In a previous comprehensive study, we compared the performance of LTQ Orbitrap XL and QSTAR® Elite for peptide identifications in complex mixtures.10 In this study, peptides labeled with four iTRAQ mass tags were analyzed using both the LTQ Orbitrap XL (referred to in the text as LTQ Orbitrap) and QSTAR Elite (Applied Biosystems, Foster City, CA) (referred to in the text as QqTOF) to assess the performance of both platforms in a quantitative proteomics experiment. We deliberately chose a relatively simple peptide mixture with high peptide concentrations and limited dynamic range for these comparative experiments so not to disadvantage the slower scanning, less sensitive instrument (QqTOF) when assessing protein sequence coverage, quantitative precision and accuracy.10 The experiments run on the LTQ Orbitrap were performed at the Thermo Fisher Scientific labs in San Jose, CA. QqTOF analyses were performed by an independent third party laboratory. The experiments were conducted by a certified SCIEX®-trained operator to ensure the highest possible quality results.

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