Peptide samples were measured by Pierce Quantitative Fluorometric Peptide Assay using a Varioskan LUX multimode microplate reader and diluted to 0.2 μg/μL. Samples (5 μL; 1 μg per injection) were analyzed using a Dionex UltiMate™ 3000 RSLCnano liquid chromatography (LC) system coupled to an Orbitrap Exploris™ 480 mass spectrometer (Thermo Fisher Scientific). Data acquisition and analysis settings are in supplementary information (Supplemental Tables S4 and S5 ). Data-dependent acquisition (DDA) sample sets spiked with Pierce™ Retention Time Calibration mixture (Thermo Fisher Scientific), and data-independent acquisition (DIA) sample sets spiked with iRT synthetic peptide mixture (Biognosys) were blocked and acquired in randomized order with digested E. coli spiked with iRT synthetic peptide mixture injected immediately before and after every sixth sample to evaluate system performance. Consistency and reproducibility of system performance were evaluated using Skyline Daily (20.2.1.315), QuiC (3.1.200602.47994), and Proteome Discoverer 2.4 (Thermo Fisher Scientific). Data files for all experiments in Table 1 are available at MassIVE (massive.ucsd.edu ; doi:10.25345/C55515 ) and experimental identifiers for each file name are provided in Supplemental Table S6 .
Skyline daily
Manufactured by Thermo Fisher Scientific
Skyline Daily is a software tool developed by Thermo Fisher Scientific. It is designed to facilitate the analysis and visualization of mass spectrometry data. The software provides users with a platform to process, manage, and interpret complex proteomic and metabolomic data.
Automatically generated - may contain errors
Lab products found in correlation
Orbitrap exploris 480 mass spectrometer, by Thermo Fisher Scientific (2 mentions)
Proteome discoverer 2, by Thermo Fisher Scientific (2 mentions)
Dionex ultimate 3000 rslcnano, by Thermo Fisher Scientific (2 mentions)
Irt synthetic peptide mixture, by Biognosys (2 mentions)
Pierce retention time calibration mixture, by Thermo Fisher Scientific (2 mentions)
2 protocols using skyline daily
1
Peptide Quantification and Mass Spectrometry
2
Peptide Quantification and Mass Spectrometry
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Peptide samples were measured by Pierce Quantitative Fluorometric Peptide Assay using a Varioskan LUX multimode microplate reader and diluted to 0.2 μg/μL. Samples (5 μL; 1 μg per injection) were analyzed using a Dionex UltiMate™ 3000 RSLCnano liquid chromatography (LC) system coupled to an Orbitrap Exploris™ 480 mass spectrometer (Thermo Fisher Scientific). Data acquisition and analysis settings are in supplementary information (Supplemental Tables S4 and S5 ). Data-dependent acquisition (DDA) sample sets spiked with Pierce™ Retention Time Calibration mixture (Thermo Fisher Scientific), and data-independent acquisition (DIA) sample sets spiked with iRT synthetic peptide mixture (Biognosys) were blocked and acquired in randomized order with digested E. coli spiked with iRT synthetic peptide mixture injected immediately before and after every sixth sample to evaluate system performance. Consistency and reproducibility of system performance were evaluated using Skyline Daily (20.2.1.315), QuiC (3.1.200602.47994), and Proteome Discoverer 2.4 (Thermo Fisher Scientific). Data files for all experiments in Table 1 are available at MassIVE (massive.ucsd.edu ; doi:10.25345/C55515 ) and experimental identifiers for each file name are provided in Supplemental Table S6 .
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