Improving Collision Induced Dissociation (CID), High Energy Collision Dissociation (HCD), and Electron Transfer Dissociation (ETD) Fourier Transform MS/MS Degradome-Peptidome Identifications Using High Accuracy Mass Information

Journal Article · Fri Feb 03 04:00:00 EST 2012 · Journal of Proteome Research

DOI:https://doi.org/10.1021/pr200597j· OSTI ID:1037522

Shen, Yufeng; Tolic, Nikola; Purvine, Samuel O; Smith, Richard D

Identification of peptides through analysis of peptide ion fragmentation mass spectra is key to proteomic/peptidomic studies. Advanced mass spectrometry has enabled measurement of peptide fragments with {approx}ppm mass error levels; however, mass accuracy has not been widely utilized in broad aspects of peptide identification. In this work we describe how peptide high-precision fragments measured with Fourier transform mass spectrometry can provide a powerful discriminative capability to distinguish true peptide 'hits' from possible incorrect peptides. For identification of peptides having multiple termini and carrying multiple charges, we show that the simple utilization of high-precision mass fragments information results in improved peptide analysis coverage and consistency, with coverage of >95% peptides identified totally from different spectral scoring and peptide statistic probability methods developed for moderate accuracy mass spectral peptide identification.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 1037522
• Report Number(s): PNNL-SA-79420; 40072; 400412000
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research Journal Issue: 2 Vol. 11; ISSN 1535-3893
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
ACCURACY
DISSOCIATION
ELECTRON TRANSFER
Environmental Molecular Sciences Laboratory
FRAGMENTATION
FT MS/MS.
MASS SPECTRA
MASS SPECTROSCOPY
PEPTIDES
PROBABILITY
STATISTICS
mass spectrometry
peptides