Simultaneous Proteomic Discovery and Targeted Monitoring using Liquid Chromatography, Ion Mobility Spectrometry, and Mass Spectrometry.
Current proteomic approaches include both broad discovery measurements and quantitative targeted analyses. In many cases, discovery measurements are initially used to identify potentially important proteins (e.g. candidate biomarkers) and then targeted studies are employed to quantify a limited number of selected proteins. Both approaches, however, suffer from limitations. Discovery measurements aim to sample the whole proteome but have lower sensitivity, accuracy, and quantitation precision than targeted approaches, whereas targeted measurements are significantly more sensitive but only sample a limited portion of the proteome. Herein, we describe a new approach that performs both discovery and targeted monitoring (DTM) in a single analysis by combining liquid chromatography, ion mobility spectrometry and mass spectrometry (LC-IMS-MS). In DTM, heavy labeled target peptides are spiked into tryptic digests and both the labeled and unlabeled peptides are detected using LC-IMS-MS instrumentation. Compared with the broad LC-MS discovery measurements, DTM yields greater peptide/protein coverage and detects lower abundance species. DTM also achieved detection limits similar to selected reaction monitoring (SRM) indicating its potential for combined high quality discovery and targeted analyses, which is a significant step toward the convergence of discovery and targeted approaches.
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Kristin E
KE
Burnum-Johnson
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Song
S
Nie
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Cameron P
CP
Casey
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Matthew E
ME
Monroe
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Daniel J
DJ
Orton
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Yehia M
YM
Ibrahim
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Marina A
MA
Gritsenko
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Therese R W
TR
Clauss
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Anil K
AK
Shukla
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Ronald J
RJ
Moore
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Samuel O
SO
Purvine
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Tujin
T
Shi
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Weijun
W
Qian
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington.
Tao
T
Liu
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington rds@pnnl.gov erin.baker@pnnl.gov.
Erin S
ES
Baker
From the ‡Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington rds@pnnl.gov erin.baker@pnnl.gov.
Richard D
RD
Smith
D000818:Animals; D001943:Breast Neoplasms / Q000378:metabolism*; D002853:Chromatography, Liquid / Q000379:methods; D005260:Female; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D051379:Mice; D009368:Neoplasm Transplantation; D010455:Peptides / Q000032:analysis*; D020543:Proteome / Q000302:isolation & purification*; D040901:Proteomics / Q000379:methods*
D010455:Peptides; D020543:Proteome
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