Improving CID, HCD, and ETD FT MS/MS degradome-peptidome identifications using high accuracy mass information

Journal Article · Mon Nov 07 04:00:00 EST 2011 · Journal of Proteome Research

DOI:https://doi.org/10.1021/pr200597j· OSTI ID:1030469

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

The peptidome (i.e. processed and degraded forms of proteins) of e.g. blood can potentially provide insights into disease processes, as well as a source of candidate biomarkers that are unobtainable using conventional bottom-up proteomics approaches. MS dissociation methods, including CID, HCD, and ETD, can each contribute distinct identifications using conventional peptide identification methods (Shen et al. J. Proteome Res. 2011), but such samples still pose significant analysis and informatics challenges. In this work, we explored a simple approach for better utilization of high accuracy fragment ion mass measurements provided e.g. by FT MS/MS and demonstrate significant improvements relative to conventional descriptive and probabilistic scores methods. For example, at the same FDR level we identified 20-40% more peptides than SEQUEST and Mascot scoring methods using high accuracy fragment ion information (e.g., <10 mass errors) from CID, HCD, and ETD spectra. Species identified covered >90% of all those identified from SEQUEST, Mascot, and MS-GF scoring methods. Additionally, we found that the merging the different fragment spectra provided >60% more species using the UStags method than achieved previously, and enabled >1000 peptidome components to be identified from a single human blood plasma sample with a 0.6% peptide-level FDR, and providing an improved basis for investigation of potentially disease-related peptidome components.

• 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: 1030469
• Report Number(s): PNNL-SA-81060; 40072; KP1601010
• Journal Information: Journal of Proteome Research, Journal Name: Journal of Proteome Research
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
ACCURACY
BLOOD
BLOOD PLASMA
CID
DISEASES
DISSOCIATION
ETD
Environmental Molecular Sciences Laboratory
FT MS/MS
HCD
PEPTIDES
PROTEINS
SPECTRA
degradome
merging of spectra
scoring of spectra.
non-tryptic peptides
peptides
peptidome