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<0.01, medium=FDR<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<0.01, medium=FDR<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.