An LC-IMS-MS Platform Providing Increased Dynamic Range for High-Throughput Proteomic Studies

Journal Article · Fri Feb 05 04:00:00 EST 2010 · Journal of Proteome Research, 9(2):997-1006

DOI:https://doi.org/10.1021/pr900888b· OSTI ID:974911

Baker, Erin Shammel; Livesay, Eric A; Orton, Daniel J; Moore, Ronald J; Danielson, William F; Prior, David C; Ibrahim, Yehia M; Lamarche, Brian L; Mayampurath, Anoop M; Schepmoes, Athena A; Hopkins, Derek F; Tang, Keqi; Smith, Richard D; Belov, Mikhail E

A high-throughput approach and platform using 15 minute reversed-phase capillary liquid chromatography (RPLC) separations in conjunction with ion mobility spectrometry-mass spectrometry (IMS-MS) measurements was evaluated for the rapid analysis of complex proteomics samples. To test the separation quality of the short LC gradient, a sample was prepared by spiking twenty reference peptides at varying concentrations from 1 ng/mL to 10 µg/mL into a tryptic digest of mouse blood plasma and analyzed with both a LC-Linear Ion Trap Fourier Transform (FT) MS and LC-IMS-TOF MS. The LC-FT MS detected thirteen out of the twenty spiked peptides that had concentrations ≥100 ng/mL. In contrast, the drift time selected mass spectra from the LC-IMS-TOF MS analyses yielded identifications for nineteen of the twenty peptides with all spiking level present. The greater dynamic range of the LC-IMS-TOF MS system could be attributed to two factors. First, the LC-IMS-TOF MS system enabled drift time separation of the low concentration spiked peptides from the high concentration mouse peptide matrix components, reducing signal interference and background, and allowing species to be resolved that would otherwise be obscured by other components. Second, the automatic gain control (AGC) in the linear ion trap of the hybrid FT MS instrument limits the number of ions that are accumulated to reduce space charge effects, but in turn limits the achievable dynamic range compared to the TOF detector.

• Research Organization: Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC05-76RL01830
• OSTI ID: 974911
• Report Number(s): PNNL-SA-67461; 24698; 17797; 32707; 31590; KP1704020
• Journal Information: Journal of Proteome Research, 9(2):997-1006, Journal Name: Journal of Proteome Research, 9(2):997-1006
• Country of Publication: United States
• Language: English

Related Subjects

Environmental Molecular Sciences Laboratory
IMS-MS
Ion mobility spectrometry
LC-IMS-MS
RPLC separations
TOF mass spectrometry
biomarker discovery
cancer
capillary liquid-chromatography
funnel trap
high-throughput RPLC
human plasma proteome
ion-cyclotron resonance
mobility spectrometry