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Edited Transition and RT Information in Skyline Library Improves DIA Quantification of Cerebral Spinal Fluid (CSF) Proteomes
2016.06.05Skyline User Metting
Potential Problems
2
Prolonged Sample-collection Period in Clinical Projects
Combine one “project-dependent Library”
DDA3DDA2DDA1 DDA4 DDA5
DIA1 DIA3DIA2 DIA4 DIA5
Inconsistent RTs require wider search window, causing
inaccurate identification & quantitation
Our Solution Build a “DIA-dependent library” for each DIA file
3
DDA1
RT: 10’ 30’ 50’
ReferencePeptide 1 Peptide
x
ReferencePeptide 2
DIAx
RT: 13’ 53’
ReferencePeptide 1
ReferencePeptide 2
RT calibration for peptide x
RT: 13’ 33’ 53’
ReferencePeptide 1 Peptide
x
ReferencePeptide 2
DDA2
DDA3
13’ 33.51’ 53’
13’ 31.54’ 53’
Assign “median RT” for Pep xwrite into “DIAx-dependent Library”
“iRT”calibration
Each DIA Filegets its own Library !
Data Improvement
4
90%
95%
100%
105%
110%
115%
120%
rep CSF 1 rep CSF 2 rep CSF 3 rep CSF 4 rep CSF 5
Increased Quantitative Peptide Number by 10.3% in Average
Project-dependent Lib
DIA-dependent Lib
Increased Quantitative Accuracy(e.g. Pep GLEWVANIK)
Aknowledgement
5
Dr.Jie LiNIH, YaleProteinT
A Clinical Proteomic Company
