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org/10.1002/sscp.201900057
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(2009) The detection, correlation, and comparison of peptide precursor and product ions
from data independent LC-MS with data
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9:1683–1695.
https://doi.org/10.1002/
pmic.200800562
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An investigation of the mobility separation of
some peptide and protein ions using a new
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261:1–12. https://doi.org/10.1016/j.ijms.
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quantitative accuracy and precision in complex
proteomics samples. Anal Bioanal Chem
404:1127–1139. https://doi.org/10.1007/
s00216-012-6197-y
23. Helm D, Vissers JPC, Hughes CJ et al (2014)
Ion mobility tandem mass spectrometry
enhances performance of bottom-up proteomics. Mol Cell Proteomics 13:3709–3715.
https://doi.org/10.1074/mcp.M114.
041038
24. Lanucara F, Holman SW, Gray CJ, Eyers CE
(2014) The power of ion mobility-mass spectrometry for structural characterization and the
study of conformational dynamics. Nat Chem
6:281–294.
https://doi.org/10.1038/
nchem.1889
25. Distler U, Kuharev J, Navarro P, Tenzer S
(2016) Label-free quantification in ion
mobility-enhanced data-independent acquisition proteomics. Nat Protoc 11:795–812.
https://doi.org/10.1038/nprot.2016.042
26. Distler U, Kuharev J, Navarro P et al (2014)
Drift time-specific collision energies enable
deep-coverage data-independent acquisition
proteomics. Nat Methods 11:167–170.
https://doi.org/10.1038/nmeth.2767
27. Souza GHMF, Guest PC, Martins-de-Souza D
(2017) LC-MS, multiplex MS/MS, ion mobility, and label-free quantitation in clinical proteomics. Methods Mol Biol 1546:57–73.
https://doi.org/10.1007/978-1-4939-67308_4
28. Silva JC, Gorenstein MV, Li G-Z et al (2006)
Absolute quantification of proteins by LCMSE:
a virtue of parallel MS acquisition. Mol Cell
Proteomics 5:144–156. https://doi.org/10.
1074/mcp.M500230-MCP200
Human Blood Plasma Investigation Employing 2D UPLC-UDMS
E Data. . .
165
Exp Med Biol 974:193–203
18. Silva-Costa LC, Garcia-Rosa S, Smith BJ et al
(2019) Blood plasma high abundant protein
depletion unintentionally carries over 100 proteins. Sep Sci Plus 2:449–456. https://doi.
org/10.1002/sscp.201900057
19. Link AJ, Eng J, Schieltz DM et al (1999)
Direct analysis of protein complexes using
mass
spectrometry.
Nat
Biotechnol
17:676–682.
https://doi.org/10.1038/
10890
20. Geromanos SJ, Vissers JPC, Silva JC et al
(2009) The detection, correlation, and comparison of peptide precursor and product ions
from data independent LC-MS with data
dependant
LC-MS/MS.
Proteomics
9:1683–1695.
https://doi.org/10.1002/
pmic.200800562
21. Pringle SD, Giles K, Wildgoose JL et al (2007)
An investigation of the mobility separation of
some peptide and protein ions using a new
hybrid quadrupole/travelling wave IMS/oaToF instrument. Int J Mass Spectrom
261:1–12. https://doi.org/10.1016/j.ijms.
2006.07.021
22. Geromanos SJ, Hughes C, Ciavarini S et al
(2012) Using ion purity scores for enhancing
quantitative accuracy and precision in complex
proteomics samples. Anal Bioanal Chem
404:1127–1139. https://doi.org/10.1007/
s00216-012-6197-y
23. Helm D, Vissers JPC, Hughes CJ et al (2014)
Ion mobility tandem mass spectrometry
enhances performance of bottom-up proteomics. Mol Cell Proteomics 13:3709–3715.
https://doi.org/10.1074/mcp.M114.
041038
24. Lanucara F, Holman SW, Gray CJ, Eyers CE
(2014) The power of ion mobility-mass spectrometry for structural characterization and the
study of conformational dynamics. Nat Chem
6:281–294.
https://doi.org/10.1038/
nchem.1889
25. Distler U, Kuharev J, Navarro P, Tenzer S
(2016) Label-free quantification in ion
mobility-enhanced data-independent acquisition proteomics. Nat Protoc 11:795–812.
https://doi.org/10.1038/nprot.2016.042
26. Distler U, Kuharev J, Navarro P et al (2014)
Drift time-specific collision energies enable
deep-coverage data-independent acquisition
proteomics. Nat Methods 11:167–170.
https://doi.org/10.1038/nmeth.2767
27. Souza GHMF, Guest PC, Martins-de-Souza D
(2017) LC-MS, multiplex MS/MS, ion mobility, and label-free quantitation in clinical proteomics. Methods Mol Biol 1546:57–73.
https://doi.org/10.1007/978-1-4939-67308_4
28. Silva JC, Gorenstein MV, Li G-Z et al (2006)
Absolute quantification of proteins by LCMSE:
a virtue of parallel MS acquisition. Mol Cell
Proteomics 5:144–156. https://doi.org/10.
1074/mcp.M500230-MCP200
Human Blood Plasma Investigation Employing 2D UPLC-UDMS
E Data. . .
165