A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F22%3A73610275" target="_blank" >RIV/61989592:15310/22:73610275 - isvavai.cz</a>

Výsledek na webu

<a href="https://www.sciencedirect.com/science/article/pii/S1387380621002049" target="_blank" >https://www.sciencedirect.com/science/article/pii/S1387380621002049</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.ijms.2021.116723" target="_blank" >10.1016/j.ijms.2021.116723</a>

Jazyk výsledku

angličtina

Název v původním jazyce

A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge

Popis výsledku v původním jazyce

The core of peptide detection in tandem mass spectrometry lies in associating fragment spectra with promising peptide candidates. We examined such detection in a synthetic combinatorial peptide library using four scoring metrics, against all theoretical peptides, and with a varying level of probabilistic prior knowledge—analyzing more than a trillion peptide-spectrum matches in total. Even after adjusting for peptide-length scoring bias, most MS/MS spectra had multiple at-least-as-good candidates as the correct peptide, showing that the highest spectral match was not a guarantee of correctness. As a remedy, we probabilistically integrated prior knowledge about expected cleavage behavior and expected peptide sequences into peptide scoring, reaching and even overcoming the performance of state-of-the-art de novo sequencing algorithms. Overall, we found that even partial and weak beliefs considerably improved peptide detection and are, in principle, generally applicable to any detection approach. Detection of peptides in a complete search thus often resulted in multiple admissible candidates near the maximal score, and the use of probabilistic prior knowledge substantially improved their discrimination.

Název v anglickém jazyce

A complete search of combinatorial peptide library greatly benefited from probabilistic incorporation of prior knowledge

Popis výsledku anglicky

The core of peptide detection in tandem mass spectrometry lies in associating fragment spectra with promising peptide candidates. We examined such detection in a synthetic combinatorial peptide library using four scoring metrics, against all theoretical peptides, and with a varying level of probabilistic prior knowledge—analyzing more than a trillion peptide-spectrum matches in total. Even after adjusting for peptide-length scoring bias, most MS/MS spectra had multiple at-least-as-good candidates as the correct peptide, showing that the highest spectral match was not a guarantee of correctness. As a remedy, we probabilistically integrated prior knowledge about expected cleavage behavior and expected peptide sequences into peptide scoring, reaching and even overcoming the performance of state-of-the-art de novo sequencing algorithms. Overall, we found that even partial and weak beliefs considerably improved peptide detection and are, in principle, generally applicable to any detection approach. Detection of peptides in a complete search thus often resulted in multiple admissible candidates near the maximal score, and the use of probabilistic prior knowledge substantially improved their discrimination.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

ISSN

1387-3806

e-ISSN

1873-2798

Svazek periodika

471

Číslo periodika v rámci svazku

JAN

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

13

Strana od-do

"116723-1"-"116723-13"

Kód UT WoS článku

000718289200005

EID výsledku v databázi Scopus

2-s2.0-85118576568