Dataset Information


Using power spectrum analysis to evaluate (18)O-water labeling data acquired from low resolution mass spectrometers.

ABSTRACT: We describe a method for ratio estimations in (18)O-water labeling experiments acquired from low resolution isotopically resolved data. The method is implemented in a software package specifically designed for use in experiments making use of zoom-scan mode data acquisition. Zoom-scan mode data allow commonly used ion trap mass spectrometers to attain isotopic resolution, which makes them amenable to use in labeling schemes such as (18)O-water labeling, but algorithms and software developed for high resolution instruments may not be appropriate for the lower resolution data acquired in zoom-scan mode. The use of power spectrum analysis is proposed as a general approach that may be uniquely suited to these data types. The software implementation uses a power spectrum to remove high-frequency noise and band-filter contributions from coeluting species of differing charge states. From the elemental composition of a peptide sequence, we generate theoretical isotope envelopes of heavy-light peptide pairs in five different ratios; these theoretical envelopes are correlated with the filtered experimental zoom scans. To automate peptide quantification in high-throughput experiments, we have implemented our approach in a computer program, MassXplorer. We demonstrate the application of MassXplorer to two model mixtures of known proteins and to a complex mixture of mouse kidney cortical extract. Comparison with another algorithm for ratio estimations demonstrates the increased precision and automation of MassXplorer.


PROVIDER: S-EPMC2922858 | BioStudies | 2010-01-01

REPOSITORIES: biostudies

Similar Datasets

2011-01-01 | S-EPMC3070069 | BioStudies
2014-01-01 | S-EPMC4037588 | BioStudies
1000-01-01 | S-EPMC3044303 | BioStudies
2008-01-01 | S-EPMC5831358 | BioStudies
2019-01-01 | S-EPMC7017751 | BioStudies
2015-01-01 | S-EPMC4350035 | BioStudies
2019-01-01 | S-EPMC7150547 | BioStudies
2020-01-01 | S-EPMC7071446 | BioStudies
2010-01-01 | S-EPMC2896157 | BioStudies
2016-01-01 | S-EPMC5031130 | BioStudies