Abstract
Examination of multiple proteomics datasets within or between species increases the reliability of protein identification. We report here proteomes of inner-ear hair bundles from three species (chick, mouse, and rat), which were collected on LTQ or LTQ Velos ion-trap mass spectrometers; the constituent proteins were quantified using MS2 intensities, which are the summed intensities of all peptide fragmentation spectra matched to a protein. The data are available via ProteomeXchange with identifiers PXD002410 (chick LTQ), PXD002414 (chick Velos), PXD002415 (mouse Velos), and PXD002416 (rat LTQ). The two chick bundle datasets compared favourably to a third, already-described chick bundle dataset, which was quantified using MS1 peak intensities, the summed intensities of peptides identified by high-resolution mass spectrometry (PXD000104; updated analysis in PXD002445). The mouse bundle dataset described here was comparable to a different mouse bundle dataset quantified using MS1 intensities (PXD002167). These six datasets will be useful for identifying the core proteome of vestibular hair bundles.
Highlights
Background & SummaryThe inner ear’s sensory hair cells detect mechanical stimuli from the environment using their hair bundles, each of which consists of ~100 actin-filled stereocilia and an axonemal kinocilium[1]
Shotgun proteomics[6,7], which is used as a discovery technique, offers quantitation even of unexpected proteins
By comparing results with standard proteins diluted in an E. coli protein background, we demonstrated that normalized summed MS2 intensities derived from ion-trap mass spectrometer data yields quantitation results that are nearly as accurate as measurement of those same proteins with MS1 peak areas using an Orbitrap mass spectrometer[8]
Summary
The inner ear’s sensory hair cells detect mechanical stimuli from the environment using their hair bundles, each of which consists of ~100 actin-filled stereocilia and an axonemal kinocilium[1]. Complicating protein identification, mass spectrometry suffers from the wellknown peptide assignment problem[9], where identical peptides found in two different proteins cannot be definitively assigned to one or the other For these reasons, it is essential to compare bundle proteomes of one species with those of other species, which should lead to the most reliable results. We have previously generated chick and mouse hair bundle and utricle datasets using MS1 peak areas for quantitation[2,10], and we show here that the ion-trap data compares favourably to the Orbitrap-acquired MS1 data. To further assist in achieving this goal, we provide combined tables with common protein grouping for the six chick datasets and, separately, for all twelve datasets analysed here
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