LTQ‐iQuant: A freely available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments

Pulsed Q dissociation enables combining LTQ ion trap instruments with isobaric peptide tagging. Unfortunately, this combination lacks a technique which accurately reports protein abundance ratios and is implemented in a freely available, flexible software pipeline. We developed and implemented a technique assigning collective reporter ion intensity‐based weights to each peptide abundance ratio and calculating a protein's weighted average abundance ratio and p‐value. Using an iTRAQ‐labeled standard mixture, we compared our technique's performance to the commercial software MASCOT, finding that it performed better than MASCOT's nonweighted averaging and median peptide ratio techniques, and equal to its weighted averaging technique. We also compared performance of the LTQ‐Orbitrap plus our technique to 4800 MALDI TOF/TOF plus Protein Pilot, by analyzing an iTRAQ‐labeled stem cell lysate. We found highly correlated protein abundance ratios, indicating that the LTQ‐Orbitrap plus our technique yields results comparable to the current standard. We implemented our technique in a freely available, automated software pipeline, called LTQ‐iQuant, which is mzXML‐compatible; supports iTRAQ 4‐plex and 8‐plex LTQ data; and can be modified for and have weights trained to a user's LTQ and other isobaric peptide tagging methods. LTQ‐iQuant should make LTQ instruments and isobaric peptide tagging accessible to more proteomic researchers.