FAIMS interface is gaining popularity because of the impressive 100-fold signal to noise enhancement in addition to the recent coupling to the Orbitrap technology, the most important analyzer developed in the last 20 years. The selection of group of ions and effective removal of single-charged ones at particular compensation voltages increases around 50% the proteome coverage at expenses of lower peptides coverage. However, specific setting for phosphoproteome analysis is yet poorly described. Here we have found the maximum transmission for several tryptic phosphopeptides isolated from a single complex mixture and we have set an experimental method based on five compensation voltages partially different to the ones described previously, demonstrating the relevance of voltages higher than 47 V, with an increase of around 20% of unique phosphopeptides. Using this experimental setup two complex phosphoproteomes isolates (SH-SY5Y cell line and plasma) were analyzed and found increments of 50% on phosphopeptides identification with the proposed method with respect to a previous one, for the cell line extract. Meanwhile for plasma 109 of the detected phosphopeptides are found for first time in this body fluid, presumably due to the release of intracellular proteins. With this FAIMS setup, 60% of the proteins identified are classified as very low abundant proteins.

FAIMS接口之所以受欢迎，是因为其信噪比提高了100倍，此外还与最近20年来开发的最重要的分析仪Orbitrap技术相结合。离子组的选择和在特定补偿电压下有效去除单电荷离子组的蛋白质组覆盖率增加了约50％，但肽覆盖率较低。但是，磷酸化蛋白质组分析的具体设置还很少描述。在这里，我们发现了从单一复杂混合物中分离出的几种胰蛋白酶磷酸肽的最大透射率，并基于部分不同于先前所述的五个补偿电压，设置了一种实验方法，证明了高于47 V的电压的相关性，约增加20％的独特磷酸肽。使用此实验设置，分析了两个复杂的磷酸化蛋白质组分离物（SH-SY5Y细胞系和血浆），发现与拟定方法相比，针对细胞系提取物，所提出的方法鉴定的磷酸肽的增量为50％。同时，对于血浆109，在该体液中首次发现了检测到的磷酸肽，这可能是由于细胞内蛋白质的释放。通过此FAIMS设置，已鉴定出的60％的蛋白质被归类为极低丰度的蛋白质。同时，对于血浆109，在该体液中首次发现了检测到的磷酸肽，这可能是由于细胞内蛋白质的释放。通过此FAIMS设置，已鉴定出的60％的蛋白质被归类为极低丰度的蛋白质。同时，对于血浆109，在该体液中首次发现了检测到的磷酸肽，这可能是由于细胞内蛋白质的释放。通过这种FAIMS设置，已鉴定出的60％的蛋白质被归类为非常低的丰富蛋白质。