Transferred AGP fractions were analysed in PMI Intact Mass v3.4 (Protein Metrics, Cupertino, CA, USA). For each separation, time slices of 15 or 30 s were created to cover the peak containing the different AGP glycoforms. Mass spectra in these time slices were deconvoluted to obtain a mass list for each time slice. The obtained masses were matched to the theoretical masses with an allowed deviation of 0.5 Da. If one measured mass matched to multiple theoretical masses, the match with the lowest deviation was chosen. This results in a list of putative glycoform assignments.
Pmi intact mass v3
Manufactured by Protein Metrics
Sourced in United States
The PMI Intact Mass v3.4 is a software solution for the analysis of intact protein mass data. It provides a suite of tools for the processing, visualization, and interpretation of high-resolution mass spectrometry data. The software supports a wide range of mass spectrometry instruments and file formats, enabling researchers to analyze a variety of protein samples.
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Lab products found in correlation
2 protocols using pmi intact mass v3
1
AGP Glycoform Analysis Protocol
2
Mass Spectrometry Data Analysis Protocol
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TOF MS data analysis, including charge state deconvolution was performed using Agilent Masshunter Workstation (BioConfirm B.06.00). Orbitrap MS data were analyzed using Freestyle 1.5 and deconvolution was performed with PMI Intact Mass v3.4 (Protein Metrics, Cupertino, CA, USA). In general, extracted ion electropherograms (EIEs) were created by summation of the intensity of the three most abundant charge states for a protein. EIEs were smoothed with default parameters in Agilent Mass Hunter, and with the moving mean algorithm (7 data points) in Freestyle. All quantification results were obtained by peak integration of these EIEs. Relative quantification of glycated and carbamylated and -Hb was performed by dividing the peak area of the glycated /carbamylated peak by the sum of peak areas of all identified or -chains. MS/MS data were analyzed using ProSight Lite v1.4 (Northwestern University, Evanston, IL, USA) after deconvolution of the fragment spectra with the Xtract algorithm embedded in Freestyle. Fragment maps were created by using primary sequences obtained from Uniprot with a fragment tolerance of 5 ppm.
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