Neutral Loss Is a Very Common Occurrence in Phosphotyrosine-Containing Peptides Labeled with Isobaric Tags

While developing a multiplexed phosphotyrosine peptide quantification assay, an unexpected observation was made: significant neutral loss from phosphotyrosine (pY) containing peptides. Using a 2000-member peptide library, we sought to systematically investigate this observation by comparing unlabeled peptides with the two highest-plex isobaric tags (iTRAQ8 and TMT10) across CID, HCD, and ETD fragmentation using high resolution high mass accuracy Orbitrap instrumentation. We found pY peptide neutral loss behavior was consistent with reduced proton mobility, and does not occur during ETD. The site of protonation at the peptide N-terminus changes from a primary to a tertiary amine as a result of TMT labeling which would increase the gas phase basicity and reduce proton mobility at this site. This change in fragmentation behavior has implications during instrument method development and interpretation of MS/MS spectra, and therefore ensuing follow-up studies. We show how sites not localized to tyrosine by search and site localization algorithms can be confidently reassigned to tyrosine using neutral loss and phosphotyrosine immonium ions. We believe these findings will be of general interest to those studying pY signal transduction using isobaric tags.

Transcriptomic and iTRAQ proteomic approaches reveal novel short-term hyperosmotic stress responsive proteins in the gill of the Japanese eel (Anguilla japonica)

Osmoregulation is critical for the survival of fishes that migrate between freshwater (FW) and seawater (SW). The eel, as a catadromous fish, has been studied for decades to reveal the mechanisms of osmoregulation. These studies, however, have been limited by the lack of a genomic database to decipher the mechanism of osmoregulation at a molecular level. In this study, using high-throughput transcriptomic and proteomic technologies, we have provided the first genome-wide study to identify hyperosmotic responsive proteins in the gills of the Japanese eel. Deep sequencing using the 454 platform produced over 660,000 reads with a mean length of 385 bp. For the proteomic study, we collected gill samples from three different treatment groups of fish that had fully adapted to FW/SW or were transferred from FW to SW for 6h. The respective group of gill proteins were extracted and labeled using an isobaric tag for relative and absolute quantitation (iTRAQ) using LTQ-Orbitrap, a high resolution mass spectrometer. Among the 1519 proteins identified from the gill samples, 96 proteins were differentially expressed between FW and SW adapted fish. Nineteen hyperosmotic responsive proteins were detected (10 up-regulated and 9 down-regulated proteins) after 6h post FW to SW transfer.

BIOLOGICAL SIGNIFICANCE

The study has provided the most comprehensive, targeted investigation of eel gill proteins to date, and shown the powerfulness of combining transcriptomic and proteomic approaches to provide molecular insights of osmoregulation mechanisms in a non-model organism, eel.

Mass Spectrometry Imaging and Structural Analysis of Lipids Directly on Tissue Specimens by Using a Spiral Orbit Type Tandem Time-of-Flight Mass Spectrometer, SpiralTOF-TOF

In this paper, we report the use of mass spectrometry imaging and structural analysis of lipids directly on a tissue specimen, carried out by means of matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry, using a combination of spiral orbit-type and reflectron-type time-of-flight mass spectrometers. The most intense peak observed in the mass spectrum from a brain tissue specimen was confirmed as phosphatidylcholine (34 : 1) [M+K](+), using tandem mass spectrometry. The charge remote fragmentation channels, which are characteristically observed using high-energy collision-induced dissociation, contributed significantly to this confirmation. Accurate mass analysis was further facilitated by mass correction using the confirmed peak. In mass spectrometry imaging, the high resolving power of our system could separate doublet peak of less than 0.1 u difference, which would otherwise be problematic when using a low-resolution reflectron type time-of-flight mass spectrometer. Two compounds, observed at m/z 848.56 and 848.65, were found to be located in complementary positions on a brain tissue specimen. These results demonstrate the importance of a high-performance tandem time-of-flight mass spectrometer for mass spectrometry imaging and analysis of observed compounds, to allow distinction between biological molecules.