Quantitative comparison of CrkL-SH3 binding proteins from embryonic murine brain and liver: Implications for developmental signaling and the quantification of protein species variants in bottom-up proteomics

• Quantitative proteomics reveals tissue-specificity in CrkL-SH3 binding proteins.
• High standard deviations in peptide quantification suggest hidden protein variants.
• CrkL-SH3-binding C3G variants exhibit functional domain-specific variability.

A major aim of proteomics is to comprehensively identify and quantify all protein species variants from a given biological source. However, in spite of its tremendous utility, bottom-up proteomic strategies can do little to provide true quantification of distinct whole protein species variants given its reliance on proteolysis. This is particularly true when molecular size information is lost as in gel-free proteomics. Crk and CrkL comprise a family of adaptor proteins that couple upstream phosphotyrosine signals to downstream effectors by virtue of their SH2 and SH3 domains respectively. Here we compare the identification and quantification of CrkL-SH3 binding partners between embryonic murine brain and liver. We also uncover and quantify tissue-specific variants in CrkL-SH3 binding proteins.

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