diaTracer enables spectrum-centric analysis of diaPASEF proteomics data
Abstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent acquisition analysis, such as the diaPASEF techn...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55448-8 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559241688612864 |
|---|---|
| author | Kai Li Guo Ci Teo Kevin L. Yang Fengchao Yu Alexey I. Nesvizhskii |
| author_facet | Kai Li Guo Ci Teo Kevin L. Yang Fengchao Yu Alexey I. Nesvizhskii |
| author_sort | Kai Li |
| collection | DOAJ |
| description | Abstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent acquisition analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves the quantification accuracy and protein depth achievable using data-independent acquisition. We introduce diaTracer, a spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (mass to charge ratio, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved “pseudo-tandem mass spectra”, facilitating direct (“spectral-library free”) peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from triple-negative breast cancer, cerebrospinal fluid, and plasma samples, data from phosphoproteomics and human leukocyte antigens immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass-offset searches. |
| format | Article |
| id | doaj-art-c8a8762e47c348b28de83d1a3e975ed9 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-c8a8762e47c348b28de83d1a3e975ed92025-01-05T12:40:51ZengNature PortfolioNature Communications2041-17232025-01-0116111410.1038/s41467-024-55448-8diaTracer enables spectrum-centric analysis of diaPASEF proteomics dataKai Li0Guo Ci Teo1Kevin L. Yang2Fengchao Yu3Alexey I. Nesvizhskii4Gilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of MichiganDepartment of Pathology, University of MichiganGilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of MichiganDepartment of Pathology, University of MichiganGilbert S. Omenn Department of Computational Medicine and Bioinformatics, University of MichiganAbstract Data-independent acquisition has become a widely used strategy for peptide and protein quantification in liquid chromatography-tandem mass spectrometry-based proteomics studies. The integration of ion mobility separation into data-independent acquisition analysis, such as the diaPASEF technology available on Bruker’s timsTOF platform, further improves the quantification accuracy and protein depth achievable using data-independent acquisition. We introduce diaTracer, a spectrum-centric computational tool optimized for diaPASEF data. diaTracer performs three-dimensional (mass to charge ratio, retention time, ion mobility) peak tracing and feature detection to generate precursor-resolved “pseudo-tandem mass spectra”, facilitating direct (“spectral-library free”) peptide identification and quantification from diaPASEF data. diaTracer is available as a stand-alone tool and is fully integrated into the widely used FragPipe computational platform. We demonstrate the performance of diaTracer and FragPipe using diaPASEF data from triple-negative breast cancer, cerebrospinal fluid, and plasma samples, data from phosphoproteomics and human leukocyte antigens immunopeptidomics experiments, and low-input data from a spatial proteomics study. We also show that diaTracer enables unrestricted identification of post-translational modifications from diaPASEF data using open/mass-offset searches.https://doi.org/10.1038/s41467-024-55448-8 |
| spellingShingle | Kai Li Guo Ci Teo Kevin L. Yang Fengchao Yu Alexey I. Nesvizhskii diaTracer enables spectrum-centric analysis of diaPASEF proteomics data Nature Communications |
| title | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| title_full | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| title_fullStr | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| title_full_unstemmed | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| title_short | diaTracer enables spectrum-centric analysis of diaPASEF proteomics data |
| title_sort | diatracer enables spectrum centric analysis of diapasef proteomics data |
| url | https://doi.org/10.1038/s41467-024-55448-8 |
| work_keys_str_mv | AT kaili diatracerenablesspectrumcentricanalysisofdiapasefproteomicsdata AT guociteo diatracerenablesspectrumcentricanalysisofdiapasefproteomicsdata AT kevinlyang diatracerenablesspectrumcentricanalysisofdiapasefproteomicsdata AT fengchaoyu diatracerenablesspectrumcentricanalysisofdiapasefproteomicsdata AT alexeyinesvizhskii diatracerenablesspectrumcentricanalysisofdiapasefproteomicsdata |