title: MaRiMba: a software application for spectral library-based MRM transition list assembly.
abstract: 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.
authors: Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA.
authors: Carly A
authors: CA
authors: Sherwood
authors: Ashley
authors: A
authors: Eastham
authors: Lik Wee
authors: LW
authors: Lee
authors: Amelia
authors: A
authors: Peterson
authors: Jimmy K
authors: JK
authors: Eng
authors: David
authors: D
authors: Shteynberg
authors: Luis
authors: L
authors: Mendoza
authors: Eric W
authors: EW
authors: Deutsch
authors: Jenni
authors: J
authors: Risler
authors: Natalie
authors: N
authors: Tasman
authors: Ruedi
authors: R
authors: Aebersold
authors: Henry
authors: H
authors: Lam
authors: Daniel B
authors: DB
authors: Martin
mesh_terms: D000818:Animals; D030562:Databases, Protein; D008168:Lung / Q000737:chemistry; D008297:Male; D013058:Mass Spectrometry / Q000379:methods*; D051379:Mice; D008807:Mice, Inbred BALB C; D010455:Peptides / Q000737:chemistry; D011506:Proteins / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D049490:Systems Biology; D014584:User-Computer Interface
chemical_list: D010455:Peptides; D011506:Proteins