Onat Bora, Momenzadeh Amanda, Haghani Ali, Jiang Yuming, Song Yang, Parker Sarah J, Meyer Jesse G
Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States.
J Proteome Res. 2025 Apr 4;24(4):1586-1595. doi: 10.1021/acs.jproteome.4c00632. Epub 2025 Jan 24.
Single cell transcriptomics (SCT) has revolutionized our understanding of cellular heterogeneity, yet the emergence of single cell proteomics (SCP) promises a more functional view of cellular dynamics. A challenge is that not all mass spectrometry facilities can perform SCP, and not all laboratories have access to cell sorting equipment required for SCP, which together motivate an interest in sending bulk cell samples through the mail for sorting and SCP analysis. Shipping requires cell storage, which has an unknown effect on SCP results. This study investigates the impact of cell storage conditions on the proteomic landscape at the single cell level, utilizing Data-Independent Acquisition (DIA) coupled with Parallel Accumulation Serial Fragmentation (diaPASEF). Three storage conditions were compared in 293T cells: (1) 37 °C (control), (2) 4 °C overnight, and (3) -196 °C storage followed by liquid nitrogen preservation. Both cold and frozen storage induced significant alterations in the cell diameter, elongation, and proteome composition. By elucidating how cell storage conditions alter cellular morphology and proteome profiles, this study contributes foundational technical information about SCP sample preparation and data quality.
单细胞转录组学（SCT）彻底改变了我们对细胞异质性的理解，然而单细胞蛋白质组学（SCP）的出现有望为细胞动力学提供更具功能性的视角。一个挑战是并非所有质谱设施都能进行SCP，而且并非所有实验室都能使用SCP所需的细胞分选设备，这共同激发了人们通过邮寄批量细胞样本进行分选和SCP分析的兴趣。运输需要细胞储存，而这对SCP结果的影响尚不清楚。本研究利用数据非依赖采集（DIA）与平行累积连续碎裂（diaPASEF）相结合的方法，在单细胞水平上研究细胞储存条件对蛋白质组格局的影响。在293T细胞中比较了三种储存条件：（1）37°C（对照），（2）4°C过夜，以及（3）-196°C储存后液氮保存。冷藏和冷冻储存均导致细胞直径、伸长率和蛋白质组组成发生显著变化。通过阐明细胞储存条件如何改变细胞形态和蛋白质组谱，本研究为SCP样本制备和数据质量提供了基础技术信息。
