii novo peptide sequencing samasya appudu sequence prediction samasyaga roopondinchabadutundi. gatamlo anchanaa vesina pakshika peptide kramam ichinatlayithe, neural-network aadhaarita dii novo peptide kramam namuunaalu anchanaa vesina peptide dravyarashi puurvagaami dravyaraasitoe saripolenta varaku atyanta sambhaavya tadupari amaino aamlanni padepade utpatti chestaayi. ganana samayamlo, ganana kharchunu takkuvagaa unchutuu pedda shodhana sthalaanni anveshinchadaaniki punjam shodhana vanti shodhana vyuuhaalanu avalambinchavacchu. munupati paddhathulatho polchinappudu, neural-network aadhaarita namuunaalu gananeeyamgaa merugaina khachitatvam mariyu sunnitatvaanni pradarsinchaayi. antekakunda, jagrattagaa namuunaa roopakalpanatho, deep-learning-aadhaarita dii novo peptide sequencing algorithamlu kooda real-time peptide dii novo sequencingnu saadhinchadaaniki taginanta vaegamgaa untaayi. peaks software eee neural network lerningnu vaari novo sequencing algaarithamlalo ponduparustundi.
software packagelu.
andreotti mariyu itarulu vivarinchinatlugaa."2012loe, antilope anedi lagrangian sadalimpu mariyu yenn yokka keey chinna maargaala anusarana kalayika. idhi 'spectrum graph' paddhatipai aadharapadi untundi mariyu vividha scoring functionlanu kaligi untundi, mariyu nadustunna samayam mariyu khachitatvampai "prajaadarana pondina atyaadhunika prograamlu" pepnovo mariyu novohmto polchavachhu.
grossman "mariyu itarulu."2005loe audeoni svayamchaalaka dii novo peptide sequencing saadhanamgaa samarpinchaaru, idhi signal sikharaalu mariyu sabdam sikharaalanu gurtinchagala preprocessing maadyuulnu kaligi undhi.
lutefisk anedi sid maas spectraanu upayoginchi novo sequencingnu parishkarinchagaladu. eee algorithamlo, mukhyamaina ayanlu modata kanugonabadataayi, taruvaata n-mariyu c-terminal saakshyaala jaabitaanu nirnayistaayi. krama jabita aadhaaramgaa, idhi varnapatamlo puurti shrenulanu utpatti chestundi mariyu prayogaatmaka varnapatamtho vaatini score chestundi. ayithe, phalitamlo chaalaa takkuva vyatyaasam unna aneka kramam abhyardhulanu kaligi undavacchu, kabatti saraina peptide kramaanni kanugonadam kashtam. rendava programme, cidentify, idhi bill piersone yokka fasta algorithm yokka alex taylor dwara savarinchabadina version, aaa anischita saaruupya abhyardhulanu vaeru cheyadaaniki vartinchavachhu.
moe "mariyu itarulu."2007loe emsnovo algorithamnu samarpinchi, idhi" "bahula dayta setlalo unna noothana saadhanaala kante merugga panichesindani niroopinchindi". eee algorithm lcq, ltq maas spectrometers mariyu singli, rettimpu, tripley chaarj ayanla yokka novo sequencing vivarananu cheyagaladu. itara algorithamla nundi bhinnamgaa, idhi oka kotta scoring functionnu vartimpajesindi mariyu spectrum graphku badulugaa maas arrenu upayogistundi.
matsyakaarulu "mariyu itarulu."novo sequencing yokka novom paddhatini pratipaadinchaaru. oka rahasya markov modal (hcmm) nuu beyesian frameworklo dii novo sequencingnu parishkarinchadaaniki kotta maargamgaa vartinchabadutundi. kramam yokka oke chihnalaku score cheyadaaniki badulugaa, eee paddhati amaino aamlaala kosam posterior sambhaavyatanu pariganistundi. kaagitamlo, eee paddhati pepnovo vanti itara prasiddha dii novo peptide sequencing paddhatula kante merugaina paniteerunu kaligi undani niroopinchabadindi.
peaks anedi peptide maas spectraanu ardham chesukovadaniki puurti software packagy. indulo kotta kramam, database shodhana, pii. tii. emm gurtimpu, homology shodhana mariyu dayta vislaeshanhaloo parimaanam untaayi. maa mariyu itarulu. sikharaalalo dii novo sequencing kosam oka kotta modal mariyu algorithamnu vivarinchindi, mariyu kwadrupol time-off-flight (q-tof) maas spectrometer dwara praamaanika proteinla yokka aneka tryptic peptidela yokka lutefisk panitiirutoe polchindi.
pepnovo anedi adhika nirgamaamsamtoe kuudina novo peptide sequencing sadhanam mariyu idhi scoring paddhatigaa sambhaavya netvarknu upayogistundi. idhi saadhaaranamgaa oka varnapatam yokka vivaranaku 0.2 sekanla kante takkuva samayam padutundi. fraank mariyu itarulu varninchaaru.", pepnovo sherenga, peaks, lutefisk vanti aneka prasiddha algorithamla kante merugga panichestundi. ippudu kotta version pepnovo + andubaatulo undhi.
