Simulacija de-novo sekvenciranja kratkih proteina pomoću masenog spektrometra, koristeći vjerojatnosne modele

undergraduate thesis

• Title (english): Simulating Short Protein De-novo Sequencing by Mass Spectrometry Using Probabilistic Models
• Author: Ante Grgurević
• Mentor: Krešimir Križanović (mentor)
• Committee member: Krešimir Križanović (predsjednik povjerenstva)
• Committee member: Marko Subašić (član povjerenstva)
• Committee member: Filip Bosnić (član povjerenstva)
• Granter: University of Zagreb; Faculty of Electrical Engineering and Computing; Zagreb
• Defense date and country: 2021-07-15, Croatia
• Scientific / art field, discipline and subdiscipline: TECHNICAL SCIENCES; Computing

Abstract

De-novo sekvenciranje kratkih proteina je proces u kojem dobivamo sekvencu aminokiselina iz podataka iščitanih iz masenog spektrometra. Prednost de-novo sekvenciranja je sposobnost dobivanja sekvence bez prethodne identifikacije peptida u bazi podataka. Čest problem kod pristupa koji koristi bazu podataka se temelji na činjenici da peptidi mogu biti derivirani iz nepoznatih proteina, ili pak mogu proći kroz brojne posttranslacijske ili kemijske modifikacije.
Za potrebe de-novo sekvenciranje, treba nam izlaz iz masenog spektrometra koji je generiran pomoću simulatora razvijenog u suradnji sa kolegom Andrijom Arbanasićem.
Koristeći modificirani algoritam za rješavanje problema ruksaka, pronalazimo sekvencu aminokiselina koja odgovara rješenju problema.
Nedvojbeno suboptimalni rezultati i preciznost programa su posljedica kompleksnosti problema te mnogih komplikacija kod samog određivanja sekvence aminokiselina koje su navedene u samom radu.

Abstract (english)

Short protein de-novo sequencing is a process in which we get an aminoacid sequence from the data read from mass spectrometer. One of the advantages of de-novo sequencing is the ability to provide an aminoacid sequence without previous peptide identification in the database. One of the most reccurring problems in approaches that use database identification is that peptides can be derived from unknown proteins, or they can go through many post-translational or chemical modifications.
For short protein de-novo sequencing, we need outputs gained from mass spectrometer, which are generated with the help of mass spectrometry simulator that has been developed in colaboration with Andrija Arbanasić.
Using the modified knapsack problem algorithm, we find an aminoacid sequence that represents the solution to the problem.
Undoubtedly suboptimal results and software accuracy are consequences of problem complexity and many more complications brought to light when trying to predict amino-acid sequence, which have been covered in this study.

• Keywords: de-novo sekvenciranje proteina; masena spektrometrija; problem ruksaka
• Keywords (english): short protein de-novo sequencing; mass spectrometry; knapsack problem
• Language: croatian
• URN:NBN: urn:nbn:hr:168:615104
• Study programme: Title: Computing; Study programme type: university; Study level: undergraduate; Academic / professional title: sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva (sveučilišni/a prvostupnik/ prvostupnica (baccalaureus/baccalaurea) inženjer/inženjerka računarstva)
• Type of resource: Text
• File origin: Born digital
• Access conditions: Closed access
• Created on: 2023-01-15 10:14:28