Tandem-affinity purification of OOPS-1 and SPE-11 and identification of phosphorylation sites on OOPS-1 and SPE-11
Data files
May 30, 2025 version files 18.68 GB
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Experiment_I_OOPS-1_Mass_spec_X_Taplin.tgz
561.11 KB
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Experiment_II_OOPS-1_Mass_spec_W_lab_code_17731.tgz
1.07 GB
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Experiment_III_OOPS-1_Mass_spec_Y_Lab_code_17794.tgz
1.18 GB
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Experiment_IV_SPE-11_Mass_spec_A_Lab_code_18822.tgz
5.09 GB
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Experiment_V_SPE-11_Mass_spec_B_Lab_code_18850.tgz
4.17 GB
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Experiment_VI_SPE-11_Mass_Spec_C_Lab_code_18879.tgz
3.25 GB
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Experiment_VII_SPE-11_Mass_spec_D_Lab_codd_18902.tgz
3.92 GB
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README.md
9.66 KB
Abstract
Fertilization triggers the completion of female meiosis and launches the oocyte-to-embryo transition. C. elegans spe-11 is one of the few known paternal-effect embryonic lethal genes. We report that the sperm protein, SPE-11, forms a complex with an oocyte protein, OOPS-1 (Oocyte Partner of SPE-11) at fertilization, and that the protein complex is required for the completion of meiosis, the block to polyspermy, and eggshell formation. Tandem-affinity purification and mass spectrometry from C. elegans extracts was used to establish that OOPS-1 and SPE-11 associate. This supplemental dataset provides the mass spectrometry data supporting the finding that OOPS-1 and SPE-11 associate in C. elegans extracts. These data were analyzed and are summarized in Table 3, Table S1, and Table S2 of the manuscript. This supplemental dataset also provides evidence that both OOPS-1 and SPE-11 are phosphoproteins. The mass spectra from the tandem-affinity purifications were analyzed for instances of protein phosphorylation. This supplemental data associated with this dataset displays the mass spectra used to identify sites of phosphorylation on OOPS-1 and SPE-11. We found multiple examples in which phosphorylation was supported at high-confidence levels by multiple diagnostic b- and y-type fragment ions in the mass spectra. These phosphorylation sites are summarized in Figure 7 of the manuscript.
Dataset DOI: 10.5061/dryad.931zcrjxk
Description of the data and file structure
The data were collected as part of a study of early post-fertilization developmental mechanisms in the nematode Caenorhabditis elegans (Tsukamoto et al., 2025). In this study, it was found that an oocyte protein, OOPS-1, and a sperm protein, SPE-11, interact at fertilization, and that the complex is required for the completion of meiosis, the block to polyspermy, and eggshell formation. Tandem-affinity purification and mass spectrometry from C. elegans extracts showed that OOPS-1 and SPE-11 associate. This dataset presents the primary mass spectral evidence that OOPS-1 and SPE-11 associate. These data are analyzed in Table 3, Table S1, and Table S2 of the publication. These data are converted from the proprietary ThermoFisher .raw format to .mzML and a .txt files containing metadata using ThermoRawFileParser and presented as .tgz archives for each experiment (Experiments I-VII). Each archive contains the spectra files in which proteins found in individual gel slices are identified.
A supplemental pdf file presents the evidence that OOPS-1 and SPE-11 are phosphoproteins, as reported in Figure 7 of the publication. Specifically, these data identify sites of phosphorylation, which are supported at high-confidence levels through the identification of multiple diagnostic b- and y-type ions. In the mass spectra in the accompanying pdf file, the peaks highlighted in yellow, show the diagnostic fragment ions supporting the phosphorylation identifications.
Files and variables
OOPS-1 Tandem-Affinity Purifications (Experiments I-III)
Experiment I (Mass spec experiment X) from the C. elegans strain DG4800 with genotype oops-1(tn1908[gfp::tev::3xflag::oops-1]). For references on C. elegans genetic nomenclature, please see the WormBook Nomenclature chapter, http://www.wormbook.org/chapters/www_nomenclature/caenornomenclature.html.
File: Experiment_I_OOPS-1_Mass_spec_X_Taplin.tgz. Component files in csv, xlsx, and txt file formats. This folder contains the same data in three different formats (.csv, .xlsx, ans .txt files). Checksum: 2c8f3921e0c9466c67e7536bb33ae1fb Experiment_I_OOPS-1_Mass_spec_X_Taplin.tgz.
For the X#-C.elegans_Protein files, the column headers are:
Unique: Unique peptides mapping to the protein.
Total: Total peptides mapping to the protein.
Reference: Protein entry in the UniProt database.
Gene Symbol: WormBase gene symbol (https://wormbase.org/#012-34-5).
MWT(kDa): Molecular mass of the protein in kilo Daltons.
Annotation: The name of the protein and its description.
AVG: Mean intensity of each isotopic peak across replicate measurements.
Length: Number of amino acids in the protein.
Coverage: Number of amino acids of the protein detected in the mass spectrometry experiment.
% Coverage: The percentage of the protein’s amino acid sequence that has been identified in the mass spectrometry experiment.
For the X#-C.elegans_Peptide files, the column headers are:
Scan F: Scan number from which the MS/MS spectrum was acquired.
z: charge state of the ion, used to calculate the true mas from the measured m/z value.
XCorr: Cross-correlation score between observed and theoretical spectra for the peptide.
