Standardization of retention time data for AMT tag proteomics database generation

Tarasova, Irina A.; Guryča, Vilém; Pridatchenko, M. L.; Gorshkov, A. V.; Kieffer‐Jaquinod, Sylvie; Evreinov, V. V.; Masselon, Christophe; Gorshkov, Mikhail V.

doi:10.1016/j.jchromb.2008.12.047

Cited by 22 publications

(18 citation statements)

References 22 publications

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“…Such experiments are currently being carried out to screen the impact of different environmental conditions or of knock-out mutations at the chloroplast level. Moreover, such an AT_CHLORO database is usable by any laboratory having a high resolution mass spectrometer (FT-ICR or Orbitrap) provided that standardization of the retention times is achieved (104) and that tools dedicated to the AMT strategy are used.…”

Section: Resultsmentioning

confidence: 99%

AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins

Ferro

Brugière

Salvi

et al. 2010

Molecular & Cellular Proteomics

425

490

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Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www. grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further validated as the compartmentation of well known pathways (for instance, photosynthesis and amino acid, fatty acid, or glycerolipid biosynthesis) within chloroplasts could be dissected. It also allowed revisiting the compartmentation of the chloroplast metabolism and functions. Molecular & Cellular Proteomics 9:1063-1084, 2010.Plastids are semiautonomous organelles that are ubiquitously found in plant cells. They are derived from an endosymbiotic event and are thought to have evolved from an ancient photosynthetic prokaryote related to present-day cyanobacteria. Following endosymbiosis, the plastid genome has been reduced to ϳ100 genes, mainly coding for housekeeping functions (translation and transcription of the plastid genome), proteins required for primary photosynthetic reactions, and a few, yet poorly characterized, gene products (1). The most conspicuous plastid type is the chloroplast, found in leaves and carrying out photosynthesis as its main function. Photosynthesis is an integrated biological process involving the coordinated functioning of ...

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Section: Resultsmentioning

confidence: 99%

AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins

Ferro

Brugière

Salvi

et al. 2010

Molecular & Cellular Proteomics

425

490

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“…Outlier data are marked by a black square and are indicative of incorrect identifications or interfered ion intensity measurements. The value and specificity of f1 and f2 increases substantially by supplementing the fragment ion signature with additional orthogonal information, such as standardized peptide retention time [49], drift time [51,55] or collision cross section [56]. Supplementary Figure 3 illustrates the addition of the standardized retention time to f1 and f2, thereby creating a subset ion map for the three fragment ions of interest, indicating substantially improved specificity compared with the results shown in Figs.…”

Section: Resultsmentioning

confidence: 95%

“…Panel (a) of Supplementary Figure 3 illustrates that experimental retention time correlate linearly with predicted normalized hydrophobicity. Panel (b) shows f1 and f2 as a function of non-standardized (raw) retention time, and panel (c) f1 and f2 as a function of retention time after normalization and standardization [49]. Drift time and collision cross section information were not acquired and/or available for the results described.…”

Section: Resultsmentioning

confidence: 99%

“…Their definition and an explanation are provided in Results section. In addition, the peptide retention times are standardized as described by Tarasova et al [49], by obtaining linear fit parameters based on hydrophobicity [50] and standardizing to a reference. This approach affords initial population of the repository with orthogonal identification information from different instruments and laboratories.…”

Section: Relational Database Repositorymentioning

confidence: 99%

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Design and Application of a Data-Independent Precursor and Product Ion Repository

Thalassinos

Vissers

Levin

et al. 2012

J. Am. Soc. Mass Spectrom.

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The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide-and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species.Konstantinos Thalassinos, Johannes P.C. Vissers and Scott J. Geromanos contributed equally to this work. Electronic supplementary material The online version of this article (doi:10.1007/s13361-012-0416-9) contains supplementary material, which is available to authorized users.Correspondence to: Johannes Vissers; e-mail: hans_vissers@waters.com Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.

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“…Absolute retention times vary from instrument to instrument and from column to column (even between columns of the same make and model), and are therefore considered to be of limited use for highconfidence inter-laboratory peak identification. However, relative retention times (or retention indices), where the retention time of each peak is expressed relative to one or two other peaks in the same chromatogram, are far more stable (Tarasova et al, 2009) and may provide an avenue to the compilation of LC-MS reference libraries capable of providing MSI-compliant peak identifications by combining accurate mass MS or MS/MS spectra with meaningful and highly reproducible retention index (RI) properties. Complementary to this approach would be the further development of RI-prediction models that can accurately predict the LC retention indices of metabolites based on their structures (Hagiwara et al, 2010).…”

Section: The Need For Chromatographic Retention Data In Lc/ms Referenmentioning

confidence: 99%

Online Metabolomics Databases and Pipelines

Carroll¹

2012

Metabolomics

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Standardization of retention time data for AMT tag proteomics database generation

Cited by 22 publications

References 22 publications

AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins

AT_CHLORO, a Comprehensive Chloroplast Proteome Database with Subplastidial Localization and Curated Information on Envelope Proteins

Design and Application of a Data-Independent Precursor and Product Ion Repository

Online Metabolomics Databases and Pipelines

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