The utility of accurate mass and LC elution time information in the analysis of complex proteomes

Journal Article · Mon Aug 01 00:00:00 EDT 2005 · Journal of the American Society for Mass Spectrometry, 16(8):1239-1249

DOI:https://doi.org/10.1016/j.jasms.2005.05.009· OSTI ID:859971

Norbeck, Angela D.; Monroe, Matthew E.; Adkins, Joshua N.; Anderson, Kevin K.; Daly, Don S.; Smith, Richard D.

Theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity and possible utility of combined peptide accurate mass and predicted LC normalized elution time (NET) information. The uniqueness of each peptide was evaluated using its combined mass (+/- 5 ppm and 1 ppm) and NET value (no constraint, +/- 0.05 and 0.01 on a 0-1 NET scale). The set of peptides both underestimates actual biological complexity due to the lack of specific modifications, and overestimates the expected complexity since many proteins will not be present in the sample or observable on the mass spectrometer because of dynamic range limitations. Once a peptide is identified from an LCMS/MS experiment, its mass and elution time is representative of a unique fingerprint for that peptide. The uniqueness of that fingerprint in comparison to that for the other peptides present is indicative of the ability to confidently identify that peptide based on accurate mass and NET measurements. These measurements can be made using HPLC coupled with high resolution MS in a high-throughput manner. Results show that for organisms with comparatively small proteomes, such as Deinococcus radiodurans, modest mass and elution time accuracies are generally adequate for peptide identifications. For more complex proteomes, increasingly accurate easurements are required. However, the majority of proteins should be uniquely identifiable by using LC-MS with mass accuracies within +/- 1 ppm and elution time easurements within +/- 0.01 NET.

• Research Organization: Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 859971
• Report Number(s): PNNL-SA-44395; JAMSEF; 400412000
• Journal Information: Journal of the American Society for Mass Spectrometry, 16(8):1239-1249, Vol. 16, Issue 8; ISSN 1044-0305
• Country of Publication: United States
• Language: English

Related Subjects

Protein Identification
High-Throughput
Liquid-Chromatography
Yeast Proteome
Spectrometry
Prediction
Tags
Technology
Retention
Mixtures