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. Author manuscript; available in PMC: 2022 Jul 2.
Published in final edited form as: J Proteome Res. 2021 May 27;20(7):3678–3688. doi: 10.1021/acs.jproteome.1c00247

Figure 1.

Figure 1.

Workflow for whole proteome tryptic digest data sets. A mouse embryonic cell line (NIH/3T3) was harvested, lysed, and processed further using the SL-TMT protocol.37 The tryptic peptide pool was divided into three aliquots: (1) unlabeled, (2) labeled with TMT11 reagents, and (3) labeled with TMTpro16 reagents. Each aliquot of peptides was fractionated into 96 fractions using basic-pH reversed-phase (BPRP) chromatography and concatenated into 24 superfractions. Each superfraction was analyzed on an Orbitrap Eclipse mass spectrometer with and without FAIMS.