The complexity of the functional proteome extends considerably beyond the coding genome, resulting in millions of proteoforms. Investigation of proteoforms and their functional roles is important to understand cellular physiology and its deregulation in diseases but challenging to perform systematically. Here we applied thermal proteome profiling with deep peptide coverage to detect functional proteoform groups in acute lymphoblastic leukemia cell lines with different cytogenetic aberrations. We detected 15,846 proteoforms, capturing differently spliced, cleaved and post-translationally modified proteins expressed from 9,290 genes. We identified differential co-aggregation of proteoform pairs and established links to disease biology. Moreover, we systematically made use of measured biophysical proteoform states to find specific biomarkers of drug sensitivity. Our approach, thus, provides a powerful and unique tool for systematic detection and functional annotation of proteoform groups.

功能蛋白质组的复杂性远远超出了编码基因组的范围，产生了数百万种蛋白质形式。蛋白质型及其功能作用的研究对于理解细胞生理学及其在疾病中的失调很重要，但系统地进行具有挑战性。在这里，我们应用具有深度肽覆盖的热蛋白质组分析来检测具有不同细胞遗传学畸变的急性淋巴细胞白血病细胞系中的功能性蛋白质组。我们检测到了 15,846 种蛋白质形式，捕获了 9,290 个基因表达的不同剪接、切割和翻译后修饰的蛋白质。我们鉴定了蛋白质型对的差异共聚集，并建立了与疾病生物学的联系。此外，我们系统地利用测量的生物物理蛋白状态来寻找药物敏感性的特定生物标志物。因此，我们的方法为蛋白质组的系统检测和功能注释提供了强大且独特的工具。