MassIVEapplication/xmlftp://massive-ftp.ucsd.edu/v04/MSV000089718/primaryOK2000000Erwin Marten Schoofhttps://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=9864774e7b7a4b8abbea0d7cc3315723erws@dtu.dkMassIVE631MS:1002864 - No post-translational-modifications are included in the identified peptides of this datasetProteomicsOrbitrap EclipseHomo Sapiens (ncbitaxon:9606)Technical University of DenmarkIn recent years, the concept of cell heterogeneity in biology has gained increasing attention, concomitant with a push toward technologies capable of resolving such biological complexity at the molecular level. For single-cell proteomics using Mass Spectrometry (scMS) and low-input proteomics experiments, the sensitivity of an orbitrap mass analyzer can sometimes be limiting. Therefore, low-input proteomics and scMS could benefit from linear ion traps, which provide faster scanning speeds and higher sensitivity than an orbitrap mass analyzer, however at the cost of resolution. We optimized an acquisition method that combines the orbitrap and linear ion trap, as implemented on a tribrid instrument, while taking advantage of the high-field asymmetric waveform ion mobility spectrometry (FAIMS) pro interface, with a prime focus on low-input applications. First, we compared the performance of orbitrap- versus linear ion trap mass analyzers. Subsequently, we optimized critical method parameters for low-input measurement by data-independent acquisition on the linear ion trap mass analyzer. We conclude that linear ion traps mass analyzers combined with FAIMS and Whisper flow chromatography are well-tailored for low-input proteomics experiments, and can simultaneously increase the throughput and sensitivity of large-scale proteomics experiments where limited material is available, such as clinical samples and cellular subpopulations.High Sensitivity Limited Material Proteomics Empowered by Data-Independent Acquisition on Linear Ion Traps.Phlairaharn Teeradon T, Grégoire Samuel S, Woltereck Lukas R LR, Petrosius Valdemaras V, Furtwängler Benjamin B, Searle Brian C BC, Schoof Erwin M EMallergic reaction, Specificity and Sensitivity, Ionen, ion, Ion, sensitive, Peptidomics, iones, periodic FEVER, familial, Specificity, Sensitivity, FPF., ions, sensitivity, autosomal dominant, DIADCR1, Ghrfr, CDF, l(2)k07135, peptides, POF2, DCR1-TNFR, F27C12_24, Desmoplastic astrocytoma of infancy, HeLa, F27C12.24, lit, CG1768, DIASP, DRF2, TRAIL-R3, DIA, Dia, CD263, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, polypeptide, peptide, Polypeptides, ms(2)04138, Desmoplastic infantile astrocytoma, POF, TRAILR3, peptido, DmelCG1768, MLPLI, DIANA, 38E.16, HILDA, Peptid, peptidos, AGAMOUS-like 61, RCB0007, Polypeptide, LIT, DIA2, Dias, Peptide., DiA, TRID, littleallergic reaction, Specificity and Sensitivity, Ionen, ion, Ion, sensitive, Peptidomics, iones, periodic FEVER, familial, Specificity, Sensitivity, FPF., ions, sensitivity, autosomal dominant, DIAl(3)rK137, scale tissue, ms(2)5970, Product, ion, instrument configuration, Mbp1, Measure, CG17228, Cost-Minimization, 1135/09, dmTAF[[II]]230, 1135/07, Techniques, POE, Biological, Method, DmelCG14472, 0451/09, Analysis, ms(2)3420, Biological Product, Cost Comparison, myd, WMS, Mass Spectrum Analysis, 0244/09, me75, 3420, Biologic Drugs, TFIID TAF250, Analyses, cel, MUB3_18, Natural, Cost-Minimization Analyses, plant peltate hair, calo, DROPROSA, HardwareType, Mbp-1, Comparison, analyzer, Biological Drugs, MUB3.18, l(3)j6E2, D17Mit170, T1, DIA, Social, allergic reaction, 671/2, Cost Analysis, 0320/10, Biological Medicine, DMPROSPER, ms(2)27C, Methodological Studies, Medicine, Medicines, Comparisons, Affordabilities, GPHYSD2, Biologic Drug, SGS, dTAF[[II]]230, Biologic Products, l(3)rO534, gyltl1b-b, PRO, Pro, familial, TAF200, Attention Focus, TAFII-250, Procedure, TAF250/230, Tl3, Tl2, Spectrum Analysis, CYS, Calo, ACMICD, Spectroscopy, TAFII250, PROS-1, Attention, PROS-2, Ionen, Biopharmaceuticals, pro, MDDGA6, mKIAA0609, 1316/02, Biologic Product, BcDNA:HL08040, KIAA0609, and GLY protein 2, ms(2)01659, finances, FPF, fg, and GLY protein 1, gyltl1b, instrument, Voila, Biological Medicines, Biological Drug, 0664/07, 1167/13, mdc1d, Spectrometry, expanded, salaries, Biologics, Methodological, MASS, CG17603, TAF[[II]], Methodological Study, MDC1D, enr, Taf250, Specificity and Sensitivity, enlarged, SR3-5, FAIMS, l(1)16Fg, financial management, 0989/01, TAF230, Cost Analyses, pds, Mental, big, d230, Procedures, Biologic Pharmaceuticals, Peptidomics, peltate hair, FBN, dTAFII250, Selective, Cost Comparisons, Spectrum Analyses, EfW1, 0763/13, CG14472, autosomal dominant, froggy, hardware, Gyltl1a, l(3)10419, dmTAF8, method, large, DmelCG17228, Cost Minimization Analysis, dmTAF1, Taf230, sensitive, ECTOL1, method used in an experiment, push, HL-VIII, Mass, Studies, anon-WO0140519.15, F15E12.6, Low, Prosp, sensitivity, Technique, Mass Spectroscopy, TAF250, Biologicals, Drugs, PROS, Taf200, F15E12_6, 0585/13, dTAF[[II]]250, FOCUS, cell, Cost Measures, iones, MDDGB6, Affordability, Natural Product, CG7128, Measures, Taf1p, LARGE, financing, ions, l(3)rH013, OCTD, Study, dTAF250, funding, BPFD#36, prod, Prodos, Social Attention, Concentration, great, Sensitivity, TAF, 0563/18, Chromatographies, Biologic, Pharmaceuticals, 0671/02, Peptidomics., l(3)j12C8, Products, fees, TAF[[II]]250, cou, Biologic Medicines, l(3)84Ab, BG:DS00004.13, Cell, l(3)rJ806, dTAF230, Pros, l(3)rL433, MS, Lr, Selective Attention, l(3)rI160, 0441/16, p230, Biopharmaceutical, periodic FEVER, TAF[[II]]250/230, TFIID, MFS1, Focus of Attention, scales, Mass Spectrum Analyses, MET, ATCMPG1, WMS2, ATCMPG2, Costs and Cost Analyses, Taf[[II]]250, Mass Spectrum, Costs, TAF[[II]]230, scale, Cost, Specificity, Cost-Minimization Analysis, Mental Concentration, TAF[II]250, Pricing, Drug, plan specification, l(3)rK204, cost, DmelCG17603, DmelCG7128, Ion, SSKS, Bra, Natural Products, Cost Measure, TAF8, TAF10PXD034862falseHigh sensitivity limited material proteomics empowered by data-independent acquisition on linear ion trapsLIT-DIA data from HeLa tryptic peptide dilution seriesFri Jun 24 05:18:00 BST 2022MSV00008971836287219