PT  - JOURNAL ARTICLE
AU  - Benjamín J. Sánchez
AU  - Petri-Jaan Lahtvee
AU  - Kate Campbell
AU  - Sergo Kasvandik
AU  - Rosemary Yu
AU  - Iván Domenzain
AU  - Aleksej Zelezniak
AU  - Jens Nielsen
TI  - Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in <em>Saccharomyces cerevisiae</em>
AID  - 10.1101/2020.03.23.998237
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.03.23.998237
4099  - http://biorxiv.org/content/early/2020/03/23/2020.03.23.998237.short
4100  - http://biorxiv.org/content/early/2020/03/23/2020.03.23.998237.full
AB  - Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for determining genome-wide absolute protein abundances. A known caveat of this approach is the poor technical reproducibility, i.e. how consistent the estimations are when the same sample is measured repeatedly. Here, we measured proteomics data for Saccharomyces cerevisiae with both biological and inter-batch technical triplicates, to analyze both accuracy and precision of protein quantification via MS. Moreover, we analyzed how these metrics vary when applying different methods for converting MS intensities to absolute protein abundances. We found that a simple normalization and rescaling approach performs as accurately yet more precisely than methods that rely on external standards. Additionally, we show that inter-batch reproducibility is worse than biological reproducibility for all evaluated methods. These results subsequently serve as a benchmark for assessing MS data quality for protein quantification, whilst also underscoring current limitations in this approach.