PT  - JOURNAL ARTICLE
AU  - Alejandro Brenes
AU  - Jens Hukelmann
AU  - Dalila Bensaddek
AU  - Angus I. Lamond
TI  - Optimising multi-batch TMT analysis to mitigate inflation of missing values, false positives and diminished inter batch accuracy
AID  - 10.1101/497396
DP  - 2018 Jan 01
TA  - bioRxiv
PG  - 497396
4099  - http://biorxiv.org/content/early/2018/12/16/497396.short
4100  - http://biorxiv.org/content/early/2018/12/16/497396.full
AB  - Multiplexing strategies for large-scale proteomic analyses have become increasingly prevalent, TMT in particular. Here we used a large iPSC proteomic experiment with twenty-four 10-plex TMT batches to evaluate the effect of integrating multiple TMT batches within a single analysis. We reveal a significant inflation rate of missing protein and peptide values and show that precision decreases as multiple batches are integrated. Additionally, we explore the effect of false positives using Y chromosome specific peptides as an internal control to quantify the effect of co-isolation interference, as well as primary and secondary reporter ion interference. Based on the results we suggest solutions to mitigate these effects. We show using a reference line can increase precision by normalising the quantification across batches and we propose experimental designs that minimise the effect of cross population reporter ion interference.