title: AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction.
abstract: BACKGROUND
  Comprehensive description of the behavior of cellular components in a quantitative manner is essential for systematic understanding of biological events. Recent LC-MS/MS (tandem mass spectrometry coupled with liquid chromatography) technology, in combination with the SILAC (Stable Isotope Labeling by Amino acids in Cell culture) method, has enabled us to make relative quantitation at the proteome level. The recent report by Blagoev et al. (Nat. Biotechnol., 22, 1139-1145, 2004) indicated that this method was also applicable for the time-course analysis of cellular signaling events. Relative quatitation can easily be performed by calculating the ratio of peak intensities corresponding to differentially labeled peptides in the MS spectrum. As currently available software requires some GUI applications and is time-consuming, it is not suitable for processing large-scale proteome data.
  
  
  RESULTS
  To resolve this difficulty, we developed an algorithm that automatically detects the peaks in each spectrum. Using this algorithm, we developed a software tool named AYUMS that automatically identifies the peaks corresponding to differentially labeled peptides, compares these peaks, calculates each of the peak ratios in mixed samples, and integrates them into one data sheet. This software has enabled us to dramatically save time for generation of the final report.
  
  
  CONCLUSIONS
  AYUMS is a useful software tool for comprehensive quantitation of the proteome data generated by LC-MS/MS analysis. This software was developed using Java and runs on Linux, Windows, and Mac OS X. Please contact ayums@ims.u-tokyo.ac.jp if you are interested in the application. The project web page is http://www.csml.org/ayums/.
authors.affiliation: The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, Japan. s-ayumu@ims.u-tokyo.ac.jp
authors.forename: Ayumu
authors.initials: A
authors.lastname: Saito
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Masaaki
authors.initials: M
authors.lastname: Oyama
authors.forename: Hiroko
authors.initials: H
authors.lastname: Kozuka-Hata
authors.forename: Kentaro
authors.initials: K
authors.lastname: Semba
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Tadashi
authors.initials: T
authors.lastname: Yamamoto
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000465:Algorithms; D002294:Carcinoma, Squamous Cell / Q000378:metabolism*; D045744:Cell Line, Tumor; D002853:Chromatography, Liquid / Q000379:methods*; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods*; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000378:metabolism*; D010449:Peptide Mapping / Q000379:methods; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction; D012984:Software
chemical_list: D009363:Neoplasm Proteins; D020543:Proteome