Machine learning based prediction for peptide drift times in ion mobility spectrometry.
BACKGROUND
Ion mobility spectrometry (IMS) has gained significant traction over the past few years for rapid, high-resolution separations of analytes based upon gas-phase ion structure, with significant potential impacts in the field of proteomic analysis. IMS coupled with mass spectrometry (MS) affords multiple improvements over traditional proteomics techniques, such as in the elucidation of secondary structure information, identification of post-translational modifications, as well as higher identification rates with reduced experiment times. The high throughput nature of this technique benefits from accurate calculation of cross sections, mobilities and associated drift times of peptides, thereby enhancing downstream data analysis. Here, we present a model that uses physicochemical properties of peptides to accurately predict a peptide's drift time directly from its amino acid sequence. This model is used in conjunction with two mathematical techniques, a partial least squares regression and a support vector regression setting.


RESULTS
When tested on an experimentally created high confidence database of 8675 peptide sequences with measured drift times, both techniques statistically significantly outperform the intrinsic size parameters-based calculations, the currently held practice in the field, on all charge states (+2, +3 and +4).


BACKGROUND
The software executable, imPredict, is available for download from http:/omics.pnl.gov/software/imPredict.php


BACKGROUND
rds@pnl.gov


BACKGROUND
Supplementary data are available at Bioinformatics online.
Shah
Anuj R
AR
Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, 999 Battelle Boulevard, Richland, WA 99352, USA.
Agarwal
Khushbu
K
Baker
Erin S
ES
Singhal
Mudita
M
Mayampurath
Anoop M
AM
Ibrahim
Yehia M
YM
Kangas
Lars J
LJ
Monroe
Matthew E
ME
Zhao
Rui
R
Belov
Mikhail E
ME
Anderson
Gordon A
GA
Smith
Richard D
RD
D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D007477:Ions; D013058:Mass Spectrometry; D010455:Peptides / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software; D013057:Spectrum Analysis
D007477:Ions; D010455:Peptides