The patellogastropod shell proteome

Transcriptome data for Patelloida mimula and MGF data for shell and tissue proteomics analyses from various patellogastropods. The results of the ID nanoLC ESI MS/MS liquid chromatography/mass spectrophotometry are presented for individual specimens (in MGF format) in the “MGF data” folder. Note that the prefix DC is appended to the sample numbers. The spreadsheets output from the proteomics analyses are presented in the subfolders of the “Peptide and protein reports ex SearchGUI” folder. The subfolder “Lottia gigantea proteome on tissue extractions” contains default protein and peptide reports from comparisons with the Lotgi1_GeneModels_FilteredModels1_aa (at ttps://mycocosm.jgi.doe.gov/Lotgi1/Lotgi1.home.html). The subfolder “Lottia gigantea shell proteome comparisons” includes reports for comparisons with the sequences in Lottia_shell_proteome_associated_proteins.fas (see below); reports for comparisons with the file “P_mimula_getorf_output.fasta“ are shown in the subfolder “Patelloida mimula overall comparisons”; and those for “P_mimula_shell_proteome_associated_proteins.fsa” in “Patelloida mimula shell protein comparisons” The “Tables and combined files” folder includes summaries of the combined protein reports for comparisons with the L. gigantea shell-associated proteins (“combined_lottia_shell_protein_reports.csv”) and possible descriptions and Blast2GO identifications of contigs in the Patelloida mimula transcriptome (“P_mimula_orfs_with_possible_identification_blast2GO.csv”). The "Proteins found in all tissues" file lists the proteins found confidently in all the tissue samples using either the Lottia gigantea gene models or the identified ORFS in the Patelloida mimula transcriptome. The "mascot search summary" file lists proteins identified in shell extractions using MASCOT searches (Matrix Science, Boston, MA) of general protein databases conducted by Matthew Fitzhenry of the Australian Proteomics Analysis Facility. There are five files In the folder “Transcriptome and sequence data”. “PM1_ATV9B_TAGCTT_L001_R1 (paired) trimmed (paired) contig list.fa” is the fasta format transcriptome assembly. Amino acid sequences from the getorf analysis of these data are shown in “P_mimula_getorf_output.fasta” (getorf parameters: minimum length of 200 and “translation of regions between START and STOP codons”, with searches on both strands). The “Peroxidases_mafft_aligned.fasta’ file contains gastropod peroxidases aligned by the program MAFFT. Patelloida mimula shell-associated proteins found in the transcriptome are shown in “P_mimula_shell_proteome_associated_proteins.fsa” and L gigantea shell-associated proteins in “Lottia_shell_proteome_associated_proteins.fas”