MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v08/MSV000095009/primaryOK200ProteomicsAaron O. BaileyOrbitrap EclipseBos Taurus (ncbitaxon:9913)https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=bcc2df88716f405ebedca37d5cfa9cd0aaron.bailey@abcellera.comAbCellera Biologics, Inc.MassIVE36oxidationGene., measuring, peptides, determination, protein complex, Proteins, Maps, proteins, protein, protein-containing complex, Gaps, Peptide, Protein Gene Products, polypeptide, peptide, Gene Proteins, Polypeptides, protein polypeptide chains, Prgs, peptido, native protein, natural protein, polypeptide chain, scientific observation, chemical analysis, Protein, Gene Products, Peptid, peptidos, Polypeptide, assay, protein aggregateliquid chromatography tandem mass spectroscopy, sodium salt, dairy cow, WAP3, posttranslational modification, Product, determination, Liquid Chromatography Mass Spectrometry, Mbp1, High Performance Liquid Chromatography Mass Spectrometry, Ultra Performance Liquid Chromatography-Mass Spectrometry, protein, High Performance Liquid Chromatography-Mass Spectrometry, peptide, Polypeptides, protein polypeptide chains, HPLC-MS, Liquid Chromatography-Mass, peptido, Pharmaceutical Product, Fingerprinting, Software Engineering, bis(p-chlorophenyl)acetic acid, protein aggregate, Work Flow, myd, WMS, Computer Program, Ultra Performance Liquid Chromatography Mass Spectrometry, posttranslational amino acid modification, LCMSMS, peptides, Open, Bos bovis, Computer Programs and Programming, beta-particle, Mbp-1, proteins, SCAN, sampling_time_point, Fast, WFDC14, allergic reaction, alpha-Lactalbumin C, alpha-Lactalbumin B, Bos Tauurus, alpha-Lactalbumin A, e, oxen, e-, medicine, Liquid Chromatography-Mass Spectrometries, Pharmaceutical, Peptide Fingerprint, domestic cow, GPHYSD2, SGS, Diagnostic Findings, LC-MS2, SIGNS SYMPTOMS, Noise, Data Set, gyltl1b-b, DESC, LC-MS/MS, Pollution, Positrons, Protein Fingerprints, Source Softwares, Software Tools, ACMICD, Programs, Program, Computer Applications, Workflows, MDDGA6, mKIAA0609, Computer Applications Software, Fast Electron, Computer Applications Softwares, Pharmaceutic, Softwares, KIAA0609, Protein Fingerprinting, fg, Software Applications, gyltl1b, PTM, positional polypeptide feature, High Pressure Liquid Chromatography Mass Spectrometry, MS/MS, Source Software, mdc1d, Spectrometry, expanded, Peptide Fingerprints, MASS, Electron, beta(-), Protein Fingerprint, MDC1D, Applications, enr, Specificity and Sensitivity, enlarged, liquid chromatography-tandem mass spectroscopy, post-translational modification, Liquid, Polypeptide, Noise Pollution, bovine, Clinical Finding, Work Flows, Computer Software Applications, big, region or site annotation, e(-), number, FBN, Gene, electron, Computer, protein-containing complex, froggy, Symptoms and Signs, LC-MS-MS, Gyltl1a, Buffer, large, potassium salt, polypeptide chain, cattle, ECTOL1, sensitive, 14C-labeled, LC-MSMS, Gene Products, Finding, sensitivity, Application, Drugs, UPLC-MS, Open Source Softwares, Ultra-Performance Liquid Chromatography-Mass Spectrometry, Fingerprints, positional, MS2, MDDGB6, Software Application, Elektron, Aggregation, Open Source Software, Spectrometries, PTCR, LARGE, posttranslational protein modification, ESI, Probabilities, Computer Software Application, OCTD, BPFD#36, drugs, alpha-Lactalbumin, Tools, great, Sensitivity, peptidos, ETD, Preparation, Chromatography-Mass Spectrometries, ETD., Pharmaceuticals, Electrons, Positron, Applications Software, Products, Open Source, Computer Software, Mapping, cow, protein complex, Negatron, Proteins, Peptide Fingerprinting, Negatrons, High Pressure Liquid Chromatography-Mass Spectrometry, Medications, buffer, Peptide, Tool, Fingerprint, polypeptide, Signs and Symptoms, LC/MS/MS, Software Tool, native protein, natural protein, Bos primigenius taurus, chemical analysis, Protein, MFS1, domestic cattle, Fast Electrons, alpha Lactalbumin, Software, tandem MS, WMS2, DDA, negatron, Pharmaceutic Preparations, alpha Lactalbumin A, alpha Lactalbumin B, alpha Lactalbumin C, Engineering, Specificity, post-translational amino acid modification, beta, Noises, Drug, Protein Gene Products, Computer Programs, Gene Proteins, Preparations, Applications Softwares, ox, Data, Isolation of Nuclei TAgged in specific Cell Types, Chromatography-Mass Spectrometry, SSKS, cardinality, LC-MS, liquid chromatography tandem mass spectrometry, Peptid, assay, Pharmaceutical Products, Lactalbumins, Pharmaceutical PreparationfalseFilling the Gaps in Peptide Maps with a Platform Assay for Top-Down Characterization of Purified Protein SamplesLC-MS intact mass analysis and LC-MS/MS peptide mapping are foundational assays for developing biologic drugs and other commercial protein products. Certain PTM types, such as truncation and oxidation, increase the difficulty of precise proteoform characterization owing to inherent limitations in peptide and intact protein analyses. Top-down MS (TDMS) can resolve this ambiguity via fragmentation of specific proteoforms. We optimized our existing flow-programmed (fp) denaturing online buffer exchange (dOBE) approach to improve ESI sensitivity and increase TDMS sampling time for industrial applications. Using bovine alpha-lactalbumin (aLac), we tested data-dependent (DDA) and targeted strategies with 14 different MS/MS scan types featuring combinations of collisional- and electron-based fragmentation as well as proton transfer charge reduction. This large dataset was processed using a new software platform, named TDAcquireX, that improves proteoform characterization through TDMS data aggregation. A DDA-based (fp)dOBE-TDMS workflow provided high confidence identification of aLac truncation proteoforms. Targeted TDMS data were analyzed using sliding window-based fragment ion deconvolution to generate composite proteoform spectral match (cPrSM) results. This strategy facilitated probability-based noise filtering of deconvoluted fragment results, simultaneously increasing the percentage of matched fragments while decreasing the total number of fragments reported. We used fragment noise filtering to characterize aLac oxidation positional isomers, finding that electron transfer dissociation (ETD) uniquely provided accurate relative occupancy data as a result of oxidation-specific technical challenges. Wed Jun 12 12:36:00 BST 2024MSV000095009