ETISEQ - Elution time ion sequencing

Data-dependent acquisition of LC-MS/MS data has been the principal method for collecting peptide fragmentation data for protein identification and quantification. However, the method is not without limitations including dynamic range restrictions and reduced selected ion chromatographic resolution for protein quantification. Proteomics data acquired by concurrent peptide fragmentation, which has been variably termed, shotgun CID, parallel CID and MSE, has been demonstrated to overcome such limitations. Nevertheless, concurrent peptide fragmentation data acquisition (CDA) remains to be widely adopted due to the lack of direct compatibility with existing MS/MS spectra identification software.

At the bottom of this page you will find our ETISEQ – elution time ion sequencing software. ETISEQ has been developed and implemented to enable automated conversion of CDA data to pseudo LC-MS/MS data. ETISEQ has been designed to be compatible with all major MS instruments and downstream data analysis software by accepting and outputting datafiles in mzXML format.

In our experiments, we generated CDA data by alternating full survey MS scans with in-source CID data. An example of a lysozyme tryptic digest can be downloaded here.

The standlone executables for Windows (cygwin required) and Linux can be downloaded here. The source code is available to non-commercial users upon request.

Detailed description and testing of ETISEQ:

Wong JWH, Schwhan AB, Downard KM.(2009) ETISEQ - An algorithm for automated elution time ion sequencing of concurrently fragmented peptide ion mixtures for mass spectrometry-based proteomics BMC Bioinformatics 10:244

Parameters:

First scan - first scan to reconstruct MS/MS spectra (defaults to 1)

Last scan - last scan to reconstruct MS/MS spectra (defaults to last scan of file)

Max ions per scan - Maximum number of ions to select for MS/MS reconstruction from each full scan (default 5 ions)

Scans to exclude selected ions - Scans to exclude an ion once it has been selected for MS/MS reconstruction (default 4 scans)

Exclude contaminants - Exclude ions which appear to be non-peptide ions.

*It is recommended that first and last scans be set for the range where peptides are known to elute to increase the speed of conversion.