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Proteomic Profile of Daphnia pulex using Data‐Independent Acquisition Mass Spectrometry and Ion Mobility Separation
Author(s) -
Steevensz Aaron,
Gombar Robert,
Vergilino Roland,
Cristescu Melania E.,
Vacratsis Panayiotis O.
Publication year - 2018
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201700460
Subject(s) - daphnia pulex , proteome , pulex , biology , proteomics , label free quantification , mass spectrometry , computational biology , gammarus pulex , chromatography , biochemistry , chemistry , quantitative proteomics , daphnia , ecology , gene , crustacean , amphipoda
Daphnia pulex is a keystone species for aquatic habitats and an ecological/evolution model organism. Although significant progress has been made on characterizing its genome, the D. pulex proteome remains largely uncharacterized partially due to abnormally high protein degradation during homogenization and emphasis on genomic analysis. In this study, various sample preparation and mass spectrometry acquisition methods are performed for the purpose of improving D. pulex proteome exploration. Benefits for employing both in‐gel and in‐solution methods of trypsin digestion are observed. Furthermore, acquisition methods employing ion mobility separation greatly increase peptide identification and more than doubled the proteome coverage. Bioinformatic analysis suggests that mitochondrial and hydrolytic activities are enriched in D. pulex compared to closely related invertebrates or Homo sapiens . Also, novel D. pulex proteins possessing putative genome modifying functional domains are identified. Data are available via ProteomeXchange with identifier PXD008455.