MaRiMba: a software application for spectral library-based MRM transition list assembly.

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.

[1]  Leigh Anderson,et al.  Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins* , 2006, Molecular & Cellular Proteomics.

[2]  R. Aebersold,et al.  High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites*S , 2007, Molecular & Cellular Proteomics.

[3]  Ruedi Aebersold,et al.  Building consensus spectral libraries for peptide identification in proteomics , 2008, Nature Methods.

[4]  Sándor Suhai,et al.  Fragmentation pathways of protonated peptides. , 2005, Mass spectrometry reviews.

[5]  D. Lauffenburger,et al.  Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks , 2007, Proceedings of the National Academy of Sciences.

[6]  W. Ens,et al.  Sequence-specific retention calculator. A family of peptide retention time prediction algorithms in reversed-phase HPLC: applicability to various chromatographic conditions and columns. , 2007, Analytical chemistry.

[7]  Christine A. Miller,et al.  Efficient Fractionation and Improved Protein Identification by Peptide OFFGEL Electrophoresis*S , 2006, Molecular & Cellular Proteomics.

[8]  Ruedi Aebersold,et al.  The standard protein mix database: a diverse data set to assist in the production of improved Peptide and protein identification software tools. , 2008, Journal of proteome research.

[9]  Nichole L. King,et al.  Development and validation of a spectral library searching method for peptide identification from MS/MS , 2007, Proteomics.

[10]  Anna Sannino,et al.  Application of liquid chromatography with electrospray tandem mass spectrometry to the determination of a new generation of pesticides in processed fruits and vegetables. , 2004, Journal of chromatography. A.

[11]  S. Carr,et al.  Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution*S , 2007, Molecular & Cellular Proteomics.

[12]  David M Bunk,et al.  Development and evaluation of a reference measurement procedure for the determination of total 3,3',5-triiodothyronine in human serum using isotope-dilution liquid chromatography-tandem mass spectrometry. , 2004, Analytical chemistry.

[13]  Nichole L. King,et al.  Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring*S , 2008, Molecular & Cellular Proteomics.

[14]  O. Krokhin,et al.  Sequence-specific retention calculator. Algorithm for peptide retention prediction in ion-pair RP-HPLC: application to 300- and 100-A pore size C18 sorbents. , 2006, Analytical chemistry.

[15]  Jennifer A Mead,et al.  MRMaid, the Web-based Tool for Designing Multiple Reaction Monitoring (MRM) Transitions* , 2009, Molecular & Cellular Proteomics.

[16]  R. Kostiainen,et al.  Liquid chromatography/atmospheric pressure ionization-mass spectrometry in drug metabolism studies. , 2003, Journal of mass spectrometry : JMS.

[17]  M. Lee,et al.  LC/MS applications in drug development. , 2002, Mass spectrometry reviews.

[18]  R. Beavis,et al.  An Improved Model for Prediction of Retention Times of Tryptic Peptides in Ion Pair Reversed-phase HPLC , 2004, Molecular & Cellular Proteomics.

[19]  J. Mesirov,et al.  Prediction of high-responding peptides for targeted protein assays by mass spectrometry , 2009, Nature Biotechnology.

[20]  Damon May,et al.  MRMer, an Interactive Open Source and Cross-platform System for Data Extraction and Visualization of Multiple Reaction Monitoring Experiments*S⃞ , 2008, Molecular & Cellular Proteomics.

[21]  R. Aebersold,et al.  A uniform proteomics MS/MS analysis platform utilizing open XML file formats , 2005, Molecular systems biology.

[22]  Gary L. Glish,et al.  Origin of product ions in the MS/MS spectra of peptides in a quadrupole ion trap , 1998, Journal of the American Society for Mass Spectrometry.

[23]  A. P. Land,et al.  Drug quantitation on a benchtop liquid chromatography-tandem mass spectrometry system. , 1997, Journal of chromatography. A.

[24]  John P Cortens,et al.  Use of peptide retention time prediction for protein identification by off-line reversed-phase HPLC-MALDI MS/MS. , 2006, Analytical chemistry.