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https://storage.jpostdb.org/JPST003416/files/210726mi-07-HeLa500ng-1400V-GL-9-4000mm-225min_Slot2-3_1_6339.d.ziphttps://storage.jpostdb.org/JPST003416/files/240605mi-04_692D2-iPSC-DDA_Slot2-2_1_12808.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-11-HeLa1500ng-1400V-GL-9-4000mm-600min_Slot2-4_1_6343.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-15-HeLa1000ng-1500V-U3000-Rep1.9um-250mm-480min_Slot1-04_1_6261.d.ziphttps://storage.jpostdb.org/JPST003416/files/240529mk-07_test-phos_DDA_n2_Slot2-11_1_12736.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-04-HeLa1000ng-1400V-GL-9-4000mm-480min_Slot2-3_1_6336.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-06-HeLa200ng-1400V-GL-9-4000mm-90min_Slot2-3_1_6338.d.ziphttps://storage.jpostdb.org/JPST003416/files/240605mi-03_692D2-iPSC-DDA_Slot2-2_1_12807.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-03-HeLa200ng-1500V-Reprosil1.9um-75um-250mm-90min_Slot2-2_1_6242.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-03-HeLa500ng-1400V-GL-9-4000mm-225min_Slot2-3_1_6335.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-14-HeLa1000ng-1500V-U3000-Rep1.9um-250mm-480min_Slot1-04_1_6260.d.ziphttps://storage.jpostdb.org/JPST003416/files/240529mk-06_test-phos_DDA_n1_Slot2-10_1_12735.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-08-HeLa1000ng-1500V-Reprosil1.9um-75um-250mm-480min_Slot2-2_1_6247.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-10-HeLa1500ng-1400V-GL-9-4000mm-600min_Slot2-4_1_6342.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-06-HeLa500ng-1500V-Reprosil1.9um-75um-250mm-225min_Slot2-2_1_6245.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-08-HeLa1000ng-1400V-GL-9-4000mm-480min_Slot2-3_1_6340.d.ziphttps://storage.jpostdb.org/JPST003416/files/240530mk-11_test-ubi_692D2_n2_Slot2-13_1_12740.d.ziphttps://storage.jpostdb.org/JPST003416/files/240530mk-10_test-ubi_692D2_n1_Slot2-12_1_12739.d.ziphttps://storage.jpostdb.org/JPST003416/files/210706mi-07-HeLa500ng-1500V-Reprosil1.9um-75um-250mm-225min_Slot2-2_1_6246.d.ziphttps://storage.jpostdb.org/JPST003416/files/210726mi-02-HeLa200ng-1400V-GL9-4000mm-90min_Slot2-3_1_6334.d.zipprimaryOK200ProteomicsMio IwasakiHomo Sapiens (human)https://repository.jpostdb.org/entry/JPST003416Kyoto UniversityjPOSTRecent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of the data-independent acquisition (DIA) method powered by machine learning has significantly improved protein identification efficiency. However, compared with the conventional data-dependent acquisition (DDA) method, the degree to which peptides are uniquely identified by DIA and DDA has not been thoroughly examined. In this study, we identified over 10,000 proteins using the DDA and DIA methods and analyzed the characteristics of unique peptides identified by each method. Results showed that the number of peptides uniquely identified by DDA and DIA using the same column type was 19% and 32%, respectively, with shorter peptides preferentially detected by the DIA method. In addition, more DIA-specific peptides were identified, especially during the first 10% of elution time, and the overall 1/K0 and m/z shifted toward smaller values than in the DDA method. Furthermore, comparing the phosphorylation and ubiquitination proteome profiles with those of whole-cell lysates by DDA showed that the enrichment of post-translationally modified peptides resulted in wider m/z and 1/K0 ranges. Notably, the ubiquitin peptide-enriched samples displayed lower m/z values than the phospho-proteome. These findings suggest a bias in the types of peptides identified by the acquisition method and the importance of setting appropriate ranges for DIA based on the post-translational modification of peptide characteristics.Differences in Uniquely Identified Peptides Between ddaPASEF and diaPASEF.Iwasaki Mio M, Nishimura Rika R, Yamakawa Tatsuya T, Miyamoto Yousuke Y, Tabata Tsuyoshi T, Narita Megumi MPolypeptides, Peptid, peptidos, Polypeptide, peptido, peptides, Peptide.sodium salt, MGC130048, Scientific Bias, Post Translational Amino Acid Modification, CDF, posttranslational modification, degree (angle), determination, Feature, A4, protein, Protein Processing, phosphorylation, Productivity, SUB, dmTAF[[II]]230, peptide, Polypeptides, Techniques, POF, peptido, DmelCG12298, Method, Epidemiologic Biase, symptoms, SCRAMBLED, AGAMOUS-like 61, Ecological, Analysis, bis(p-chlorophenyl)acetic acid, protein aggregate, Transfer, KIF20A, DiA, Mass Spectrum Analysis, Post-Translational