Synthetic Knockout Protein Standard for Evaluating Interference in Tandem Mass Tag-Based Proteomics.
Anal Chem
; 96(17): 6836-6846, 2024 04 30.
Article
em En
| MEDLINE
| ID: mdl-38640495
ABSTRACT
Isobaric labeling is widely used for unbiased, proteome-wide studies, and it provides several advantages, such as fewer missing values among samples and higher quantitative precision. However, ion interference may lead to compressed or distorted observed ratios due to the coelution and coanalysis of peptides. Here, we introduced a synthetic KnockOut standard (sKO) for evaluating interference in tandem mass tags-based proteomics. sKO is made by mixing TMTpro-labeled tryptic peptides derived from four nonhuman proteins and a whole human proteome as background at different proportions. We showcased the utility of the sKO standard by exploring ion interference at different peptide concentrations (up to a 30-fold change in abundance) and using a variety of mass spectrometer data acquisition strategies. We also demonstrated that the sKO standard could provide valuable information for the rational design of acquisition strategies to achieve optimal data quality and discussed its potential applications for high-throughput proteomics workflows development.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Proteômica
/
Espectrometria de Massas em Tandem
Limite:
Animals
/
Humans
Idioma:
En
Revista:
Anal Chem
Ano de publicação:
2024
Tipo de documento:
Article
País de afiliação:
Estados Unidos