AbstractANPELA is widely used for quantifying traditional bulk proteomic data. Recently, there is a clear shift from bulk proteomics to the single‐cell ones (SCP), for which powerful cytometry techniques demonstrate the fantastic capacity of capturing cellular heterogeneity that is completely overlooked by traditional bulk profiling. However, the in‐depth and high‐quality quantification of SCP data is still challenging and severely affected by the large numbers of quantification workflows and extreme performance dependence on the studied datasets. In other words, the proper selection of well‐performing workflow(s) for any studied dataset is elusory, and it is urgently needed to have a significantly enhanced and accelerated tool to address this issue. However, no such tool is developed yet. Herein, ANPELA is therefore updated to its 2.0 version (https://idrblab.org/anpela/), which is unique in providing the most comprehensive set of quantification alternatives (>1000 workflows) among all existing tools, enabling systematic performance evaluation from multiple perspectives based on machine learning, and identifying the optimal workflow(s) using overall performance ranking together with the parallel computation. Extensive validation on different benchmark datasets and representative application scenarios suggest the great application potential of ANPELA in current SCP research for gaining more accurate and reliable biological insights.