Journal
JOURNAL OF PROTEOME RESEARCH
Volume 15, Issue 3, Pages 976-982Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.5b00997
Keywords
top-down proteomics; proteoform; cellular senescence; GELFrEE; Fourier transform mass spectrometry; label-free; quantitative proteomics; differential mass spectrometry
Categories
Funding
- National Institute of General Medical Sciences of the National Institutes of Health [GM067193, GM108569]
- federal funds from the National Cancer Institute (Office of Cancer Clinical Proteomics Research) [HHSN261200800001E]
- Office of Research at Northwestern University
- UIUC Center for Neuroproteomics on Cell to Cell Signaling [P30 DA018310]
- Robert H. Lurie Comprehensive Cancer Center
- Swiss National Science Foundation
- Cancer Research UK [15890] Funding Source: researchfish
Ask authors/readers for more resources
Top-down proteomics is capable of identifying and quantitating unique proteoforms through the analysis of intact proteins. We extended the coverage of the label-free technique, achieving differential analysis of whole proteins <30 kDa from the proteomes of growing and senescent human fibroblasts. By integrating improved control software with more instrument time allocated for quantitation of intact ions, we were able to collect protein data between the two cell states, confidently comparing 1577 proteoform levels. To then identify and characterize proteoforms, our advanced acquisition software, named AUTOPILOT, employed enhanced identification efficiency in identifying 1180 unique Swiss-Prot accession numbers at 1% false-discovery rate. This coverage of the low mass proteome is equivalent to the largest previously reported but was accomplished in 23% of the total acquisition time. By maximizing both the number of quantified proteoforms and their identification rate in an integrated software environment, this work significantly advances proteoform-resolved analyses of complex systems.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available