MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v05/MSV000092113/primary200OK0000ProteomicsHanna BudayevaOrbitrap EclipseHomo Sapiens (ncbitaxon:9606)Mus Musculus (ncbitaxon:10090)https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=745952e97520446295068da76b7bef2eGenentech, Inc.budayeva.hanna@gene.comMassIVE61[C] [302.216664] heavy desthiobiotin on cysUNIMOD:4 - "Iodoacetamide derivative."[C] [+329.2266] iodoTMTUNIMOD:2016 - "TMTpro 16plex Tandem Mass Tag"[C] [296.184764] desthiobiotin on cysUNIMOD:35 - "Oxidation or Hydroxylation."total expressed protein, Activity, General activity, Proteomes.Amyloid intracellular domain 57, APP, ABETA, Amyloid intracellular domain 59, Poikiloderma of Rothmund-Thomson, E 920, poikiloderma congenitale, Activity, determination, AUTSX3, A4, CTFgamma, protein, neutral molecular compounds, progressive encephalomyelitis with rigidity, Amyloid intracellular domain 50, Long Term, Abpp, and loss of purposeful hand use, ischiocoxopodopatellar syndrome, AAA, Morsch Woltman syndrome, Cvap, peptide, Polypeptides, protein polypeptide chains, Techniques, AG, AW111620, peptido, Beta-amyloid protein 42, Method, congenital coxa vara, sucrose phosphate synthetase activity, Beta-amyloid protein 40, germacrene A synthase activity, Software Engineering, 2-amino-3-mercaptopropanoic acid, Cystein, protein aggregate, dementia, Effect, AID(50), molecule, poikiloderma atrophicans and cataract, TYMSAS, tarsal synostosis, Computer Program, molecula, AI505014, RS, CG10850, C, Ag, molecules, peptides, cisteina, UDP-glucose-fructose-phosphate glucosyltransferase activity, Open, RTS, labeling., hypoplasia, RTT, Computer Programs and Programming, ataxia, purification, proteins, Molekuel, Alzheimer disease amyloid A4 protein homolog, PA1, isolation and purification, N-APP, Gamma-secretase C-terminal fragment 50, Methodological Studies, Gamma-secretase C-terminal fragment 57, Gamma-secretase C-terminal fragment 59, RecQ protein-like 4, C16orf53, AD1, Abeta, APPI, Half Cystine, Rett syndrome, C80, Long-Term Effects, AA589574, 1110046B24Rik, sucrose phosphate-uridine diphosphate glucosyltransferase activity, C83, (+)-germacrene A synthase activity, close to, IDA, Ida, AICD-50, S-APP-alpha, Zinc Cysteinate, MRXSL, Longterm Effect, Procedure, Gamma-CTF(57), Cys, Source Softwares, Software Tools, Programs, C99, Program, Computer Applications, TPSG1, S-adenosyl-L-methionine:thiol S-methyltransferase activity, RSTS, Computer Applications Software, AICD-57, Computer Applications Softwares, Softwares, GAS, (2R)-2-amino-3-sulfanylpropanoic acid, 6-trans-farnesyl-diphosphate diphosphate-lyase (germacrene-A-forming) activity, uridine diphosphoglucose-fructose phosphate glucosyltransferase activity, region, AICD-59, Cerebral vascular amyloid peptide, RecQ4, Software Applications, Source Software, DNA helicase, L-Cysteine, Methodological, Alzheimer disease amyloid protein, Protease nexin-II, MRX16, Methodological Study, ICPPS, Apc5, L-Cystein, APC5, MRSR, Applications, RecQ-like type 4, 3.6.4.12, PRSS31, l(3)SH7, Polypeptide, TMT, Proteomes, Computer Software Applications, sucrose 6-phosphate synthase activity, Cysteine Hydrochloride, Procedures, Effects, P3(40), Stiff-trunk syndrome, L-Zystein, 2-trans, Gene, MRX79, Computer, protein-containing complex, betaApp, AID(59), method, UDPglucose-fructose-phosphate glucosyltransferase activity, polypeptide chain, reduced, isolation, UDP-glucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, APP-C57, method used in an experiment, APP-C59, Gene Products, Studies, Coxo-podo-patellar syndrome, atypical, tiny, Half-Cystine, SMS, Technique, Application, SPMSY, Open Source Softwares, patella aplasia, PreA4, Longterm, sucrosephosphate-UDP glucosyltransferase activity, Zappella variant, MS3, Software Application, L Cysteine, E-920, HSRTSBETA, Open Source Software, S-APP-beta, DmelCG10850, labeling, Hcys, Long-Term, Gamma-CTF(59), Computer Software Application, Study, AID(57), UDPglucose:D-fructose-6-phosphate 2-alpha-D-glucosyltransferase activity, Tools, CYSTEINE, SELD, site, FREE CYSTEINE, peptidos, Long-Term Effect, SpS, (2R)-2-amino-3-mercaptopropanoic acid, SPS1, thiol methyltransferase activity, coxa vara, small, Applications Software, Stiff person syndrome and related disorders, Open Source, STIFF-PERSON syndrome, Amyloidogenic glycoprotein, Computer Software, protein complex, E030013M08Rik, PPMX, 6-trans-farnesyl-diphosphate diphosphate-lyase [(+)-germacrene-A-forming] activity, Proteins, preserved speech variant, MRXS13, total expressed protein, SPS, (+)-(10R)-germacrene A synthase activity, Peptide, Tool, near to, Gamma-CTF(50), APP-C99, polypeptide, Software Tool, native protein, natural protein, Adap, Long Term Effects, chemical analysis, Protein, l(3)63Fb, Software, Zystein, Data Base, Stiff-Man syndrome, P3(42), PN-II, underdeveloped, 2-amino-3-sulfanylpropanoic acid, CBP, Engineering, L-2-Amino-3-mercaptopropionic acid, SRS, Soluble APP-beta, (R)-2-amino-3-mercaptopropanoic acid, 2-Amino-3-mercaptopropionic acid, Longterm Effects, Protein Gene Products, C31, plan specification, Computer Programs, Gene Proteins, Applications Softwares, approaches, autism, vicinity of, Soluble APP-alpha, E920, Peptid, patella aplasia and tarsal synostosis, assay, PN2, Beta-APP42, Beta-APP40, General activity, CVAP, ABPP0falseIncreasing the Throughput and Reproducibility of Activity-Based Proteome Profiling Studies with Hyperplexing and Intelligent Data AcquisitionIntelligent data acquisition (IDA) strategies, such as real-time database search (RTS), have improved the depth of proteome coverage for experiments that utilize isobaric labels and gas phase purification techniques (i.e., SPS-MS3). While most applications of IDA have been focused on the analysis of protein abundance, these approaches have recently been applied to activity-based proteome profiling (ABPP) studies aimed at characterization of protein site engagement by small molecules. In this work, we extend IDA capabilities offered by vendor software through a new program called InSeqAPI. First, we demonstrate robust performance of InSeqAPI in the analysis of biotinylated cysteine peptides from ABPP experiments. Then, we describe PairQuant, a method within InSeqAPI designed for the hyperplexing approach that utilizes protein-level isotopic labeling and peptide-level TMT labeling.Tue Jun 06 14:41:00 BST 2023MSV000092113