Biomarker Candidate Identification in Yersinia pestis Using Organism-Wide Semiquantitative Proteomics

Hixson, Kim; Adkins, Joshua N.; Baker, Scott E.; Moore, Ronald J.; Chromy, Brett A.; Smith, Richard D.; McCutchen-Maloney, Sandra L.; Lipton, Mary

doi:10.1021/pr060179y

Cited by 42 publications

(45 citation statements)

References 50 publications

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“…Spectra corresponding to peptides that matched SAR11 eCDSs associated with transport functions accounted for 67% of the total spectra for SAR11. Using similar methods with cultured SAR11 cells, 28%-35% of all spectra matched transport proteins (Sowell et al, 2008), whereas when the same approach was applied to other Gram-negative bacteria, only 4%-11% of spectra matched to transport proteins Callister et al, 2006;Ding et al, 2006;Hixson et al, 2006;Elias et al, 2008). The prevalence of SAR11 periplasmic substratebinding proteins in the Sargasso Sea metaproteome was not unanticipated.…”

Section: Discussionmentioning

confidence: 91%

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

et al. 2008

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The northwestern Sargasso Sea undergoes annual cycles of productivity with increased production in spring corresponding to periods of upwelling, and oligotrophy in summer and autumn, when the water column becomes highly stratified. The biological productivity of this region is reduced during stratified periods as a result of low concentrations of phosphorus and nitrogen in the euphotic zone. To better understand the mechanisms of microbial survival in this oligotrophic environment, we used capillary liquid chromatography (LC)-tandem mass spectrometry to detect microbial proteins in surface samples collected in September 2005. A total of 2215 peptides that mapped to 236 SAR11 proteins, 1911 peptides that mapped to 402 Prochlorococcus proteins and 2407 peptides that mapped to 404 Synechococcus proteins were detected. Mass spectra from SAR11 periplasmic substrate-binding proteins accounted for a disproportionately large fraction of the peptides detected, consistent with observations that these extremely small cells devote a large proportion of their volume to periplasm. Abundances were highest for periplasmic substrate-binding proteins for phosphate, amino acids, phosphonate, sugars and spermidine. Proteins implicated in the prevention of oxidative damage and protein refolding were also abundant. Our findings support the view that competition for multiple nutrients in oligotrophic systems is extreme, but nutrient flux is sufficient to sustain microbial community activity.

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Section: Discussionmentioning

confidence: 91%

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

et al. 2008

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“…Soluble protein extracts were prepared from a clinical strain of Pseudomonas aeruginosa, isolated from a cystic fibrosis patient [21]. Briefly, the bacteria were grown to 1.2 o.d.…”

Section: Sample Preparationmentioning

confidence: 99%

On the benefits of acquiring peptide fragment ions at high measured mass accuracy

Scherl

Shaffer

Taylor

et al. 2008

J. Am. Soc. Mass Spectrom.

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The advantages and disadvantages of acquiring tandem mass spectra by collision-induced dissociation (CID) of peptides in linear ion trap Fourier-transform hybrid instruments are described. These instruments offer the possibility to transfer fragment ions from the linear ion trap to the FT-based analyzer for analysis with both high resolution and high mass accuracy. In addition, performing CID during the transfer of ions from the linear ion trap (LTQ) to the FT analyzer is also possible in instruments containing an additional collision cell (i.e., the "C-trap" in the LTQ-Orbitrap), resulting in tandem mass spectra over the full m/z range and not limited by the ejection q value of the LTQ. Our results show that these scan modes have lower duty cycles than tandem mass spectra acquired in the LTQ with nominal mass resolution, and typically result in fewer peptide identifications during data-dependent analysis of complex samples. However, the higher measured mass accuracy and resolution provides more specificity and hence provides a lower false positive ratio for the same number of true positives during database search of peptide tandem mass spectra. In addition, the search for modified and unexpected peptides is greatly facilitated with this data acquisition mode. It is therefore concluded that acquisition of tandem mass spectral data with high measured mass accuracy and resolution is a competitive alternative to "classical" data acquisition strategies, especially in situations of complex searches from large databases, searches for modified peptides, or for peptides resulting from unspecific cleavages. analyzers were introduced. These instruments greatly expand opportunities for experimental design because they combine two mass analyzers working in series. Also important to note is that even with external calibration, they deliver mass accuracies in the 2-5 ppm range on a routine basis. Furthermore, even better mass accuracies down to 1-2 ppm have been demonstrated by using the mass difference between adjacent peptide fragment ions in the FT-ICR analyzer [3] as well as injection of a normalized, stable amount of calibrant into the Orbitrap [4] analyzer. The mass accuracy of these instruments is therefore similar to the prior generations sector instruments used at the beginning of the era of mass spectrometry based peptide sequencing [5], but now at unprecedented sensitivity and data acquisition rates. While the community has embraced these new instrument platforms capable of very high mass accuracy, little attention has been paid to what is actually gained by this additional information, especially when acquired on fragment ions.Unlike other hybrid mass spectrometers such as Q-TOFs [6] or Q-FTICRs [7], which have a single detector, the LTQ-FT and LTQ-OT instruments allow parallel data acquisition in both mass analyzers by use of dual detectors. This silent revolution in mass analyzers opens up new data acquisition schemes. Typically, the FT-based analyzer performs a survey scan of MS1 ions while the linear ion trap ...

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“…Y. pestis is of current concern to human health because of its past use and future potential as a bioterrorism agent [4]. To gain a better understanding of the virulence mechanism of Y. pestis, we previously investigated the proteomic changes associated with the induction of virulence as a function of calcium and temperature on a common, attenuated laboratory strain [5,6].…”

Section: Introductionmentioning

confidence: 99%

“…KIM5 D27, biovar Mediavalis, has a deletion of the pgm locus, and is conditionally avirulent [7]. This strain was included for direct comparison to previous proteomic [5,6] and proteogenomic studies [8]. India-195/P, NYC and PEXU2 are virulent strains from the Orientalis biovar.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, Y. pestis strains were grown under conditions that mimic the induction of virulence and differential protein expression between the strains, and the growth conditions was analyzed by 2-D DIGE as previously reported [5,6]. The DeCyder software package (GE Healthcare, Piscataway, NJ) was used to process 2-D DIGE gel images, detect protein spots, match spots between gels and determine statistical differences in protein abundance levels [13,14].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Multivariate Statistical Analysis of Diverse Strains of Yersinia pestis by Comparative Proteomics

Corzett

Eldridge

Knaack

et al. 2013

J Proteomics Bioinform

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Biomarker Candidate Identification in Yersinia pestis Using Organism-Wide Semiquantitative Proteomics

Cited by 42 publications

References 50 publications

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea

On the benefits of acquiring peptide fragment ions at high measured mass accuracy

Multivariate Statistical Analysis of Diverse Strains of Yersinia pestis by Comparative Proteomics

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