2026-10-11T13:52:13Z https://api.figshare.com/v2/oai

oai:figshare.com:article/33824194 2026-09-15T21:20:55Z category_4 category_146 category_16 category_21 category_873 category_45 portal_63 item_type_3 month_year_09_2026

Evaluation of Deep and Dynamic Proteomic Screening Strategies at Sub-50 Hz Scan Speed and without Robotic Sample Preparation Bhavesh S. Parmar (24957445) Yuanyuan Liu (136992) Parviz Ghezellou (9672311) Christian Münch (8907575) Biochemistry Space Science Physiology Biotechnology Chemical Sciences not elsewhere classified Sociology well format strap tribrid orbitrap instruments reduced dynamic range psilac ), highlighting proteomic screening capabilities precise proteome coverage minimal upgrade cost many research laboratories labeled proteomic screening enabled proteomic screening capturing protein translation proteomes per day well cell culture throughput sample preparation dependent acquisition strategies data analysis strategies cell culture data acquisition static proteomes independent acquisition whereas data tmt data robust throughput robotic automation remain inaccessible procedural automation optimized workflow nonautomated high missing values key advantages core facilities c18 plates amino acids 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. 2026-09-15T00:00:00Z Dataset Dataset 10.1021/acs.jproteome.6c00312.s002 https://figshare.com/articles/dataset/Evaluation_of_Deep_and_Dynamic_Proteomic_Screening_Strategies_at_Sub-50_Hz_Scan_Speed_and_without_Robotic_Sample_Preparation/33824194 CC BY-NC 4.0