Supporting Information for manuscript "Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation"
Emma B. Timmins-Schiffman, Grace A. Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn, Steven B. Roberts (2016) Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation bioRxiv 094615; doi: https://doi.org/10.1101/094615
S1-Pgenerosa-gonad-protein-v3.fasta
Deduced protein sequences derived from gonad transcriptome sequencing.
S2-comet.params Parameter file used in Comet searches for the DDA data.
S3-technical-reps.pdf NMDS of the whole proteomic profiles (DDA data) for the three biological replicates and corresponding three technical replicates for each sex and maturation stage. Blue points represent female proteomes and orange represent male. Shapes and shade (light to dark) represent the different stages: circles for early-stage, squares for mid-stage, and triangles for late-stage.
S4-technical-reps-box-plots.pdf Box plot of the coefficients of variation for protein spectral counts from DDA data A) across technical replicates for each geoduck biological replicate and B) across biological replicates for each sex-maturation stage. CVs were calculated in R using the raster package. X-axis labels correspond to the geoduck sex and maturation stage, indicated by e.g. “EF3” represents early-stage female sample 3. The boxes represent the upper and lower quartiles of the data distribution; horizontal black line represents median value; “whiskers” extend to the greatest and least values, excluding outliers; open circles represent outliers (more or less than 3/2 times the upper or lower quartiles.
S5-spc-nsaf-prot-names.txt All identified proteins from the DDA experiment with Uniprot annotations (e-value cut-off of 1E-10), total spectral counts for each technical replicate, calculated normalized spectral abundance factor (NSAF) for combined technical replicates, and indication of significantly differentially abundant proteins by pairwise comparison. Columns containing spectral count data have headers “SpC” followed by the biological replicate number, sex, maturation stage, and technical replicate (for example, “SpC 3FE” is technical replicate 1 from early-stage female 3). Notation for NSAF is similar to SpC. The 9 columns in the sheet have headers such as “EFvLF” (comparison between early- and late-stage females) have asterisks in the cells that correspond to proteins that were differentially abundant for each given comparison. The last two columns (“NMDS Gonad” and “NMDS Hemolymph”) have asterisks in cells that correspond to the proteins with peptide transitions that contribute significantly to the SRM NMDS plot distributions.
S6-DAGs.pdf Enrichment plots for early- and mid-maturation stage geoduck (EM, EF, MM, MF). Processes colored in blue were enriched from the set of all proteins detected in the given sex-stage, while red processes are from the protein set that was uniquely detected in a sex-stage. Darker colors represent higher significance of enrichment.
S7-NMDS-SRM-tech-reps.pdf NMDS of gonad SRM data for the 3 biological replicates and corresponding three technical replicates for each sex and maturation stage. Blue points represent female proteomes and orange represent male. Shapes and shade (light to dark) represent the different stages: circles for early-stage, squares for mid-stage, and triangles for late-stage.
S8-GOterms-table.csv GO biological processes enriched in proteins that were differentially abundant between stages within a sex (e.g. early- vs. mid-stage female) or between sexes within a stage (e.g LF vs. LM). Only the most specific GO terms in the GO hierarchy are listed. No terms are listed when a comparison was not made.
S9-SRM-data.xlsx Raw Skyline output (in the tab “Skyline output) and peak intensities normalized by QC peptide abundance (“Normalized Intensities”) for the gonad and hemolymph SRM data.
S10-SRM-cv-boxplots.pdf Integrated peak area coefficient of variation values across all gonad peptide transitions (n=212) and hemolymph peptide transitions (n=171) A) across technical replicates for each geoduck biological replicate in gonad tissue, B) across biological replicates for each sex-maturation stage in gonad tissue, C) across technical replicates for each geoduck biological replicate in hemolymph, and D) across biological replicates for each sex-maturation stage in hemolymph. CVs were calculated in R using the raster package. X-axis labels correspond to the geoduck sex and maturation stage, indicated by e.g. “EF3” represents early-stage female sample 3. The boxes represent the upper and lower quartiles of the data distribution;horizontal black line represents median value;“whiskers” extend to the greatest and least values, excluding outliers; open circles represent outliers (more or less than 3/2 times the upper or lower quartiles).
[Data] Transcriptomic profiles of adult female & male gonads in Panopea generosa (Pacific geoduck).
https://www.ncbi.nlm.nih.gov/bioproject/PRJNA316216
Panopea gonad transcriptome
Open Science Framework Project
https://osf.io/3xf6m/
[Data] Geoduck (Panopea generosa) gonad DDA LC-MS/MS https://www.ebi.ac.uk/pride/archive/projects/PXD003127
[Code] Source Code for GO Analysis in Geoduck Gonad Background https://github.com/yeastrc/compgo-geoduck-public
[Data] Geoduck (Panopea generosa) gonad DIA LC-MS/MS https://www.ebi.ac.uk/pride/archive/projects/PXD004921
[Data] Selected reaction monitoring of geoduck gonad peptides to develop biomarkers of reproductive maturation status http://www.peptideatlas.org/PASS/PASS00943
[Data] Selected reaction monitoring of geoduck hemolymph peptides to develop biomarkers of reproductive maturation status http://www.peptideatlas.org/PASS/PASS00942