Protein, gamma sarcoglycan, Ecological Biases, posttranslational amino acid modification, Ubiquitylation, l(2)k07135, High Mobility Protein 20, peptides, TFIID TAF250, Analyses, cel, Post-Translational, Machine, Ubiquitin-related 1, procedures, DIASP, Posttranslational Protein Processing, DIA, Dia, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, APF-1, Methodological Studies, column, Statistical Biases, 38E.16, gamma-sarcoglycan, Ecological Bias, ubiquitination, Systematic, Epidemiologic Biases, screening, Post-Translational Modification, dTAF[[II]]230, Scientific, Epidemiologic, Learning, Modifications, SG-gamma, STRUBBELIG, TAF200, Ecological Fallacies, Procedure, TAFII-250, TAF250/230, CEP52, Spectrum Analysis, Feature., Spectroscopy, Outcome Measurement Errors, ms(2)04138, Desmoplastic infantile astrocytoma, TAFII250, Experimental, Post Translational Modifications, sarcoglycan, Truncation Bias, Ubiq, Ubiquitin, Bias, PTM, POF2, F27C12_24, Processing, F27C12.24, Spectrometry, Human Ubiquitin, signs, Methodological, Outcome Measurement, Features, gamma (35kDa dystrophin-associated glycoprotein), CG17603, Methodological Study, TAF[[II]], Experimental Bias, Outcome Measurement Error, DMDA, Amino Acid Modification, Taf250, 35kD dystrophin-associated glycoprotein, SR3-5, post-translational modification, DIANA, Posttranslational Modifications, Polypeptide, Proteomes, Posttranslational Modification, TAF230, AT1G11140, d230, SGCG_HUMAN, Post-Translational Protein Modifications, Procedures, Peptidomics, Ecological Fallacy, Truncation, Gene, Systematic Bias, dTAFII250, ATP Dependent Proteolysis Factor 1, Spectrum Analyses, Ubiquitin carboxyl extension protein 80, protein-containing complex, EfW1, TYPE, CG12298, Human, Posttranslational, DAGA4, method, potassium salt, dmTAF1, Taf230, 14C-labeled, DmelCG1768, method used in an experiment, 35DAG, Mass, Gene Products, HILDA, Studies, Post Translational Modification, HMG-20, Post-Translational Modifications, MAM, gamma-SG, SCG3, Technique, Mass Spectroscopy, Post Translational, TAF250, Fallacies, Modification, study, Transfer Learning, Taf200, dTAF[[II]]250, cell, mei-1794, Aggregation, Taf1p, posttranslational protein modification, Protein Modifications, Study, Post-Translational Amino Acid Modification, dTAF250, 40S ribosomal protein S27a, Posttranslational Amino Acid Modification, ubiquitin, Posttranslational Protein, peptidos, SRF9, Characteristics, DIA2, TAF, protein tagging activity, Biase, Fallacy, TAF[[II]]250, findings, 35 kDa dystrophin-associated glycoprotein, protein complex, Desmoplastic astrocytoma of infancy, Proteins, Phosphorylations, total expressed protein, Post-Translational Protein Modification, l(3)84Ab, Truncation Biases, BG:DS00004.13, CG1768, DRF2, Peptide, Cell, SGCG, LGMD2C, dTAF230, STRUBBELIG-RECEPTOR FAMILY 9, polypeptide, MS, Ubiquitin A-52 residue ribosomal protein fusion product 1, Characteristic, native protein, Ubiquitin-related 2, p230, Protein, chemical analysis, MLPLI, TAF[[II]]250/230, Errors, TFIID, techniques, Dias, ATP-Dependent Proteolysis Factor 1, Protein Modification, Mass Spectrum Analyses, DDA, Taf[[II]]250, Mass Spectrum, covalent modifier, TAF[[II]]230, DMDA1, Post Translational Protein Processing, Dub, Biases, TAF[II]250, arc degree, post-translational amino acid modification, Protein Gene Products, plan specification, Gene Proteins, Post Translational Protein Modification, DmelCG17603, 60S ribosomal protein L40, Error, Aggregation Bias, SCARMD2, Statistical Bias, Post-Translational Protein Processing, Peptid, Ubiquitin-related, assay, Statistical, T19D16.8, SCM, methodology, TAF1Polypeptides, Peptid, peptidos, Polypeptide, peptido, peptides, Peptide.sodium salt, Scientific Bias, Post Translational Amino Acid Modification, CDF, posttranslational modification, degree (angle), determination, Feature, protein, Protein Processing, phosphorylation, dmTAF[[II]]230, peptide, Polypeptides, Techniques, POF, peptido, Method, Epidemiologic Biase, symptoms, AGAMOUS-like 61, Ecological, Analysis, bis(p-chlorophenyl)acetic acid, protein aggregate, Transfer, DiA, Mass Spectrum Analysis, Post-Translational Protein, Ecological Biases, posttranslational amino acid modification, Ubiquitylation, l(2)k07135, High Mobility Protein 20, peptides, TFIID TAF250, Analyses, cel, Post-Translational, Machine, Ubiquitin-related 1, procedures, DIASP, Posttranslational Protein Processing, DIA, Dia, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, APF-1, Methodological Studies, Statistical Biases, 38E.16, Ecological