期刊
JOURNAL OF PROTEOME RESEARCH
卷 8, 期 10, 页码 4396-4405出版社
AMER CHEMICAL SOC
DOI: 10.1021/pr900010h
关键词
multiple reaction monitoring (MRM); selective reaction monitoring (SRM); MRM transition; transition list; spectral library; mass spectrometry; targeted proteomics
资金
- NIH [R21 CA126216, N01-HV-28179]
- Center for Systems Biology [P50 GM076547]
- National Heart, Lung, and Blood Institute
Multiple reaction monitoring mass spectrometry (MRM-MS) is a targeted analysis method that has been increasingly viewed as an avenue to explore proteomes with unprecedented sensitivity and throughput. We have developed a software tool, called MaRiMba, to automate the creation of explicitly defined MRM transition lists required to program triple quadrupole mass spectrometers in such analyses. MaRiMba creates MRM transition lists from downloaded or custom-built spectral libraries, restricts output to specified proteins or peptides, and filters based on precursor peptide and product. ion properties. MaRiMba can also create MRM lists containing corresponding transitions for isotopically heavy peptides, for which the precursor and product ions are adjusted according to user specifications. This open-source application is operated through a graphical user interface incorporated into the Trans-Proteomic Pipeline, and it outputs the final MRM list to a text file for upload to MS instruments. To illustrate the use of MaRiMba, we used the tool to design and execute an MRM-MS experiment in which we targeted the proteins of a well-defined and previously published standard mixture.
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