1 research outputs found
Deep Coverage Proteomics Identifies More Low-Abundance Missing Proteins in Human Testis Tissue with Q‑Exactive HF Mass Spectrometer
Since 2012, missing proteins (MPs)
investigation has been one of
the critical missions of Chromosome-Centric Human Proteome Project
(C-HPP) through various biochemical strategies. On the basis of our
previous testis MPs study, faster scanning and higher resolution mass-spectrometry-based
proteomics might be conducive to MPs exploration, especially for low-abundance
proteins. In this study, Q-Exactive HF (HF) was used to survey proteins
from the same testis tissues separated by two separating methods (tricine-
and glycine-SDS-PAGE), as previously described. A total of 8526 proteins
were identified, of which more low-abundance proteins were uniquely
detected in HF data but not in our previous LTQ Orbitrap Velos (Velos)
reanalysis data. Further transcriptomics analysis showed that these
uniquely identified proteins by HF also had lower expression at the
mRNA level. Of the 81 total identified MPs, 74 and 39 proteins were
listed as MPs in HF and Velos data sets, respectively. Among the above
MPs, 47 proteins (43 neXtProt PE2 and 4 PE3) were ranked as confirmed
MPs after verifying with the stringent spectra match and isobaric
and single amino acid variants filtering. Functional investigation
of these 47 MPs revealed that 11 MPs were testis-specific proteins
and 7 MPs were involved in spermatogenesis process. Therefore, we
concluded that higher scanning speed and resolution of HF might be
factors for improving the low-abundance MP identification in future
C-HPP studies. All mass-spectrometry data from this study have been
deposited in the ProteomeXchange with identifier PXD004092