A generic normalization method for proper quantification in untargeted proteomics screening

ABSTRACT: The label-free quantitative mass spectrometry methods, in particular the SWATH-MS approach, have gained popularity and became a powerful technique for comparison of large datasets. In the present work, it is introduced the use of recombinant proteins as internal standards for untargeted label-free methods. The proposed internal standard strategy reveals a similar intragroup normalization capacity when compared with the most common normalization methods, with the additional advantage of maintaining the overall proteome changes between groups (which are lost using the methods referred above). Thus, proving to be able to maintain a good performance even when large qualitative and quantitative differences in sample composition are observed, such as the ones induced by biological regulation (as observed in secretome and other biofluids’ analyses) or by enrichment approaches (such as immunopurifications). Moreover, it corresponds to a cost-effective alternative, easier to implement than the current stable-isotope labeling internal standards, therefore being an appealing strategy for large quantitative screening, as clinical cohorts for biomarker discovery.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Rattus Norvegicus (rat) Homo Sapiens (human) Escherichia Coli Aequorea Victoria

TISSUE(S): Immortal Cell Line Cell

SUBMITTER: Sandra Anjo  

LAB HEAD: Bruno Manadas

PROVIDER: PXD009068 | Pride | 2019-08-19

REPOSITORIES: Pride