Range of protein detection by selected/multiple reaction monitoring mass spectrometry in an unfractionated human cell culture lysate.

Proteomics
H Alexander EbhardtRuedi Aebersold

Abstract

Selected or multiple reaction monitoring is a targeted mass spectrometry method (S/MRM-MS), in which many peptides are simultaneously and consistently analyzed during a single liquid chromatography-mass spectrometry (LC-S/MRM-MS) measurement. These capabilities make S/MRM-MS an attractive method to monitor a consistent set of proteins over various experimental conditions. To increase throughput for S/MRM-MS it is advantageous to use scheduled methods and unfractionated protein extracts. Here, we established the practically measurable dynamic range of proteins reliably detectable and quantifiable in an unfractionated protein extract from a human cell line using LC-S/MRM-MS. Initially, we analyzed S/MRM transition peak groups in terms of interfering signals and compared S/MRM transition peak groups to MS1-triggered MS2 spectra using dot-product analysis. Finally, using unfractionated protein extract from human cell lysate, we quantified the upper boundary of copies per cell to be 35 million copies per cell, while 7500 copies per cell represents a lower boundary using a single 35 min linear gradient LC-S/MRM-MS measurement on a current, standard commercial instrument.

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Citations

Dec 28, 2012·Nature Methods·Paola PicottiRuedi Aebersold
Jul 20, 2012·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Lance A Liotta, Emanuel F Petricoin
Nov 20, 2015·Molecular Biology and Evolution·Johannes EngelkenElena Bosch
Mar 23, 2013·Biochemistry·Daniel C Liebler, Lisa J Zimmerman
Jun 23, 2015·Proteomics·H Alexander EbhardtRuedi Aebersold
Nov 8, 2014·Rapid Communications in Mass Spectrometry : RCM·H Alexander EbhardtRuedi Aebersold
Apr 10, 2013·Biochimica Et Biophysica Acta·Marianne SandinFredrik Levander
Jun 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Ryohei NarumiHiroki R Ueda
Dec 13, 2016·Journal of Proteome Research·Camille TerfveRuedi Aebersold
Apr 4, 2014·Molecular & Cellular Proteomics : MCP·Xiaofeng GuoHamid Mirzaei
Jan 8, 2017·Molecular & Cellular Proteomics : MCP·Anuli Christiana UzozieGiancarlo Marra
Mar 17, 2020·Molecular Systems Biology·Barbora SalovskaYansheng Liu
Oct 22, 2013·Expert Review of Molecular Diagnostics·Yansheng LiuRuedi Aebersold
Jul 7, 2018·NPJ Systems Biology and Applications·H Alexander EbhardtRuedi Aebersold
Aug 26, 2021·Molecular Systems Biology·Jelena ČuklinaPatrick G A Pedrioli

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