A calibration routine for efficient ETD in large-scale proteomics

Christopher M Rose; Matthew J P Rush; Nicholas M Riley; Anna E Merrill; Nicholas W Kwiecien; Dustin D Holden; Christopher Mullen; Michael S Westphall; Joshua J Coon

doi:10.1007/s13361-015-1183-1

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A calibration routine for efficient ETD in large-scale proteomics

Journal article

Open access

A calibration routine for efficient ETD in large-scale proteomics

Christopher M Rose, Matthew J P Rush, Nicholas M Riley, Anna E Merrill, Nicholas W Kwiecien, Dustin D Holden, Christopher Mullen, Michael S Westphall and Joshua J Coon

Journal of the American Society for Mass Spectrometry, Vol.26(11), pp.1848-1857

11/2015

DOI: 10.1007/s13361-015-1183-1

PMCID: PMC5642106

PMID: 26111518

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Abstract

Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment. Graphical Abstract ᅟ.

Tandem Mass Spectrometry - standards

Peptides - chemistry

Proteomics - standards

Calibration

Kinetics

Proteomics - methods

Tandem Mass Spectrometry - methods

Peptides - analysis

Details

Title: Subtitle: A calibration routine for efficient ETD in large-scale proteomics
Creators: Christopher M Rose - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Matthew J P Rush - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Nicholas M Riley - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Anna E Merrill - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Nicholas W Kwiecien - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Dustin D Holden - Thermo Fisher Scientific, San Jose, CA, USA
Christopher Mullen - Thermo Fisher Scientific, San Jose, CA, USA
Michael S Westphall - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA
Joshua J Coon - Genome Center of Wisconsin, University of Wisconsin, Madison, WI, 53706, USA. jcoon@chem.wisc.edu
Resource Type: Journal article
Publication Details: Journal of the American Society for Mass Spectrometry, Vol.26(11), pp.1848-1857
DOI: 10.1007/s13361-015-1183-1
PMID: 26111518
PMCID: PMC5642106
NLM abbreviation: J Am Soc Mass Spectrom
ISSN: 1044-0305
eISSN: 1879-1123
Publisher: United States
Grant note: R01 GM080148 / NIGMS NIH HHS T32GM008505 / NIGMS NIH HHS 5T15LM007359 / NLM NIH HHS T32 GM008505 / NIGMS NIH HHS T15 LM007359 / NLM NIH HHS
Language: English
Date published: 11/2015
Academic Unit: Pathology; Injury Prevention Research Center
Record Identifier: 9984046935102771

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