Direct Identification of Urinary Tract Pathogens by MALDI-TOF/TOF Analysis and De Novo Peptide Sequencing
peer-reviewed · Molecules · 2022
| Date | 2022-08-25 |
| Type | peer-reviewed |
| Venue | Molecules |
| Publisher | MDPI |
| Contribution | downstream-application |
| DOI | 10.3390/molecules27175461 |
| Citations (OpenAlex) | 9 |
Abstract
For mass spectrometry-based diagnostics of microorganisms, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is currently routinely used to identify urinary tract pathogens. However, it requires a lengthy culture step for accurate pathogen identification, and is limited by a relatively small number of available species in peptide spectral libraries (≤3329). Here, we propose a method for pathogen identification that overcomes the above limitations, and utilizes the MALDI-TOF/TOF MS instrument. Tandem mass spectra of the analyzed peptides were obtained by chemically activated fragmentation, which allowed mass spectrometry analysis in negative and positive ion modes. Peptide sequences were elucidated de novo, and aligned with the non-redundant National Center for Biotechnology Information Reference Sequence Database (NCBInr). For data analysis, we developed a custom program package that predicted peptide sequences from the negative and positive MS/MS spectra. The main advantage of this method over a conventional MALDI-TOF MS peptide analysis is identification in less than 24 h without a cultivation step. Compared to the limited identification with peptide spectra libraries, the NCBI database derived from genome sequencing currently contains 20,917 bacterial species, and is constantly expanding. This paper presents an accurate method that is used to identify pathogens grown on agar plates, and those isolated directly from urine samples, with high accuracy.
Methods and tools
- Direct UTI pathogen ID (MALDI-TOF): Culture-independent MALDI-TOF/TOF de novo peptide sequencing workflow (using Protein Acrobat + NCBInr alignment) that identifies uropathogens directly from native patient urine in under 24 h, side-stepping the standard 24–72 h culture step in clinical microbiology.
- Protein Acrobat: De novo peptide sequencing tool from the Cindrić group, coupling MALDI-TOF/TOF fragmentation of chemically activated peptides with de novo sequence elucidation and NCBInr alignment for organism identification (bacteria, viruses, meat-species markers).
Cites (3)
Cited by (4)
- Identification of Species-Specific Peptide Markers in Highly Processed Meat Products Using De Novo Sequencing (2026) crossref
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2024) both
- Algorithms for de-novo sequencing of peptides by tandem mass spectrometry: A review (2023) crossref
- Deep learning-driven fragment ion series classification enables highly precise and sensitive de novo peptide sequencing (2023) crossref