SWATH-MS data independent acquisition is now commonly used to determine the abundance of proteins in complex biological samples. It is well suited for quantitative studies across many biological samples, but has not yet been fully exploited for applications of human plasma biomarker discovery.

In this paper, we used SWATH-MS to profile changes in plasma proteins associated with healthy human infant development. We profiled 40 individual plasma samples from four sample age groups (neonates, < 1-year olds, 1-5 year olds, adults, n=10 each). A local SWATH peptide library was built by combining 1D nanoLC MS/MS IDA runs from each pooled group, and an extended SWATH peptide library was also evaluated by merging the local library with publicly available MS spectral repository in SWATHAtlas.

Using undepleted plasma, 118 proteins with minimum of two peptides were quantified when the local library was used which contained 146 proteins while the extended library allowed for putative identification and quantification of more than 900 proteins. Overall, the changes in neonatal plasma proteins were the most significant when compared with the other three groups. Using both protein and peptide cut-off criteria to determine proteins changed in expression, the local library yielded 17 and 26 proteins up- and down-regulated respectively when compared with children under one year of age. Correspondingly, 8 and 35 proteins were found to be up- and down-regulated respectively when compared to 1-5 year old children; and 9 and 25 proteins with adults group. Interestingly, the number of differentially expressed proteins was only slightly higher with the extended library. In summary, this is the first description of using SWATH-MS to profile the expression of plasma proteins associated with human infant development.