Using Ion Mobility Data to Improve Peptide Identification: Intrinsic Amino Acid Size Parameters

Abstract

A new method for enhancing peptide ion identification in proteomics analyses using ion mobility data is presented. Ideally, direct comparisons of experimental drift times (tD) with a standard mobility database could be used to rank candidate peptide sequence assignments. Such a database would represent only a fraction of sequences in protein databases and significant difficulties associated with the verification of data for constituent peptide ions would exist. A method that employs intrinsic amino acid size parameters to obtain ion mobility predictions that can be used to rank candidate peptide ion assignments is proposed. Intrinsic amino acid size parameters have been determined for doubly-charged peptide ions from an annotated yeast proteome. Predictions of ion mobilities using the intrinsic size parameters are more accurate than those obtained from a polynomial fit to tD versus molecular weight data. More than a two-fold improvement in prediction accuracy has been observed for a group of arginine-terminated peptide ions twelve residues in length. The use of this predictive enhancement as a means to aid peptide ion identification is discussed and a simple peptide ion scoring scheme is presented.

Examining the Influence of Phosphorylation on Peptide Ion Structure by Ion Mobility Spectrometry-Mass Spectrometry

“…One IMS-based strategy proposed for improving peptide identification is the utilization of intrinsic size parameters (ISPs) [14, 41–45]. ISPs provide the average value each amino acid residue or modification contributes to a peptide’s cross section.…”

Design and Application of a Data-Independent Precursor and Product Ion Repository

“…Outlier data are marked by a black square and are indicative of incorrect identifications or interfered ion intensity measurements. The value and specificity of f1 and f2 increases substantially by supplementing the fragment ion signature with additional orthogonal information, such as standardized peptide retention time [49], drift time [51,55] or collision cross section [56]. Supplementary Figure 3 illustrates the addition of the standardized retention time to f1 and f2, thereby creating a subset ion map for the three fragment ions of interest, indicating substantially improved specificity compared with the results shown in Figs.…”

“…Drift time and collision cross section information were not acquired and/or available for the results described. Drift time is expected to further increase specificity [51], whereas cross section information is believed to be useful for the analysis of post-translationally modified peptides [56]. Median values for f1 and f2 were 31.8% and 28.5%, respectively.…”

“…In addition, accurate precursor and product ion mass information is uploaded into the relational database, as well as, if applied, their associated ion mobility values. Direct comparison of the experimental drift time with a standard mobility database is likely to enhance peptide ion identification [51]. As for mass, drift time values are not normalized or standardized.…”

Challenges and developments in protein identification using mass spectrometry

“…The additional level of separation is exploited in a bottom-up approach in resolving the chimera MS/MS spectra of co-eluting peptides in DDA (if within the mass-selection window) or in DIA (e.g., HDMS E on Waters Q-TOF instruments) [6,26,31,32].…”