Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer.
Anal Chem
; 87(2): 1241-9, 2015 Jan 20.
Article
in En
| MEDLINE
| ID: mdl-25521595
ABSTRACT
As a driver for many biological processes, phosphorylation remains an area of intense research interest. Advances in multiplexed quantitation utilizing isobaric tags (e.g., TMT and iTRAQ) have the potential to create a new paradigm in quantitative proteomics. New instrumentation and software are propelling these multiplexed workflows forward, which results in more accurate, sensitive, and reproducible quantitation across tens of thousands of phosphopeptides. This study assesses the performance of multiplexed quantitative phosphoproteomics on the Orbitrap Fusion mass spectrometer. Utilizing a two-phosphoproteome model of precursor ion interference, we assessed the accuracy of phosphopeptide quantitation across a variety of experimental approaches. These methods included the use of synchronous precursor selection (SPS) to enhance TMT reporter ion intensity and accuracy. We found that (i) ratio distortion remained a problem for phosphopeptide analysis in multiplexed quantitative workflows, (ii) ratio distortion can be overcome by the use of an SPS-MS3 scan, (iii) interfering ions generally possessed a different charge state than the target precursor, and (iv) selecting only the phosphate neutral loss peak (single notch) for the MS3 scan still provided accurate ratio measurements. Remarkably, these data suggest that the underlying cause of interference may not be due to coeluting and cofragmented peptides but instead from consistent, low level background fragmentation. Finally, as a proof-of-concept 10-plex experiment, we compared phosphopeptide levels from five murine brains to five livers. In total, the SPS-MS3 method quantified 38â¯247 phosphopeptides, corresponding to 11â¯000 phosphorylation sites. With 10 measurements recorded for each phosphopeptide, this equates to more than 628â¯000 binary comparisons collected in less than 48 h.
Full text:
1
Database:
MEDLINE
Main subject:
Phosphopeptides
/
Mass Spectrometry
/
Brain Chemistry
/
Chromatography, High Pressure Liquid
/
Proteomics
/
Liver
Type of study:
Evaluation_studies
Limits:
Animals
Language:
En
Journal:
Anal Chem
Year:
2015
Type:
Article
Affiliation country:
United States