Figure 1.

Optimization of the minimal sample protocol. The panels describe testing of the need for a carrier channel, carrier channel input size, and position. (a) Panel shows an overview of cell numbers used for different purposes in the protocol and comparisons. (b) Comparison of TMT setups for using 1000 cells with and without carrier channel and using 60 000, 20 000, and 10 000 cells for the carrier channel. The graph shows the numbers of protein groups detected using the experimental setup below. The error bars show standard deviation. (c) Effects of carrier channel on neighboring channels at 1 Thompson distance using a 10plex TMT experiment with empty channels 2–8 and a sample from 10 000 cells in channels 1 and 10. ESC—embryonic stem cell, MN—motor neuron, FACS—fluorescence-activated cell sorting, and TMT—tandem mass tag.