GPMDB00255OtherDyrlund TF, et al.InstrumentNot AvailableNot availableHomo_sapiens_viruses, Human, Acholeplasma_laidlawii_pg_8a,escherichia_coli_k_12_substr__mg1655,escherichia_coli_o157_h7_sakai,escherichia_coli_se11,mycoplasma_fermentans_jer,mycoplasma_hominis_atcc_23114,mycoplasma_hyorhinis_gdl_1tfd@mb.au.dk25164020Department of Molecular Biology and Genetics, Aarhus University, et al.http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029260http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029261http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029262http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029263http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029264http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029220http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029221http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029265http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029211http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029255http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029212http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029256http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029213http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029257http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029258http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029259http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029218http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029219http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029250http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029251http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029252http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029253http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029210http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029254http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029200http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029244http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029201http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029245http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029246http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029202http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029203http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029247http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029204http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029248http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029249http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029205http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029206http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029207http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029208http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029209http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029240http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029241http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029242http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029243http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029233http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029234http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029235http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029236http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029237http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029238http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029239http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029230http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029231http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029232http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029199http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029222http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029223http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029225http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029226http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029227http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029228http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029229Not availableGPMDBUsing advanced mass spectrometry and high confidence criteria for accepting proteins (P < 0.01), a total of 110 proteins other than HSA were identified. The average HSA content was found to be 94% (92-97%) of total protein. Other individual proteins accounted for up to 4.7% of the total protein. Analysis of purified HSA strongly suggests that these non-declared proteins are introduced to the media when the albumin is added. GO analysis showed that many of these proteins have roles in defence pathways, for example 18 were associated with the innate immune response and 17 with inflammatory responses. Eight proteins have been reported previously as secreted embryo proteins.For six of the commercial embryo culture media only one batch was analyzed. However, this does not affect the overall conclusions.The results showed that the HSA added to IVF media contained many other proteins and that the amount varies from batch to batch. These variations in protein profiles are problematic when attempting to identify proteins derived from the embryos. Therefore, when studying the embryo secretome and analyzing conditioned media with the aim of finding potential biomarkers that can distinguish normal and abnormal embryo development, it is important that the medium used in the experimental and control groups is from the same batch. Furthermore, the proteins present in unconditioned media could potentially influence embryonic development, gestation age, birthweight and perhaps have subsequent effects on health of the offspring.The following eight commercial embryo culture media were included in this study: G-1 PLUS and G-2 PLUS G5 Series from Vitrolife, Sydney IVF Cleavage Medium and Sydney IVF Blastocyst Medium from Cook Medical and EmbryoAssist, BlastAssist, Sequential Cleav and Sequential Blast from ORIGIO. Two batches were analyzed from each of the Sydney IVF media and one batch from each of the other media. All embryo culture media are supplemented by the manufacturers with purified human serum albumin (HSA 5 mg/ml). The purified HSA (HSA-solution from Vitrolife) and the recombinant human albumin supplement (G-MM from Vitrolife) were also