Protein identification by liquid chromatography–mass spectrometry using retention time prediction

Palmblad, Magnus; Ramström, Margareta; Bailey, Christopher G.; McCutchen-Maloney, Sandra L.; Bergquist, Jonas; Zeller, Loreen C.

doi:10.1016/j.jchromb.2003.11.007

Cited by 50 publications

(48 citation statements)

References 31 publications

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“…To overcome these drawbacks, we have compared the possible combinations obtained by software analysis with the sequences of the main rapeseed proteins (cruciferin and napin) (Schwenke, 1994). The purpose of that investigation was to keep only the peptides which can be encountered in rapeseed proteins (Palmblad et al, 2004). As a result, the list was reduced to only two possible sequences for the peptide with a MM of 343.4 g/ mol: VLI or LVI, which correspond to only one combination.…”

Section: Description Of the Prediction Methodsmentioning

confidence: 99%

Prediction of the amino acid composition of small peptides contained in a plant protein hydrolysate by LC–MS and CE–MS

Tessier¹,

Schweizer²,

Fournier³

et al. 2005

Food Research International

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Section: Description Of the Prediction Methodsmentioning

confidence: 99%

Prediction of the amino acid composition of small peptides contained in a plant protein hydrolysate by LC–MS and CE–MS

Tessier¹,

Schweizer²,

Fournier³

et al. 2005

Food Research International

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“…The medium was experimentally derived to elicit the best growth parameters for vegetative Y. pestis cells and was previously shown to permit full-scale growth under all the conditions used here (22). Therefore, BCS medium ensures that differences in protein expression are not due to growth arrest, and the growth parameters of temperature and calcium used here have previously been employed to study changes in gene (52) and protein (54,74) expression. Taken together, the observed changes in protein expression detected in this study reflect adaptations to growth conditions rather than changes due to a cessation of growth.…”

Section: Differential Protein Expression Following Change From 26°cmentioning

confidence: 99%

Proteomic Characterization ofYersinia pestisVirulence

et al. 2005

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The Yersinia pestis proteome was studied as a function of temperature and calcium by two-dimensional differential gel electrophoresis. Over 4,100 individual protein spots were detected, of which hundreds were differentially expressed. A total of 43 differentially expressed protein spots, representing 24 unique proteins, were identified by mass spectrometry. Differences in expression were observed for several virulence-associated factors, including catalase-peroxidase (KatY), murine toxin (Ymt), plasminogen activator (Pla), and F1 capsule antigen (Caf1), as well as several putative virulence factors and membrane-bound and metabolic proteins. Differentially expressed proteins not previously reported to contribute to virulence are candidates for more detailed mechanistic studies, representing potential new virulence determinants.Yersinia pestis, the etiological agent of plague, is a gram-negative bacterium that is both a natural environmental pathogen and a biothreat agent (4,8,32). Early studies of Yersinia physiology uncovered the low calcium response (LCR), whereby bacterial cultures grown in rich medium at an elevated temperature (37°C) exhibit a growth defect upon chelation of calcium ions. The growth arrest was shown to be a result of one of the two type III secretion systems (TTSSs) in Y. pestis, the Ysc TTSS, and is responsible for the secretion of virulence factors known as Yersinia outer proteins, or Yops (21, 29; for a review, see reference 61). This TTSS can be activated in vitro and virulence factors can be released into the medium when Y. pestis is grown at 37°C with submillimolar calcium (for a review, see reference 16). Upon interaction with the host, the TTSS enables virulence factors to enter the host cell through a specialized apparatus, the injectisome (15). Once inside the host cell, Yops affect a variety of host pathways, with detectable expression changes in the pathogen as well as the host (14,52,82).The Y. pestis proteome was previously examined using twodimensional electrophoresis (57,60,71,72). These studies demonstrated that virulence factors were not induced at 26°C or 37°C in the presence of calcium concentrations similar to that found in mammalian plasma (2.5 mM) (71). More recently, the introduction of two-dimensional differential gel electrophoresis (2-D DIGE) has significantly improved the quality of gel-based proteomics through fluorescence-based multiplex analyses providing relative quantitation of expression differences and improved gel-to-gel comparisons (75). Several examples of 2-D DIGE bacterial proteomics have been reported (23), including characterizations of the gram-negative bacterium Escherichia coli (1, 76, 81). Here we report the characterization of the soluble cell-associated proteome of Y. pestis as a function of temperature and calcium, which were used to effect virulence induction. Differentially expressed proteins include virulence-associated factors, membrane-bound proteins, metabolic and housekeeping proteins, and potential new virulence determinants.Bacterial ...

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“…However, as the genomic, and thus, the proteomic, complexity of an organism increases, the ability to identify proteins (or peptides) on the basis of mass measurements alone decreases. Additional information such as isoelectric point, LC elution time or, most commonly, the analysis of peptide fragment ions must be used to distinguish peptides that have identical or very similar masses [11][12][13][14]. Experimental approaches to address this complexity include more extensive protein or peptide separations, or focusing on only those peptides with a specific physical characteristic (e.g., isolation of cysteinyl peptides by chemical labeling or solid phase extraction techniques [15][16][17], and fractionation techniques to add a second separation dimension, e.g., MudPIT [2, 18 -23], in addition to the use of peptide ion fragmentation patterns.…”

mentioning

confidence: 99%

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

Norbeck

Monroe

Adkins

et al. 2005

J. Am. Soc. Mass Spectrom.

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The combination of mass and normalized elution time (NET) of a peptide identified by liquid chromatography-mass spectrometry (LC-MS) measurements can serve as a unique signature for that peptide. However, the specificity of an LC-MS measurement depends upon the complexity of the proteome (i.e., the number of possible peptides) and the accuracy of the LC-MS measurements. In this work, theoretical tryptic digests of all predicted proteins from the genomes of three organisms of varying complexity were evaluated for specificity. Accuracy of the LC-MS measurement of mass-NET pairs (on a 0 to 1.0 NET scale) was described by bivariate normal sampling distributions centered on the peptide signatures. Measurement accuracy (i.e., mass and NET standard deviations of Ϯ0.1, 1, 5, and 10 ppm, and Ϯ0.01 and 0.05, respectively) was varied to evaluate improvements in process quality. The spatially localized confidence score, a conditional probability of peptide uniqueness, formed the basis for the peptide identification. Application of this approach to organisms with comparatively small proteomes, such as Deinococcus radiodurans, shows that modest mass and elution time accuracies are generally adequate for confidently identifying most peptides. For more complex proteomes, more accurate measurements are required. However, the study suggests that the majority of proteins for even the human proteome should be identifiable with reasonable confidence by using LC-MS measurements with mass accuracies within Ϯ1 ppm and high efficiency separations having elution time measurements within Ϯ0.01

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Protein identification by liquid chromatography–mass spectrometry using retention time prediction

Cited by 50 publications

References 31 publications

Prediction of the amino acid composition of small peptides contained in a plant protein hydrolysate by LC–MS and CE–MS

Prediction of the amino acid composition of small peptides contained in a plant protein hydrolysate by LC–MS and CE–MS

Proteomic Characterization ofYersinia pestisVirulence

The Utility of Accurate Mass and LC Elution Time Information in the Analysis of Complex Proteomes

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