chii "mariyu itarulu."2013loe pinovo + nuu complimentary hechsidi mariyu etdi tandum maas spectraanu upayoginchi kotta dii novo peptide sequencing saadhanamgaa pradarsinchaaru. eee paddhatiloo, oka bhaaga algorithm, pdag, peptide sequencing yokka samuparjana samayanni sagatuna 0.018s kii vegavantam chestundi, idhi itara prasiddha dii novo sequencing software kante moodu retlu vaegamgaa untundi.
jiong mariyu itarulu vivarinchinatlugaa.", konni rakaala spectraalapai matrame baga panichese itara novo peptide sequencing toolstho poliste, annovo anedi vividha rakaala spectraalu ledhaa spectral jatalapai manchi paniteerunu kaligi unna marinta saarvatrika sadhanam, sid, ett, hechsidi, cid/ett, modalainavi. idhi pepnovo + ledhaa sikharaala kante merugaina khachitatvanni kaligi untundi. antekakunda, idhi nivedinchabadina peptide shrenula dosha retunu utpatti chestundi.
maa 2015loe real time dii novo peptide sequencing injinga novernu prachurinchindi. parimaanam yokka kramamlo kotta vegaanni meruguparachadaaniki mariyu marketloni itara kotta saadhanaala maadirigaane khachitatvanni nilupukovadaaniki eee sadhanam prayatninchabadindi. macbook proo laptaplo, nover sekanuku 300 ms/ms spectraanu saadhinchaadu.
pevtsov mariyu itarulu. paina perkonna aidu dii novo sequencing algorithamla paniteerunu polcharu audins, lutefisk, novom, pepnovo mariyu peaks. qstar mariyu lcq maas spectrometer dayta vislaeshanhaloo upayoginchabaddaayi, mariyu saapeksha kramam dhooram (rsd) viluva dwara moolyaankanam cheyabaddaayi, idhi dynamic prograaming paddhati dwara lekkinchina dii novo peptide sequencing mariyu nijamaina peptide kramam madhya saaruupyata. anni algorithamlu elsq dayta kante custar detaalo merugaina paniteerunu kaligi unnayani phalitaalu choopinchaayi, ayithe uttamamainavi custar detaalo <id1> vijaya retunu kaligi unnaayi, mariyu novomm uttamamainavi elsq detaalo <id2> vijaya retunu kaligi unnaayi. qstar detaalo paniteeru kramam sikharaalu> lutefisk, pepnovo> audins, novom, mariyu lcq detaalo novom> pepnovo, sikharaalu> lutefisk> audins. spectrum naanhyata shrenitho poliste, sikharaalu mariyu novomm kooda mottam 5 algorithamlalo rendu detaalo uttama paniteerunu choopinchaayi. sikharaalu mariyu novomm custar mariyu elsq dayta rendintiloonuu uttama sunnitatvaanni kaligi unnaayi. ayithe, yea moolyaankanam chesina algorithamlu rendu dayta setlaku khachitamaina gurtimpulo 50 saataanni minchaledu.
maas spectrometerlalo iteevali purogati ultra-hye resolution maas spectraanu utpatti cheyadam saadhyapadindi. merugaina khachitatvam, utpatti cheyabadutunna maas spectrometry dayta yokka perigina mottamto paatu, dii novo peptide sequencingku lothaina abhyasa paddhatulanu vartimpajese aasaktulanu aakarshistundi. 2017 loe traan mariyu itarulu. pratipaadita deepnovo, modati deep learning aadhaarita dii novo sequencing software. asalu prachuranalooni benchmark vislaeshanha, deepnovo sikharaalu, nover mariyu pepnovolatho sahaa munupati paddhatulanu gananeeyamaina thedaatho adhigaminchindani niroopinchindi. deepnovo anedi tensorflo framework thoo pythonlo amalu cheyabadutundi. neural-netvarkku sthira-dimensional inputgaa maas spectramnu suuchimchadaaniki, deepnovo prati spectramnu 150,000 vector podavulo vibhajinchindi. eee anavasaramaina pedda spectrum praatinidhyam, mariyu asalu amalulo single-thread cpu vadakam, nija samayamlo peptide sequencingnu pradarsinchakundaa deepnovonu nirodhistundi. dii novo peptide sequencing namuunaala saamarthyaanni marinta meruguparachadaaniki, kviao mariyu itarulu. 2020loe pratipaadita payintnovo. payintnovo anedi pitorch frameworktho amalu cheyabadina paithan software mariyu idhi deepnovo sweekarinchina space viniyoginche spectrum-vector-praatinidhyaanni tolagistundi. deepnovonu polchinappudu, payintnovo oka varnapataanni neerugaa m/z mariyu teevrata jatala samitigaa soochinchadam dwara adhe samayamlo merugaina khachitatvam mariyu saamarthyaanni saadhinchagaligindi.