Evaluation of Deep and Dynamic Proteomic Screening Strategies at Sub-50 Hz Scan Speed and without Robotic Sample Preparation.
- 1Institute of Molecular Systems Medicine, Goethe University, Frankfurt am Main60528, Germany.
Abstract
Advances in ultrafast mass analyzer technology and procedural automation have enabled proteomic screening at the throughput of hundreds of proteomes per day. However, these approaches often require expensive instrumentation upgrades and robotic automation that remain inaccessible to many research laboratories and core facilities. In this study, we address the feasibility of scaling up proteomic screening capabilities with minimal upgrade cost by focusing on (a) strategies for nonautomated high-throughput sample preparation from 96-well cell culture, (b) data acquisition on sub-50 Hz scan speed hybrid and tribrid Orbitrap instruments, and (c) data analysis strategies for label-free and labeled proteomic screening. We find that the 96-well format STrap, in combination with C18 plates, provides the most robust throughput for a nonautomated sample preparation workflow. Furthermore, we show that for static proteomes, an isobaric tandem mass tag (TMT)-based multiplexing approach provides deeper and more precise proteome coverage, whereas data-independent acquisition (DIA) is more accurate, albeit with a reduced dynamic range and more missing values. Finally, we extend the optimized workflow to proteome turnover studies using pulsed stable isotope labeling by amino acids in cell culture (pSILAC), highlighting the key advantages and trade-offs of DIA and TMT data-dependent acquisition strategies for capturing protein translation.
Related
- In situ polymerized monolith tips for reproducible, format-flexible proteomic sample preparation applied to biofluids
- Orthogonal Chemical Proteomic Strategies Reveal the Cholesteryl Ester Interactome in Mammalian Cells
- ［2+4］型手性多孔有机笼Pim高效液相色谱固定相的制备及其手性拆分性能评价 Preparation and chiral separation performance evaluation of a high performance liquid chromatography stationary phase based on a ［2+4］-type chiral porous organic cage Pim
- Cross-Platform Evaluation Reveals Sample Preparation-Driven Biological Biases despite Advances in Mass Spectrometry Performance in Serum Proteomics.
- Preparation, Emulsion Stability and Preliminary Demoulding Evaluation of a Wax-Free Water-Based Soybean Oil-Mineral Oil Concrete Release Agent
BibTeX
@article{parmar2026evaluation,
title = {{Evaluation of Deep and Dynamic Proteomic Screening Strategies at Sub-50 Hz Scan Speed and without Robotic Sample Preparation.}},
author = {Bhavesh S Parmar and Yuanyuan Liu and Parviz Ghezellou and Christian Münch},
journal = {Journal of proteome research},
year = {2026},
month = oct,
doi = {10.1021/acs.jproteome.6c00312},
url = {https://europepmc.org/article/MED/42918129},
note = {CC BY},
}
RIS
TY - JOUR
TI - Evaluation of Deep and Dynamic Proteomic Screening Strategies at Sub-50 Hz Scan Speed and without Robotic Sample Preparation.
AU - Bhavesh S Parmar
AU - Yuanyuan Liu
AU - Parviz Ghezellou
AU - Christian Münch
PY - 2026
DA - 2026/10/01
JO - Journal of proteome research
DO - 10.1021/acs.jproteome.6c00312
UR - https://europepmc.org/article/MED/42918129
AB - Advances in ultrafast mass analyzer technology and procedural automation have enabled proteomic screening at the throughput of hundreds of proteomes per day. However, these approaches often require expensive instrumentation upgrades and robotic automation that remain inaccessible to many research laboratories and core facilities. In this study, we address the feasibility of scaling up proteomic screening capabilities with minimal upgrade cost by focusing on (a) strategies for nonautomated high-throughput sample preparation from 96-well cell culture, (b) data acquisition on sub-50 Hz scan speed hybrid and tribrid Orbitrap instruments, and (c) data analysis strategies for label-free and labeled proteomic screening. We find that the 96-well format STrap, in combination with C18 plates, provides the most robust throughput for a nonautomated sample preparation workflow. Furthermore, we show that for static proteomes, an isobaric tandem mass tag (TMT)-based multiplexing approach provides deeper and more precise proteome coverage, whereas data-independent acquisition (DIA) is more accurate, albeit with a reduced dynamic range and more missing values. Finally, we extend the optimized workflow to proteome turnover studies using pulsed stable isotope labeling by amino acids in cell culture (pSILAC), highlighting the key advantages and trade-offs of DIA and TMT data-dependent acquisition strategies for capturing protein translation.
SN - 1535-3893
SN - 1535-3907
ER -