MASPIC: Intensity-Based Tandem Mass Spectrometry Scoring Scheme That Improves Peptide Identification at High Confidence

Journal Article · Sat Jan 01 04:00:00 EST 2005 · Analytical Chemistry

DOI:https://doi.org/10.1021/ac0501745· OSTI ID:931842

Narasimhan, Chandrasegaran NMN ^[1]; Tabb, Dave L ^[1]; Verberkmoes, Nathan C ^[1]; Thompson, Melissa R ^[1]; Uberbacher, Edward C ^[1]

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1. ORNL

Algorithmic search engines bridge the gap between large tandem mass spectrometry data sets and the identification of proteins associated with biological samples. Improvements in these tools can greatly enhance biological discovery. We present a new scoring scheme for comparing tandem mass spectra with a protein sequence database. The MASPIC (Multinomial Algorithm for Spectral Profile-based Intensity Comparison) scorer converts an experimental tandem mass spectrum into a m/z profile of probability and then scores peak lists from potential candidate peptides using a multinomial distribution model. The MASPIC scoring scheme incorporates intensity, spectral peak density variations, and m/z error distribution associated with peak matches into a multinomial distribution. The scoring scheme was validated on two standard protein mixtures and an additional set of spectra collected on a complex ribosomal protein mixture from Rhodopseudomonas palustris. The results indicate a 5-15% improvement over Sequest for high-confidence identifications. The performance gap grows as sequence database size increases. Additional tests on spectra from proteinase-K digest data showed similar performance improvements demonstrating the advantages in using MASPIC for studying proteins digested with less specific proteases. All these investigations show MASPIC to be a versatile and reliable system for peptide tandem mass spectral identification.

• Research Organization: Oak Ridge National Laboratory (ORNL)
• Sponsoring Organization: SC USDOE - Office of Science (SC)
• DOE Contract Number: AC05-00OR22725
• OSTI ID: 931842
• Journal Information: Analytical Chemistry, Journal Name: Analytical Chemistry Journal Issue: 23 Vol. 77; ISSN ANCHAM; ISSN 0003-2700
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
ALGORITHMS
DATA PROCESSING
DISTRIBUTION
MASS SPECTRA
MASS SPECTROSCOPY
MIXTURES
PEPTIDES
PERFORMANCE
PROBABILITY
PROTEINS
RHODOPSEUDOMONAS
SPECTRA