SWATH-MS in quality control of biologicals: Towards confident label-free and non-targeted quantification with single injection? - An illustration with plasma residuals profiling in human immunoglobulin.

ABSTRACT: By performing data-independent acquisition (DIA), SWATH-MS is expected to provide comprehensive and repeatable spectral data that can be perpetually interrogated by reference spectral libraries. In the context of biological sample quality control, a benchmark spectral library could index all the possible low-abundant contaminants that should be screened in the sample. Here, the case study concerns the profiling of plasma residuals in human immunoglobulin (Ig) preparations. Yet with such an application, a strong repeatability issue in protein quantification calls for a MS2-level data quality criterion. A MS device intrinsic relationship between MS2 quantification CV and peak area allows using peak area range instead of CV threshold as such a criterion, and by this flagging confident data from single injections. A Python script is provided to perform this flagging. Using such flagging becomes increasingly important as the library becomes more distant from the actual sample. Using appropriated sample fractionation, Ig residuals profiles based on flagged MS2-level quantifications are remarkably consistent with MS1-level quantifications based on classical shotgun (DDA) approach. Sensitivity, which is around three to four orders of magnitude in the concentration dynamic range with a TripleTOF5600 device, remains the main pitfall to gain confident quantification of proteins which were not identified with DDA in the sample and to fully benefit from the SWATH potential for QC applications: provide MS2 specific, comprehensive, label-free and non-targeted quantitative profiles with single injections.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Maarten Dhaenens  

LAB HEAD: Dieter Deforce

PROVIDER: PXD007656 | Pride | 2022-10-04

REPOSITORIES: Pride