DOI: 10.5061/dryad.w0vt4b8z5
title: Data from: Transcriptome and exosome proteome analyses provide insights into the mantle exosome involved in nacre color formation of pearl oyster Pinctada fucata martensii

description: The pearl oyster Pinctada fucata martensii is an economically
 important species of marine pearl culture, and tissue of mantle plays an
 essential role in pearl formation. Here, the extracted
 exosomes from mantle of P. f. martensii were analyzed by
 quantitative protein TMT sequencing. We wanted to verify if exosomes are
 the important vehicle in the process of biomineralization (e.g., pearl and
 shell formation), especially the color formation in shellfish. Finally, we
 got some results which indicated the importance of exosomes in sides of
 proteins, and it can also contribute to other researches related to the
 exosomes or pearl oyster.
description: All the individuals were
 collected in the Liusha Bay, Leizhou (2022), and this dataset described
 the peptide groups and proteins of <em>Pinctada fucata
 martensii</em> in mantle using TMT method.
description: # Data from: Transcriptome and exosome proteome analyses provide insights
 into the mantle exosome involved in nacre color formation of pearl oyster
 Pinctada fucata martensii **Paper:** Transcriptome and exosome proteome
 analyses provide insights into the mantle exosome involved in nacre color
 formation of pearl oyster *Pinctada fucata martensii* **Authors:** Yong
 Liu, Ziman Wang, Chengao Guo, Siyao Li, Youxi Li, Ronglian Huang, Yuewen
 Deng *** ### **File list** HFX\_TMT\_F\_PeptideGroups.xls
 HFX\_TMT\_F\_Proteins.xls *** ### **File descriptions** The process of
 proteome identification involves enzymatic digestion of proteins into
 peptides, identification of peptides by mass spectrometry, and later
 derivation of possible proteins. Therefore, in order to assess the overall
 situation of the obtained proteomic data, we can evaluate the two levels
 of peptides and proteins in terms of each physicochemical property and
 other aspects. * **HFX\_TMT\_F\_PeptideGroups.xls: peptide groups in
 exosome of mantle by TMT** The variables in this file: * Peptide Groups
 Peptide Group ID: Peptide number; * Confidence: High=FDR&lt;0.01,
 medium=FDR&lt;0.05; * Annotated Sequence: Amino acids before and after
 annotated peptides; * Modifications: Type of peptide modification; *
 Qvality PEP: Posterior Error Probability of the identification, this value
 essentially operates as a p-value, where smaller is better; * Qvality
 q-value: Corrected FDR (false discovery rate), smaller values are better;
 * Proteins: Number of proteins, how many proteins contain this peptide; *
 Master Protein Accessions: Login number of the best matching protein in
 the proteome; * Positions in Master Proteins: Position of the peptide
 sequence on the protein; * Modifications in Master Proteins: Modification
 site; * Missed Cleavages: Number of missed cleavages; * Theo. MH+ [Da]:
 Molecular weight of the measured peptide in theory; * Sequence Length; *
 Abundances (Scaled) & Abundances (Normalized): Corrected peptide
 quantification values; * Abundance: Raw quantitative values; * Quan Info:
 Indicates whether the peptide is used for quantification; * Found in
 Sample: Indication of identification in the sample; * Charge: Sequest HT:
 Number of charges on the peptide; * m/z [Da]: Sequest HT: M/Z of peptides;
 * DeltaM [ppm]: Sequest HT: Error between detected and theoretical
 molecular weights; * RT [min]: Sequest HT: retention time.
 **HFX\_TMT\_F\_Proteins.xls: proteins in exosome of mantle by TMT** The
 variables in this file: * Proteins Unique Sequence ID: Number of unique
 peptides identified; * Protein FDR Confidence: Combined:
 High=FDR&lt;0.01, medium=FDR&lt;0.05; * Master: Indicates whether
 it is a Master protein; * Accession: Protein accession number, the
 accession number of the protein in that proteome in the database matched
 to the database, the main sources of the database are UniProt/NCBI, other
 species-specific databases, and customer-supplied databases (derived from
 transcriptome data); * Description: information describing the function of
 the protein in the database, containing the protein name, species name
 (OS=species Latin name), and gene name (GN=\*\*); * Exp. q-value:
 Combined: Demonstrate the q-value, which will be greater than a certain
 threshold value; * Coverage [%]: Coverage (percentage), the number of
 amino acids identified by the protein on mass spectrometry analysis as a
 proportion of the total number of amino acids of the highest scoring
 protein in the proteome; * Peptides: Peptide number, identifies the total
 number of peptides in a given proteome, which corresponds to the number of
 peptides used for characterization; * PSMs: number of secondary peptide
 maps. Reactive peptides were captured by mass spectrometry, with a higher
 average number of PSMs indicating a higher reliability of individual
 peptide identification; * Unique Peptides: The number of peptides that are
 specialized to a particular proteome; * AAs: number of amino acids; * MW:
 molecular weight of protein; * calc. pI: calculated isoelectric point of
 the protein; * Score Sequest HT: Sequest HT: Protein search library
 scoring: sum of peptide scores; * Abundances (Scaled) & Abundances
 (Normalized): Corrected peptide quantification values; * Abundance: Raw
 quantitative values; * Found in Sample: Indicates whether the current
 sample was identified; * Protein Groups: Number of protein groups; *
 Modifications: Types of protein modifications. **You need to open these
 two files in Microsoft Excel.** **Note**: Missing values are denoted by
 N/A.