analyzed.A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable and therefore represent the majority of the total protein in the media samples.The study was supported by the Danish Agency for Science, Technology and Innovation. Research at the Fertility Clinic, Aarhus University Hospital is supported by an unrestricted grant from Merck Sharp & Dohme Corp and Ferring. The authors declare no conflicts of interest.There are no data in the literature on what non-declared proteins are present in unconditioned (fresh media in which no embryos have been cultured) commercial embryo media.For protein quantification, media samples were in-solution digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For in-depth protein identification, media were albumin depleted, dialyzed and concentrated before sodium dodecyl sulfate polyacrylamide gel electrophoresis. The gel was cut into 14 slices followed by in-gel trypsin digestion, and analysis by LC-MS/MS. Proteins were further investigated using gene ontology (GO) terms analysis.Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media?STUDY QUESTION: Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media? SUMMARY ANSWER: A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable and therefore represent the majority of the total protein in the media samples. WHAT IS KNOWN ALREADY: There are no data in the literature on what non-declared proteins are present in unconditioned (fresh media in which no embryos have been cultured) commercial embryo media. STUDY DESIGN, SIZE, DURATION: The following eight commercial embryo culture media were included in this study: G-1 PLUS and G-2 PLUS G5 Series from Vitrolife, Sydney IVF Cleavage Medium and Sydney IVF Blastocyst Medium from Cook Medical and EmbryoAssist, BlastAssist, Sequential Cleav and Sequential Blast from ORIGIO. Two batches were analyzed from each of the Sydney IVF media and one batch from each of the other media. All embryo culture media are supplemented by the manufacturers with purified human serum albumin (HSA 5 mg/ml). The purified HSA (HSA-solution from Vitrolife) and the recombinant human albumin supplement (G-MM from Vitrolife) were also analyzed. PARTICIPANTS/MATERIALS, SETTING, METHODS: For protein quantification, media samples were in-solution digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For in-depth protein identification, media were albumin depleted, dialyzed and concentrated before sodium dodecyl sulfate polyacrylamide gel electrophoresis. The gel was cut into 14 slices followed by in-gel trypsin digestion, and analysis by LC-MS/MS. Proteins were further investigated using gene ontology (GO) terms analysis. MAIN RESULTS AND THE ROLE OF CHANCE: Using advanced mass spectrometry and high confidence criteria for accepting proteins (P < 0.01), a total of 110 proteins other than HSA were identified. The average HSA content was found to be 94% (92-97%) of total protein. Other individual proteins accounted for up to 4.7% of the total protein. Analysis of purified HSA strongly suggests that these non-declared proteins are introduced to the media when the albumin is added. GO analysis showed that many of these proteins have roles in defence pathways, for example 18 were associated with the innate immune response and 17 with inflammatory responses. Eight proteins have been reported previously as secreted embryo proteins. LIMITATIONS, REASONS FOR CAUTION: For six of the commercial embryo culture media only one batch was analyzed. However, this does not affect the overall conclusions. WIDER IMPLICATIONS OF THE FINDINGS: The results showed that the HSA added to IVF media contained many other proteins and that the amount varies from batch to batch. These variations in protein profiles are problematic when attempting to identify proteins derived from the embryos. Therefore, when studying the embryo secretome and analyzing conditioned media with the aim of finding potential biomarkers that can distinguish normal and abnormal embryo development, it is important that the medium used in the experimental and control groups is from the same batch. Furthermore, the proteins present in unconditioned media could potentially influence embryonic development, gestation age, birthweight and perhaps have subsequent effects on health of the offspring. STUDY FUNDING/COMPETING INTERESTS: The study was supported by the Danish Agency for Science, Technology and Innovation. Research at the Fertility Clinic, Aarhus University Hospital is supported by an unrestricted grant from Merck Sharp & Dohme Corp and Ferring. The authors declare no conflicts of interest.<h4>Study question</h4>Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media?<h4>Summary answer</h4>A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable and therefore represent the majority of the total protein in the media samples.<h4>What is known already</h4>There are no data in the literature on what non-declared proteins are present in unconditioned (fresh media in which no embryos have been cultured) commercial embryo media.<h4>Study design, size, duration</h4>The following eight commercial embryo culture media were included in this study: G-1 PLUS and G-2 PLUS G5 Series from Vitrolife, Sydney IVF Cleavage Medium and Sydney IVF Blastocyst Medium from Cook Medical and EmbryoAssist, BlastAssist, Sequential Cleav and Sequential Blast from ORIGIO. Two batches were analyzed from each of the Sydney IVF media and one batch from each of the other media. All embryo culture media are supplemented by the manufacturers with purified human serum albumin (HSA 5 mg/ml). The purified HSA (HSA-solution from Vitrolife) and the recombinant human albumin supplement (G-MM from Vitrolife) were also analyzed.<h4>Participants/materials, setting, methods</h4>For protein quantification, media samples were in-solution digested with trypsin and analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). For in-depth protein identification, media were albumin depleted, dialyzed and concentrated before sodium dodecyl sulfate polyacrylamide gel electrophoresis. The gel was cut into 14 slices followed by in-gel trypsin digestion, and analysis by LC-MS/MS. Proteins were further investigated using gene ontology (GO) terms analysis.