title: Automated iterative MS/MS acquisition: a tool for improving efficiency of protein identification using a LC-MALDI MS workflow.
abstract: We have developed an information-dependent, iterative MS/MS acquisition (IMMA) tool for improving MS/MS efficiency, increasing proteome coverage, and shortening analysis time for high-throughput proteomics applications based on the LC-MALDI MS/MS platform. The underlying principle of IMMA is to limit MS/MS analyses to a subset of molecular ions that are likely to identify a maximum number of proteins. IMMA reduces redundancy of MS/MS analyses by excluding from the precursor ion peak lists proteotypic peptides derived from the already identified proteins and uses a retention time prediction algorithm to limit the degree of false exclusions. It also increases the utilization rate of MS/MS spectra by removing "low value" unidentifiable targets like nonpeptides and peptides carrying large loads of modifications, which are flagged by their "nonpeptide" excess-to-nominal mass ratios. For some samples, IMMA increases the number of identified proteins by ∼20-40% when compared to the data dependent methods. IMMA terminates an MS/MS run at the operator-defined point when "costs" (e.g., time of analysis) start to overrun "benefits" (e.g., number of identified proteins), without prior knowledge of sample contents and complexity. To facilitate analysis of closely related samples, IMMA's inclusion list functionality is currently under development.
authors.affiliation: UCSF Sandler-Moore Mass Spectrometry Core Facility and Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, California 94143, United States.
authors.forename: Haichuan
authors.initials: H
authors.lastname: Liu
authors.forename: Lee
authors.initials: L
authors.lastname: Yang
authors.forename: Nikita
authors.initials: N
authors.lastname: Khainovski
authors.forename: Ming
authors.initials: M
authors.lastname: Dong
authors.forename: Steven C
authors.initials: SC
authors.lastname: Hall
authors.forename: Susan J
authors.initials: SJ
authors.lastname: Fisher
authors.forename: Mark D
authors.initials: MD
authors.lastname: Biggin
authors.forename: Jian
authors.initials: J
authors.lastname: Jin
authors.forename: H Ewa
authors.initials: HE
authors.lastname: Witkowska
mesh_terms: D000465:Algorithms; D002853:Chromatography, Liquid / Q000379:methods*; D007477:Ions; D011506:Proteins / Q000032:analysis* / Q000737:chemistry; D040901:Proteomics / Q000379:methods*; D012984:Software; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods*; D057188:Workflow
chemical_list: D007477:Ions; D011506:Proteins