Using power spectrum analysis to evaluate (18)O-water labeling data acquired from low resolution mass spectrometers.
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.
Sadygov
Rovshan G
RG
Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas 77555, USA. rovshan.sadygov@utmb.edu
Zhao
Yingxin
Y
Haidacher
Sigmund J
SJ
Starkey
Jonathan M
JM
Tilton
Ronald G
RG
Denner
Larry
L
D000465:Algorithms; D000818:Animals; D002417:Cattle; D002853:Chromatography, Liquid; D019295:Computational Biology / Q000379:methods; D045304:Cytochromes c / Q000032:analysis; D006736:Horses; D007553:Isotope Labeling / Q000379:methods*; D007672:Kidney Cortex / Q000737:chemistry; D051379:Mice; D010103:Oxygen Isotopes / Q000032:analysis; D011506:Proteins / Q000032:analysis* / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012710:Serum Albumin, Bovine / Q000032:analysis; D012984:Software; D013057:Spectrum Analysis / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*
D010103:Oxygen Isotopes; D011506:Proteins; D012710:Serum Albumin, Bovine; D045304:Cytochromes c