ETISEQ – an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics

An algorithm called Elution Time Ion Sequencing (ETISEQ), has been developed to enable automated conversion of concurrent peptide fragmentation data acquisition data to LC-MS/MS data. ETISEQ generates MS/MS-like spectra based on the correlation of precursor and product ion elution profiles. The performance of ETISEQ is demonstrated using concurrent peptide fragmentation data from tryptic digests of standard proteins and whole influenza virus. It is shown that the number of unique peptides identified from the digests is broadly comparable between ETISEQ processed concurrent peptide fragmentation data and the data-dependent acquired LC-MS/MS data.The ETISEQ algorithm has been designed for easy integration with existing MS/MS analysis platforms. It is anticipated that it will popularize concurrent peptide fragmentation data acquisition in proteomics laboratories.Liquid chromatography (LC) coupled electrospray ionization (ESI)-tandem mass spectrometry (MS/MS) [1] has been one of the essential proteomics enabling technologies [2,3]. While technological improvements are continually being made in chromatography [4], mass spectrometry [5,6] and mass spectra interpretation algorithms [7], the detection of lower abundance proteins or proteolytic peptides in complex mixtures remains an obstacle in most proteomics experiments [8,9]. These dynamic range limitations arise in LC-MS/MS experiments, in part, as a result of the inability to completely resolve all peptide ions by liquid chromatography. The use of multidimensional liquid chromatography, where peptides are resolved using two or more separation principles, can improve the dynamic range of detection [10]. Nevertheless, in complex proteomic samples, multiple peptides are still likely to co-elute.In order to acquire tandem mass spectra for as many peptide ions as possible, the vast majority of tandem mass spectrometers are able to perform data-dependent acquisition (DDA). Data-dependent acquisition of LC-MS/MS data has been