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  • Fig shows the representative protein sequence

    2018-10-25

    Fig. 2 shows the representative protein sequence identified with confidence interval ≥95% in the study. (A) Protein sequence with identified peptide sequences highlighted in green. (B) Table with details of identified peptides. (C) MS/MS spectrum of the identified peptide MANQANIPVITLDR. (D) Assignment of fragmentation for the identified peptide. Fig. 3 shows the representative protein sequence identified with confidence level <95% but ≥50% in the study. (A) Protein sequence with identified peptide sequences highlighted in yellow. (B) Table with details of identified peptides. (C) MS/MS spectrum of the identified peptide IEDDLKVR. (D) Assignment of fragmentation for the identified peptide.
    Materials and methods
    Acknowledgments This work was supported by a research grant from the Singapore National Research Foundation under its Environmental and Water Technologies Strategic Research Programme and administered by the Environment and Water Industry Programme Office (EWI) of the PUB, Singapore׳s National Water Agency, (NRF-EWI-IRIS, R-706-000-010-272 and R-706-000-040-279). We also acknowledge Keppel Club, Singapore, for granting us permission to collect the mangrove leaf samples from Berlayer Creek.
    Data, experimental design, materials and methods The data in the PRIDE Archive provide a comprehensive protein identification of different stages of peanut gynophores [2]. This data can be analyzed using a variety of commercial tandem mass spectrometry tools. The data provide variable information for researchers to study the functions of potential key SBI-0206965 in peanut pod development. The following sections present a detail description about the materials and methods, will help the investigators to design novel procedures that rely on 1 DE with nano LC–MS/MS approaches (Fig. 1).
    Acknowledgments This work is supported by the Ministry of Science and Technology of China (2013AA102602, 2011BAD35B04, and 2012BAD33B07), the National Natural Science Foundation of China (31101427), Shandong Provincial Foundation (BS2014SW017, ZR2015YL061), Shandong Province Taishan Scholar Foundation (tshw20100416), and the Young Talents Training Program of Shandong Academy of Agricultural Sciences.
    Specifications Table
    Experimental design and data Fig. 1 shows the schematic flowchart of experiments, data processing and results that were presented in.xls tables. s Amphipods were sampled from rivers in mid-eastern France or from laboratory husbandries. Ovaries were taken and then treated for shotgun mass spectrometry analysis. Five biological replicates per species were analyzed, resulting in 25 proteome samples. The peptides from each sample were analyzed by tandem mass spectrometry with an LTQ-Orbitrap-XL spectrometer (Thermo). A first round of MS/MS spectra search was done with four different databases to assign them to tryptic peptide sequences. Two databases derived from RNASeq were used, GFOSS, described by Trapp et al. [2] which is G. fossarum specific and PHAWA, P. hawaiensis specific [3]. These two databases contain the six frame translation of the sequenced transcriptome. As a consequence, these databases comprised both the true protein sequences and a lot of false translated protein sequences as usually handled by proteogenomics [4,5]. To complete the search, two more databases, the Daphnia pulex whole-genome protein sequence database and the non-redundantd database NCBInr were used. In this case, the MS/MS spectra files acquired on the five biological replicates of the same species were merged before spectra assignation. The list of the overall assigned spectra and the peptide characteristics are described in Table S1, while the proteins identified are listed in Table S2. Table S3 summarizes the ratio of each database contribution in terms of spectra assignation. The 2192 identified proteins were then selected to create a specific ovary amphipod restricted database, which was named AMPHI-MERGE. For the second step, spectra assignation of ovary proteome was performed with the AMPHI-MERGE database, for each of the 25 animal proteomes separately. The list of assigned spectra and the corresponding peptide characteristics are described in Table S4 whereas the proteins identified and their spectral count quantitation are listed in Table S5. Then, protein homologs were searched for the resulting identified proteins using the Blastp alignment tool. Homologous proteins were found for almost the entire protein list. Based on their most-closely homologs (same protein GeneID), the detected proteins were grouped together under one protein group. Finally, homolog proteins GeneID were used to associate a function to the detected proteins with the Gene Ontology annotation system. These data were used to define the core ovary proteome of the five amphipods [1].