Advancing Urinary Protein Biomarker Discovery by Data-Independent Acquisition on a Quadrupole-Orbitrap Mass Spectrometer
| Autor: | Jan Muntel, Richard G. Bachur, Hanno Steen, Yue Xuan, Alex Kentsis, Sebastian T. Berger, Lukas Reiter |
|---|---|
| Rok vydání: | 2015 |
| Předmět: |
Male
Urinary protein Analytical chemistry Biology Proteomics Orbitrap Mass spectrometry Sensitivity and Specificity Biochemistry Mass Spectrometry Article law.invention Peptide Library law Data Mining Humans Data-independent acquisition Biomarker discovery Child Chromatography General Chemistry Abdominal Pain Ovarian Cysts Urinary Tract Infections Proteome Female Biomarkers |
| Zdroj: | Journal of Proteome Research. 14:4752-4762 |
| ISSN: | 1535-3907 1535-3893 |
| DOI: | 10.1021/acs.jproteome.5b00826 |
| Popis: | The promises of data-independent acquisition (DIA) strategies are a comprehensive and reproducible digital qualitative and quantitative record of the proteins present in a sample. We developed a fast and robust DIA method for comprehensive mapping of the urinary proteome that enables large scale urine proteomics studies. Compared to a data-dependent acquisition (DDA) experiments, our DIA assay doubled the number of identified peptides and proteins per sample at half the coefficients of variation observed for DDA data (DIA = ~8%; DDA = ~16%). We also tested different spectral libraries and their effects on overall protein and peptide identifications and their reproducibilities, which provided clear evidence that sample type-specific spectral libraries are preferred for reliable data analysis. To show applicability for biomarker discovery experiments, we analyzed a sample set of 87 urine samples from children seen in the emergency department with abdominal pain. The whole set was analyzed with high proteome coverage (~1300 proteins/sample) in less than 4 days. The data set revealed excellent biomarker candidates for ovarian cyst and urinary tract infection. The improved throughput and quantitative performance of our optimized DIA workflow allow for the efficient simultaneous discovery and verification of biomarker candidates without the requirement for an early bias toward selected proteins. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|