<h4>Main results and the role of chance</h4>Using advanced mass spectrometry and high confidence criteria for accepting proteins (P < 0.01), a total of 110 proteins other than HSA were identified. The average HSA content was found to be 94% (92-97%) of total protein. Other individual proteins accounted for up to 4.7% of the total protein. Analysis of purified HSA strongly suggests that these non-declared proteins are introduced to the media when the albumin is added. GO analysis showed that many of these proteins have roles in defence pathways, for example 18 were associated with the innate immune response and 17 with inflammatory responses. Eight proteins have been reported previously as secreted embryo proteins.<h4>Limitations, reasons for caution</h4>For six of the commercial embryo culture media only one batch was analyzed. However, this does not affect the overall conclusions.<h4>Wider implications of the findings</h4>The results showed that the HSA added to IVF media contained many other proteins and that the amount varies from batch to batch. These variations in protein profiles are problematic when attempting to identify proteins derived from the embryos. Therefore, when studying the embryo secretome and analyzing conditioned media with the aim of finding potential biomarkers that can distinguish normal and abnormal embryo development, it is important that the medium used in the experimental and control groups is from the same batch. Furthermore, the proteins present in unconditioned media could potentially influence embryonic development, gestation age, birthweight and perhaps have subsequent effects on health of the offspring.<h4>Study funding/competing interests</h4>The study was supported by the Danish Agency for Science, Technology and Innovation. Research at the Fertility Clinic, Aarhus University Hospital is supported by an unrestricted grant from Merck Sharp & Dohme Corp and Ferring. The authors declare no conflicts of interest.Unconditioned commercial embryo culture media contain a large variety of non-declared proteins: a comprehensive proteomics analysis.Dyrlund Thomas F TF,Kirkegaard Kirstine K,Poulsen Ebbe Toftgaard ET,Sanggaard Kristian W KW,Hindkjær Johnny J JJ,Kjems Jørgen J,Enghild Jan J JJ,Ingerslev Hans Jakob HJ,Dyrlund Thomas F TF, Kirkegaard Kirstine K, Poulsen Ebbe Toftgaard ET, Sanggaard Kristian W KW, Hindkjær Johnny J JJ, Kjems Jørgen J, Enghild Jan J JJ, Ingerslev Hans Jakob HJbig, embryo, determination, plant germ, Proteins, expanded, chemical analysis., Gene, proteins, embryo early (growth) stage, developing organism, embryo stage, Entire embryo, Culture, Protein Gene Products, Gene Proteins, polypeptide, large, embryonic organism, developmental tissue, Media, enlarged, great, Protein, Gene Products, Embryologic, assayIGF-I, data, steel factor, embryo, plant germ, Slf, hematopoietic growth factor KL, Proteins, Somatomedin-C, somatomedin, Gene, FPH2, developing organism, embryo stage, compositionality, composed of, sKITLG, Culture, polypeptide, Experiment, Media, mechano growth factor, Protein, Gene Products, Embryologic, Igf-1, study, SHEP7, mast cell growth factor, content, Stem cell factor, somatomedin-C, SF, Kitl, composition, proteins, present in organism, embryo early (growth) stage, Entire embryo, STAT5, Mast cell growth factor, Protein Gene Products, Gene Proteins, stem cell factor, proteins., KL-1, embryonic organism, developmental tissue, IGF1, MGF, c-Kit ligand, structure, Mechano growth factor, KITLG, Soluble KIT ligand, SCF, Slbig, embryo, determination, plant germ, Proteins, expanded, chemical analysis., Gene, proteins, embryo early (growth) stage, developing organism, embryo stage, Entire embryo, Culture, Protein Gene Products, Gene Proteins, polypeptide, large, embryonic organism, developmental tissue, Media, enlarged, great, Protein, Gene Products, Embryologic, assayGene., advanced, R13-Ag, embryo, determination, plant germ, nonspecific immune response, Proteins, nectadrin, Gene, innate immunity, M1/69-J11D heat stable antigen, Hsa, HSA, Spectrum Analyses, Normalcy, developing organism, embryo stage, compositionality, composed of, Spectrum Analysis, Spectroscopy, polypeptide, small cell lung carcinoma cluster 4 antigen, Protein, chemical analysis, precocious, Mass, Gene Products, Embryologic, Oxidase assembly 1-like protein, Analysis, Mass Spectrum Analyses, Mass Spectroscopy, Mass Spectrum Analysis, Normalities, average, Mass Spectrum, lymphocyte antigen 52, Analyses, Normality, content, Spectrometry, composition, proteins, embryo early (growth) stage, Entire embryo, early, Protein Gene Products, OXA1Hs, Gene Proteins, OXA1-like protein, X62 heat stable antigen, Health, embryonic organism, developmental tissue, structure, CD24A, ly-52, assay, associated, CD242505http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM11210029252dbgap_ncbi~0patentfamilies~0rfam~0merops~0complex-portal~0uniprot~0wormbaseparasite~0embl-covid19~0reactome~0emdb~0wgs_masters~0ebiweb_resources~0opentargets_genetics~0biomodels_all~0ipd-mhc~0ebiweb_teams~0taxonomy~0genome_assembly~0sc-experiments~0ebiweb_people~0enzymeportal_enzymes~0ipd-nhkir~0cellosaurus~0pdbe~0chebi~0patentproteins~0interpro7~0uniref~0chembl~0pdbekb~0gpcrdb~0hgnc~0sc-genes~0intact~0rhea~0ebiweb_training~0alphafold~0imgt-hla~0patentnucleotides~0ensemblroot~0eva_studies~0non-coding~0europepmc~0pubmed~1identifiers_registry~0pdbechem~0hpa-covid19~0eva-variants-covid19~0biosamples~0gwas_catalog~0biotools~0tls_masters~0mesh~0coding~0sra~0opentargets~0efo~0embl-pathogen~0project~0pride~1human_diseases~0geo_datasets~0embl~0treefam~0uniparc~0ols~0dgva~0intenz~0go~0tsa_masters~0biosamples-covid19~0ebiweb_corporate~0omim~0lrg~0earlycause-molecular-sequences~0ipd-kir~0empiar~0rnacentral~0orcid_data_claims~0gpmdb~2lineage-covid19~0metagenomics~0pfam~0pride archive~1varsite~00Resource Reanalysis0.00.00.00771128932757557050.01.0falseUnconditioned commercial embryo culture media contain a large variety of non-declared proteins: a comprehensive proteomics analysis.Data from ProteomeXchange, PXD ID: PXD001174. Experiment: Vitrolife G-1 Plus - 1ug, file: 2014-01-28 - TFD - Vitrolife G-1 Plus - 1ug - 3.mgf. Published as part of Hum Reprod. 2014 Aug 27 . From the Abstract: {{i}} STUDY QUESTION: Which non-declared proteins (proteins not listed on the composition list of the product data sheet) are present in unconditioned commercial embryo culture media? SUMMARY ANSWER: A total of 110 non-declared proteins were identified in unconditioned media and between 6 and 8 of these were quantifiable and therefore represent the majority of the total protein in the media samples. {{/i}}2014-09-01GPM1121002925225164020PXD001174PXD001174