Data analysis to provide a revised data set for use in peptide sequencing determination

A method of analyzing product ion data for use in peptide sequence determination by searching a database for matches to mass spectra, the method comprising:

• (a) subjecting a precursor ion with a peak abundance to fragmentation by Electron Capture Dissociation (ECD) to generate product ion data over a spectral range;
• (b) determining the ion product data quality and utilizing only ion product data of at least a predetermined quality, if any, for further processing, in subsequent steps;
• (c) identifying peaks of the ion product data of the at least predetermined quality that represent first order ion products and higher order ion products;
• (d) utilizing the ion product data of the at least predetermined quality and the identified peaks of the first and higher order ion product data to determine, by at least two different charge state analyses, tentative candidate charge states of the first order ion products;
• (e) combining the results of the at least two different charge state analyses to determine candidate charge states of the first order ion products;
• and
• (f) submitting the identified peaks and the determined candidate charge states to a nucleotide sequence database searching program for performing the peptide sequence determination.

A storage medium encoded with machine-readable computer program code for analyzing product ion data for use in peptide sequence determination by searching a database for matches to mass spectra, the storage medium including instructions for:

• (a) obtaining ion product data over a spectral range, the ion product data having been generated by Electron Transfer Dissociation (ETD);
• (b) determining the ion product data quality and utilizing only ion product data of at least a predetermined quality, if any, for further processing;
• (c) identifying peaks of the ion product data of the at least predetermined quality that represent first order ion products and higher order ion products, wherein the first order ion products comprise one or more members of the group consisting of charge reduced precursors, electron transfer products, anion adducts, side chain losses and hydrogen transfer products and wherein the higher order ion products comprise at least one ion product resulting from a dissociation reaction of a first order ion product;
• (d) utilizing the ion product data of the at least predetermined quality and the identified peaks of the first and higher order ion product data to determine candidate charge states of the first order ion products;
• and
• (e) submitting the identified peaks and the determined candidate charge states to a nucleotide sequence database searching program for performing the peptide sequence determination.