Formaldehyde Derivatization: An Unexpected Side Reaction During Filter-Aided Sample Preparation

The filter-aided
sample preparation (FASP) method has been commonly
used for proteomic sample preparation due to its high efficiency in
removing impurities. Herein, we report an overlooked +12 Da side modification
during FASP method using Microcon spin filters. We confirmed that
the side modification is caused by formaldehyde released from the
spin filter and found that the side modification leads to 10.5% and
9.5% loss in proteome-level peptide and protein identification, respectively.
We evaluated different pretreatment procedures to reduce the side
reaction. Furthermore, on the basis of the evaluation results of different
brands of spin filters, we recommend Nanosep spin filters for different
proteomic studies, especially for amine-labeling proteomic studies.
Our results would benefit researchers employing the spin filters to
improve their results and also help spin filter manufacturers to improve
the product quality. Data are available via ProteomeXchange with identifier
PXD018737.