Bias, ubiquitination, Systematic, Epidemiologic Biases, screening, Post-Translational Modification, dTAF[[II]]230, Scientific, Epidemiologic, Learning, Modifications, TAF200, Th, Ecological Fallacies, Procedure, TAFII-250, TAF250/230, CEP52, Spectrum Analysis, Feature., Spectroscopy, Outcome Measurement Errors, ms(2)04138, Desmoplastic infantile astrocytoma, TAFII250, Experimental, Post Translational Modifications, Truncation Bias, Ubiq, Ubiquitin, Bias, PTM, POF2, F27C12_24, Processing, F27C12.24, Spectrometry, Human Ubiquitin, signs, Methodological, Outcome Measurement, Features, CG17603, Methodological Study, TAF[[II]], Experimental Bias, Outcome Measurement Error, Amino Acid Modification, Taf250, SR3-5, post-translational modification, DIANA, Posttranslational Modifications, Polypeptide, Proteomes, Posttranslational Modification, TAF230, d230, Post-Translational Protein Modifications, Procedures, Peptidomics, Ecological Fallacy, Truncation, Gene, Systematic Bias, dTAFII250, ATP Dependent Proteolysis Factor 1, Spectrum Analyses, Ubiquitin carboxyl extension protein 80, protein-containing complex, thomson, EfW1, mass-to-charge ratio, Human, Posttranslational, method, potassium salt, dmTAF1, Taf230, 14C-labeled, DmelCG1768, method used in an experiment, Mass, Gene Products, HILDA, Studies, Post Translational Modification, HMG-20, Post-Translational Modifications, Technique, Mass Spectroscopy, Post Translational, TAF250, Fallacies, Modification, study, Transfer Learning, Taf200, dTAF[[II]]250, cell, Aggregation, Taf1p, posttranslational protein modification, Protein Modifications, Study, Post-Translational Amino Acid Modification, dTAF250, 40S ribosomal protein S27a, Posttranslational Amino Acid Modification, ubiquitin, Posttranslational Protein, peptidos, Characteristics, DIA2, TAF, protein tagging activity, Biase, Fallacy, TAF[[II]]250, findings, protein complex, Desmoplastic astrocytoma of infancy, Proteins, Phosphorylations, total expressed protein, Post-Translational Protein Modification, l(3)84Ab, Truncation Biases, BG:DS00004.13, CG1768, DRF2, Peptide, Cell, dTAF230, polypeptide, MS, Ubiquitin A-52 residue ribosomal protein fusion product 1, Characteristic, native protein, Ubiquitin-related 2, p230, Protein, chemical analysis, MLPLI, TAF[[II]]250/230, Errors, TFIID, techniques, Dias, ATP-Dependent Proteolysis Factor 1, Protein Modification, Mass Spectrum Analyses, DDA, Taf[[II]]250, Mass Spectrum, covalent modifier, TAF[[II]]230, Post Translational Protein Processing, Biases, TAF[II]250, arc degree, post-translational amino acid modification, Protein Gene Products, plan specification, Gene Proteins, Post Translational Protein Modification, DmelCG17603, 60S ribosomal protein L40, Error, Aggregation Bias, Statistical Bias, Post-Translational Protein Processing, Peptid, Ubiquitin-related, assay, Statistical, methodology, TAF1falseDifferences of uniquely identified peptides between ddaPASEF and diaPASEFRecent advancements in mass spectrometry-based proteomics have made it possible to conduct comprehensive protein analysis. In particular, the emergence of the data-independent acquisition (DIA) method powered by machine learning has significantly improved protein identification effi-ciency. However, compared with the conventional data-dependent acquisition (DDA) method, the degree to which peptides are uniquely identified by DIA and DDA has not been thoroughly ex-amined. In this study, we identified over 10,000 proteins using the DDA and DIA methods and analyzed the characteristics of unique peptides identified by each method. Results showed that the number of peptides uniquely identified by DDA and DIA was 19% and 32%, respectively, with shorter peptides preferentially detected by the DIA method. In addition, more DIA-specific peptides were identified, especially during the first 10% of elution, and the overall 1/K0 and m/z shifted to-ward smaller values than in the DDA method. In addition, comparing the phosphorylation and ubiquitination proteome profiles with those of whole-cell lysates by DDA showed that the en-richment of post-translationally modified peptides resulted in wider m/z and 1/K0 ranges. Notably, the ubiquitin peptide-enriched samples displayed a broader range of 1/K0 at lower m/z values than the phosphoproteome. These findings suggest a bias in the types of peptides identified by the ac-quisition method and the importance of setting appropriate ranges for DIA based on the post-translational modification of peptide characteristics.Sun Dec 01 00:00:00 GMT 2024PXD056754960639594597