Benchmarking accuracy and precision of intensity-based absolute quantification of protein abundances in Saccharomyces cerevisiae
Artikel i vetenskaplig tidskrift, 2021

Protein quantification via label-free mass spectrometry (MS) has become an increasingly popular method for predicting genome-wide absolute protein abundances. A known caveat of this approach, however, is the poor technical reproducibility, that is, how consistent predictions 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 demonstrate that our simple normalization and rescaling approach can perform as accurately, yet more precisely, than methods which rely on external standards. Additionally, we show that inter-batch reproducibility is worse than biological reproducibility for all evaluated methods. These results offer a new benchmark for assessing MS data quality for protein quantification, while also underscoring current limitations in this approach.

UPS2

mass spectrometry

batch effect

absolute proteomics

iBAQ

Författare

Benjamín José Sánchez

Chalmers, Biologi och bioteknik, Systembiologi

Novo Nordisk Foundation Center for Biosustainability

Petri-Jaan Lahtvee

Tartu Ülikool

Kate Campbell

Chalmers, Biologi och bioteknik, Systembiologi

Novo Nordisk Foundation Center for Biosustainability

S. Kasvandik

Tartu Ülikool

Tao Yu

Novo Nordisk Foundation Center for Biosustainability

Chalmers, Biologi och bioteknik, Systembiologi

Iván Domenzain Del Castillo Cerecer

Novo Nordisk Foundation Center for Biosustainability

Chalmers, Biologi och bioteknik, Systembiologi

Aleksej Zelezniak

Chalmers, Biologi och bioteknik, Systembiologi

Jens B Nielsen

Novo Nordisk Foundation Center for Biosustainability

Chalmers, Biologi och bioteknik, Systembiologi

Danmarks Tekniske Universitet (DTU)

Proteomics

1615-9853 (ISSN) 1615-9861 (eISSN)

Vol. In Press

Ämneskategorier

Analytisk kemi

Bioinformatik (beräkningsbiologi)

Bioinformatik och systembiologi

DOI

10.1002/pmic.202000093

PubMed

33452728

Mer information

Senast uppdaterat

2021-03-17