Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery

Shawn J. Rice, Xin Liu, Jianhong Zhang, Chandra Belani

Research output: Contribution to journalArticle

Abstract

The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike-in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple-reaction monitoring-high resolution (MRM-HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, the eAQ method is applied to 12 plasma samples from six non-small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.

Original languageEnglish (US)
Article number1800135
JournalProteomics
Volume19
Issue number3
DOIs
StatePublished - Feb 1 2019

Fingerprint

Biomarkers
Blood Proteins
Proteins
Plasma (human)
Monitoring
Non-Small Cell Lung Carcinoma
Proteomics
Cells
Ions
Plasmas
Peptides

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology

Cite this

@article{e6125ab7438546a8a3e3dc6b3d67e54e,
title = "Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery",
abstract = "The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike-in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple-reaction monitoring-high resolution (MRM-HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, the eAQ method is applied to 12 plasma samples from six non-small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.",
author = "Rice, {Shawn J.} and Xin Liu and Jianhong Zhang and Chandra Belani",
year = "2019",
month = "2",
day = "1",
doi = "10.1002/pmic.201800135",
language = "English (US)",
volume = "19",
journal = "Proteomics",
issn = "1615-9853",
publisher = "Wiley-VCH Verlag",
number = "3",

}

Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery. / Rice, Shawn J.; Liu, Xin; Zhang, Jianhong; Belani, Chandra.

In: Proteomics, Vol. 19, No. 3, 1800135, 01.02.2019.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Absolute Quantification of All Identified Plasma Proteins from SWATH Data for Biomarker Discovery

AU - Rice, Shawn J.

AU - Liu, Xin

AU - Zhang, Jianhong

AU - Belani, Chandra

PY - 2019/2/1

Y1 - 2019/2/1

N2 - The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike-in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple-reaction monitoring-high resolution (MRM-HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, the eAQ method is applied to 12 plasma samples from six non-small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.

AB - The current state of proteomics requires a choice between targeted and global discovery methods. A method, that combines targeted and data-independent acquisition for absolute quantification of all identified plasma proteins, in a single sequential window acquisition of all theoretical fragment ions (SWATH) acquisition run, using a panel of spike-in standards (SIS), is established and optimized. The absolute quantification (AQ) of SWATH and multiple-reaction monitoring-high resolution (MRM-HR) acquisition methods are compared using the 100 protein PlasmaDive SIS panel spiked into non-depleted human plasma. SWATH provides equivalent quantification and differentially abundant protein profiles as MRM-HR. Absolute quantities of the SIS peptides from the SWATH data are used to estimate the absolute quantities (eAQ) for all the proteins in the run. The eAQ values provide similar quantification and differentially abundant protein profiles as AQ and protein area (PA) values. As a proof-of-concept, the eAQ method is applied to 12 plasma samples from six non-small cell lung cancer (NSCLC) patients and the performance of eAQ values versus peak area quantification is evaluated. There is a strong correlation between AQ and peak area ratios producing significant overlap of differentially abundant proteins. This eAQ method can provide quantitative data equivalent to AQ or peak area values.

UR - http://www.scopus.com/inward/record.url?scp=85060243155&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060243155&partnerID=8YFLogxK

U2 - 10.1002/pmic.201800135

DO - 10.1002/pmic.201800135

M3 - Article

C2 - 30585401

AN - SCOPUS:85060243155

VL - 19

JO - Proteomics

JF - Proteomics

SN - 1615-9853

IS - 3

M1 - 1800135

ER -