DOI: 10.5061/dryad.931zcrjxk
title: Tandem-affinity purification of OOPS-1 and SPE-11 and identification of phosphorylation sites on OOPS-1 and SPE-11

description: 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.
description: # Tandem-affinity purification of OOPS-1 and SPE-11 and identification of
 phosphorylation sites on OOPS-1 and SPE-11 Dataset DOI:
 [10.5061/dryad.931zcrjxk](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](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](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](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