Differences in Uniquely Identified Peptides Between ddaPASEF and diaPASEF DOI Creative Commons
Mio Iwasaki,

Rika Nishimura,

Tatsuya Yamakawa

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(22), P. 1848 - 1848

Published: Nov. 7, 2024

Recent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of data-independent acquisition (DIA) method powered by machine learning has significantly improved identification efficiency. However, compared with conventional data-dependent (DDA) method, degree which peptides are uniquely identified DIA and DDA not been thoroughly examined. this study, we over 10,000 proteins using methods analyzed characteristics unique each method. Results showed that number same column type was 19% 32%, respectively, shorter preferentially detected addition, more DIA-specific were identified, especially during first 10% elution time, overall 1/

Language: Английский

Impact of Local Air Pressure on Ion Mobilities and Data Consistency in diaPASEF-Based High Throughput Proteomics DOI

Michael Steidel,

Sascha Knecht,

Gavain M.A. Sweetman

et al.

Journal of Proteome Research, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 24, 2025

Data-independent acquisition (DIA) on ion mobility mass spectrometers enables deep proteome coverage and high data completeness in large-scale proteomics studies. For advanced schemes such as parallel accumulation serial fragmentation-based DIA (diaPASEF) stability of (1/K0) over time is crucial for consistent quality. We found that minor changes environmental air pressure systematically affect the vacuum TIMS analyzer, causing shifts. By comparing experimental mobilities with historical weather data, we attributed observed drifts to fluctuations ground pressure. Moderate e.g. fifteen mbar induce shifts 0.025 Vs/cm2. These negatively impact peptide quantification across consecutively acquired samples due drift-dependent abundance increased missing values ions located at boundaries diaPASEF isolation windows, which cannot be corrected by postprocessing. To address this, applied an in-batch autocalibration feature a run-wise basis, leading full elimination drifts.

Language: Английский

Citations

0
Ultra-Fast Multi-Organ Proteomics Unveils Tissue-Specific Mechanisms of Drug Efficacy and Toxicity DOI
Yun Xiong, Lin Tan,

Waikin Chan

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 27, 2024

Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential systems biology. We present UFP-MS, an ultra-fast mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling >240 samples per day. This optimized MS approach identifies 6,201 7,466 human proteins 1- 2-min gradients, respectively. Our streamlined preparation workflow features high-throughput homogenization, adaptive focused acoustics (AFA)-assisted proteolysis, Evotip-accelerated desalting, allowing processing up to 96 tissue in 5 h. As a practical application, we analyzed 507 from 13 mouse tissues treated enzyme-drug L-asparaginase (ASNase) or its glutaminase-free Q59L mutant, generating quantitative profile 11,472 following drug treatment. The results confirmed impact ASNase on amino acid metabolism solid tissues. Further revealed broad suppression anticoagulants cholesterol uncovered numerous tissue-specific dysregulated pathways. In summary, UFP-MS greatly accelerates generation biological insights clinically actionable hypotheses into vulnerabilities targeted by ASNase.

Language: Английский

Citations

3
Eleven shades of PASEF DOI Creative Commons
Marta Mendes, Klara F. Borrmann, Gunnar Dittmar

et al.

Expert Review of Proteomics, Journal Year: 2024, Volume and Issue: 21(9-10), P. 367 - 376

Published: Oct. 2, 2024

The introduction of trapped ion mobility spectrometry (TIMS) in combination with fast high-resolution time-of-flight (TOF) mass to the proteomics field led a jump protein identifications and quantifications, as well lowering limit detection for proteins from biological samples. Parallel Accumulation-Serial Fragmentation (PASEF) is driving force this development has been adapted discovery targeted proteomics.

Language: Английский

Citations

3
Differences in Uniquely Identified Peptides Between ddaPASEF and diaPASEF DOI Creative Commons
Mio Iwasaki,

Rika Nishimura,

Tatsuya Yamakawa

et al.

Cells, Journal Year: 2024, Volume and Issue: 13(22), P. 1848 - 1848

Published: Nov. 7, 2024

Recent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of data-independent acquisition (DIA) method powered by machine learning has significantly improved identification efficiency. However, compared with conventional data-dependent (DDA) method, degree which peptides are uniquely identified DIA and DDA not been thoroughly examined. this study, we over 10,000 proteins using methods analyzed characteristics unique each method. Results showed that number same column type was 19% 32%, respectively, shorter preferentially detected addition, more DIA-specific were identified, especially during first 10% elution time, overall 1/

Language: Английский

Citations

1