Simulating and validating proteomics data and search results

Abstract

The computational simulation of complete proteomic data sets and their utility to validate detection and interpretation algorithms, to aid in the design of experiments and to assess protein and peptide false discovery rates is presented. The simulation software has been developed for emulating data originating from data-dependent and data-independent LC-MS workflows. Data from all types of commonly used hybrid mass spectrometers can be simulated. The algorithms are based on empirically derived physicochemical liquid and gas phase models for proteins and peptides. Sample composition in terms of complexity and dynamic range, as well as chromatographic, experimental and MS conditions, can be controlled and adjusted independently. The effect of on-column amounts, gradient length, mass resolution and ion mobility on search specificity will be demonstrated using tryptic peptides from human and yeast cellular lysates simulated over five orders of magnitude in dynamic range. Initial justification of the simulated data sets is achieved by comparing and contrasting the in silico simulated data to experimentally derived results from a 48 protein mixture, spanning a similar magnitude of five orders of magnitude. Additionally, experimental data from replicate and dilutions series experiments will be utilized to determine error rates at the peptide and protein level with respect to mass, area, retention and drift time. The data presented reveal a high degree of similarity at the ion detection, peptide and protein level when analyzed under similar conditions.

Improving Qualitative and Quantitative Performance for MSE-based Label-free Proteomics

“…Indeed, it has been estimated that at 25000 fwhm mass spectrometry resolution, around 35 and 20% of the EMRTs are composite in MS E and HDMS E , respectively. 43 Identification Transfer. Identification transfer is the process of assigning QR EMRTs with a sequence by pairing it with an IR peptide in order to retrieve quantitative measurement from QR.…”

A Computational Tool to Detect and Avoid Redundancy in Selected Reaction Monitoring

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

“…Multidimensional chromatography, when properly implemented, should have a positive impact on overall separation capacity [13,14]. Alternatively, an additional dimension of separation such as ion mobility (IM) can be very effective in reducing chimeric and composite interferences and the benefits of this approach have been demonstrated in dataindependent analysis (DIA) strategies [14,15]. The application and combination of IM with DDA is less common.…”