TY - JOUR
T1 - Parallel reaction monitoring using quadrupole-Orbitrap mass spectrometer
T2 - Principle and applications
AU - Bourmaud, Adele
AU - Gallien, Sebastien
AU - Domon, Bruno
N1 - Funding Information:
This work was supported by PEARL (CPIL) and CORE (PORT-HPP) grants from the Fonds National de la Recherche Luxembourg (FNR). Thermo Scientific is acknowledged for support in the development of the PRM methods.
Publisher Copyright:
© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
PY - 2016/8/1
Y1 - 2016/8/1
N2 - Targeted mass spectrometry-based approaches are nowadays widely used for quantitative proteomics studies and more recently have been implemented on high resolution/accurate mass (HRAM) instruments resulting in a considerable performance improvement. More specifically, the parallel reaction monitoring technique (PRM) performed on quadrupole-Orbitrap mass spectrometers, leveraging the high resolution and trapping capabilities of the instrument, offers a clear advantage over the conventional selected reaction monitoring (SRM) measurements executed on triple quadrupole instruments. Analyses performed in HRAM mode allow for an improved discrimination between signals derived from analytes and those resulting from matrix interferences translating in the reliable quantification of low abundance components. The purpose of the study defines various implementation schemes of PRM, namely: (i) exploratory experiments assessing the detectability of very large sets of peptides (100–1000), (ii) wide-screen analyses using (crude) internal standards to obtain statistically meaningful (relative) quantitative analyses, and (iii) precise/accurate quantification of a limited number of analytes using calibrated internal standards. Each of the three implementation schemes requires specific acquisition methods with defined parameters to appropriately control the acquisition during the actual peptide elution. This tutorial describes the different PRM approaches and discusses their benefits and limitations in terms of quantification performance and confidence in analyte identification.
AB - Targeted mass spectrometry-based approaches are nowadays widely used for quantitative proteomics studies and more recently have been implemented on high resolution/accurate mass (HRAM) instruments resulting in a considerable performance improvement. More specifically, the parallel reaction monitoring technique (PRM) performed on quadrupole-Orbitrap mass spectrometers, leveraging the high resolution and trapping capabilities of the instrument, offers a clear advantage over the conventional selected reaction monitoring (SRM) measurements executed on triple quadrupole instruments. Analyses performed in HRAM mode allow for an improved discrimination between signals derived from analytes and those resulting from matrix interferences translating in the reliable quantification of low abundance components. The purpose of the study defines various implementation schemes of PRM, namely: (i) exploratory experiments assessing the detectability of very large sets of peptides (100–1000), (ii) wide-screen analyses using (crude) internal standards to obtain statistically meaningful (relative) quantitative analyses, and (iii) precise/accurate quantification of a limited number of analytes using calibrated internal standards. Each of the three implementation schemes requires specific acquisition methods with defined parameters to appropriately control the acquisition during the actual peptide elution. This tutorial describes the different PRM approaches and discusses their benefits and limitations in terms of quantification performance and confidence in analyte identification.
KW - High resolution accurate mass
KW - Parallel reaction monitoring
KW - Precise quantification
KW - Targeted proteomics
KW - Technology
UR - http://www.scopus.com/inward/record.url?scp=84983293026&partnerID=8YFLogxK
U2 - 10.1002/pmic.201500543
DO - 10.1002/pmic.201500543
M3 - Review article
C2 - 27145088
AN - SCOPUS:84983293026
SN - 1615-9853
VL - 16
SP - 2146
EP - 2159
JO - Proteomics
JF - Proteomics
IS - 15-16
ER -