ΔCorr: The differencxe in correlation scores between the best scoring peptide spectrum match and the next best match
# Ions: The number of detected ions at a specific m/z for the theoretical petide sequencxe that have been matched to observed peaks in the experimental MS/MS spectrum (ions detected/expected ions predicted).
# Ions Link: The number of theoretical fragement ions from the peptide sequence thare are matched to the observed peaks in the experimental MS/MS spectrum, shown as a ratio, where the first number is the count of matched fragment ions and the second is the total number of possible theoretical fragment ions for that peptide.
Reference: The protein from the UniProt database to which the identified peptide is matched to during the database search.
Reference Link: The protein database entry that contains the identified peptide sequence. This field contains the UniProt accession number to which the identified peptide is matched to during the database search.
Redun: Redundancy, which indicates the number of times the peptide sequence has been identified in the dataset (0 indicates that the peptide identification was identified only once in the dataset).
Redun Link: An internal reference or pointer that connects peptide entries that are redundant, meaning they represent the same peptide sequence identified in different spectra.
Peptide: The amino acid sequence of the peptide that has been identified in the database search. The single-amino acid letter code is used. A period (.) is used to indicate the amino acid residue immediately before and after the identified peptide sequence in the parent protein. An asterisk (*) is used to denote a post-translational modification or a modified amino acid within the peptide sequence.
Peptide Link: An internal reference or identifier that connects all peptide-spectrum matches corresponding to the same peptide sequence within the dataset.
Gene Symbol: WormBase gene symbol (https://wormbase.org/#012-34-5)
Protein MWT(kDa): Molecular mass of the protein in kilo Daltons.
Annotation: The name of the protein and its description.
Experiment II (Mass spec experiment W, lab code 17731) from DG4800 oops-1(tn1908[gfp::tev::3xflag::oops-1]). File: Experiment_II_OOPS-1_Mass_spec_W_lab_code_17731.tgz. Component files in mzML and txt file formats. Checksum: 940821af98c2ddaea37d565446cef083 Experiment_II_OOPS-1_Mass_spec_W_lab_code_17731.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (gel slice analyzed).
Experiment III (Mass spec experiment Y, lab code 17794) from DG4800 oops-1(tn1908[gfp::tev::3xflag::oops-1]). File: Experiment_III_OOPS-1_Mass_spec_Y_Lab_code_17794.tgz. Component files in mzML and txt file formats. Checksum: e4cd77b2f7500bfbe1e91a18a1730950 Experiment_III_OOPS-1_Mass_spec_Y_Lab_code_17794.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (instrument) (instrument mode) (gel slice analyzed).
SPE-11 Tandem-Affinity Purifications (Experiments IV-VII)
Experiment IV (Mass spec experiment A, lab code 18822) from DG5430 spe-11(tn2094[gfp::tev::3xflag::spe-11]). File: Experiment_IV_SPE-11_Mass_spec_A_Lab_code_18822.tgz. Component files in mzML and txt file formats. Checksum: d88cf87f397b3427cfe4598663cd3cd2 Experiment_IV_SPE-11_Mass_spec_A_Lab_code_18822.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (instrument) (instrument mode) (liquid chromatography method) (gel slice analyzed).
Experiment V (Mass spec experiment B, lab code 18850) from DG5430 spe-11(tn2094[gfp::tev::3xflag::spe-11]). File: Experiment_V_SPE-11_Mass_spec_B_Lab_code_18850.tgz. Component files in mzML and txt file formats. Checksum: 53eebc919d4e7bd35fa9d9ec735b8205 Experiment_V_SPE-11_Mass_spec_B_Lab_code_18850.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (instrument) (instrument mode) (liquid chromatography method) (gel slice analyzed).
Experiment VI (Mass spec experiment C, lab code 18879) from DG5462 spe-11(tn2094[gfp::tev::3xflag::spe-11]); him-5(e1490). File: Experiment_VI_SPE-11_Mass_Spec_C_Lab_code_18879.tgz. Component files in mzML and txt file formats. Checksum: 4887a1e8966d61149020eec41de342c7 Experiment_VI_SPE-11_Mass_Spec_C_Lab_code_18879.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (instrument) (instrument mode) (liquid chromatography method) (gel slice analyzed).
Experiment VII (Mass spec experiment D, lab code 18902) from DG5462 spe-11(tn2094[gfp::tev::3xflag::spe-11]); him-5(e1490). File: Experiment_VII_SPE-11_Mass_spec_D_Lab_codd_18902.tgz. Component files in mzML and txt file formats. Checksum: e7de83ed9bd0ebfcf43c6cf4782e0d6e Experiment_VII_SPE-11_Mass_spec_D_Lab_codd_18902.tgz.
File naming convention:
(Experiment number) (Protein Purified) (Mass spec experiment letter ID) (lab code ID) (PI) (Scientist) (date) (lab code) (instrument) (instrument mode) (liquid chromatography method) (gel slice analyzed).
Supplemental File Supporting the Identification of Phosphorylation Sites on OOPS-1 and SPE-11
Sites of phosphorylation in OOPS-1 and SPE-11 are shown with the corresponding mass spectra supporting the identification. The high-confidence level identifications are summarized in Figure 7 in Tsukamoto et al., (2025).
Supplemental File: PhosphoID_OOPS1_SPE11_dataset_v4.pdf
Code/software
Open source software for viewing proteomics data in mzML files: OpenMS, ProteoWizard, Chromascope, MassChroViewer, Mzkit, MathIOmica MSViewer.
Proprietary software for viewing proteomics data in mzML files: Proteome Discoverer (ThermoFisher).
Adobe Acrobat Reader