A model-based method for the prediction of the isotopic distribution of peptides

Valkenborg, Dirk; Jansen, Ivy; Burzykowski, Tomasz

doi:10.1016/j.jasms.2008.01.009

Cited by 46 publications

(56 citation statements)

References 6 publications

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“…The profile is related to the isotopic distribution of the peptide. Prior knowledge about the distribution can thus be used to develop strategies for searching for the profile in the spectra and, hence, for efficient processing of the spectral information [2][3][4][5][6]. Another application can be found in the field of metabolomics.…”

Section: Introductionmentioning

confidence: 99%

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Claesen

Dittwald

Burzykowski

et al. 2012

J. Am. Soc. Mass Spectrom.

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In this article, we present a computation-and memory-efficient method to calculate the probabilities of occurrence and exact center-masses of the aggregated isotopic distribution of a molecule. The method uses fundamental mathematical properties of polynomials given by the Newton-Girard theorem and Viete's formulae. The calculation is based on the atomic composition of the molecule and the natural abundances of the elemental isotopes in normal terrestrial matter. To evaluate the performance of the proposed method, which we named BRAIN, we compare it with the results obtained from five existing software packages (IsoPro, Mercury, Emass, NeutronCluster, and IsoDalton) for 10 biomolecules. Additionally, we compare the computed mass centers with the results obtained by calculating, and subsequently aggregating, the fine isotopic distribution for two of the exemplary biomolecules. The algorithm will be made available as a Bioconductor package in R, and is also available upon request.

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Section: Introductionmentioning

confidence: 99%

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Claesen

Dittwald

Burzykowski

et al. 2012

J. Am. Soc. Mass Spectrom.

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“…[35] 2.2 Protocol-specific solutions 2.2.1 10 mM citric acid monohydrate pH 6 [29,36] ▪ 1.05 g citric acid monohydrate (Sigma-Aldrich, Japan) ▪ Dissolve in 480 mL H 2 O ▪ pH to 6.0 using 1 M NaOH (~13 mL) (Merck, Darmstadt, Germany) ▪ Make up volume to 500 mL with H 2 O 2.2.2 100 mM ammonium bicarbonate (NH 4 [32] ▪ 0.4 pmol/mL angiotensin I [34][35][36][37][38][39][40][41][42][43] ( Figure 1. Protocol for mapping the distribution and determining the identity of tryptic peptides generated in situ.…”

Section: Chemicals Consumables and Equipmentmentioning

confidence: 99%

“…SNAP using averagine [39] peptide composition) ○ Re-calibration [32] (quadratic internal re-calibration, 300 ppm tolerance using a custom mass control list [.mcl] containing the following calibrants): Figure 3. Typical MALDI-TOF/TOF spectrum (single) from an in situ acquisition (500 laser shot sum) on an FFPE ovarian cancer section prepared using the described tryptic MALDI-IMS protocol in a previous research article.…”

Section: 4mentioning

confidence: 99%

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Gustafsson

Eddes

Meding

et al. 2013

Rapid Comm Mass Spectrometry

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RATIONALE: Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry provides the means to map the in situ distribution of tryptic peptides in formalin-fixed clinical tissue samples. The ability to analyze clinical samples is of great importance to further developments in the imaging field. However, there is a requirement in this field of research for additional methods describing the characterization of tryptic peptides by MALDI imaging. METHODS AND RESULTS: This protocol gives highly detailed instructions, with examples, for (1) successfully performing tryptic peptide MALDI imaging on formalin-fixed cancer tissue using a MALDI-TOF/TOF MS instrument, (2) tentatively generating identifications through nLC/MS/MS, and (3) validating these identifications by in situ MS/MS of peptides of interest. CONCLUSIONS: This protocol provides a detailed and straightforward description of the methods required for groups new to MALDI imaging to begin analysis of formalin-fixed clinical samples.

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“…With a high resolution mass spectrometer such as the LTQ-Orbitrap XL, monoisotopic mass, i.e. nomination of the correct peak of an isotopically resolved group of peptides peak as a monoisotopic peak (29), is determined using an algorithm based on the study reported by Senko et al (30). These authors proposed the concept of a virtual amino acid, Averagine, constructed using the statistical occurrences of amino acids in the PIR protein data base (31).…”

Section: ϩmentioning

confidence: 99%

Revisiting Iodination Sites in Thyroglobulin with an Organ-oriented Shotgun Strategy

Dedieu

Gaillard

Pourcher³

et al. 2011

Journal of Biological Chemistry

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Thyroglobulin (Tg) is secreted by thyroid epithelial cells. It is essential for thyroid hormonogenesis and iodine storage. Although studied for many years, only indirect and partial surveys of its post-translational modifications were reported. Here, we present a direct proteomic approach, used to study the degree of iodination of mouse Tg without any preliminary purification. A comprehensive coverage of Tg was obtained using a combination of different proteases, MS/MS fragmentation procedures with inclusion lists and a hybrid mass highresolution LTQ-Orbitrap XL mass spectrometer. Although only 16 iodinated sites are currently known for human Tg, we uncovered 37 iodinated tyrosine residues, most of them being mono-or diiodinated. We report the specific isotopic pattern of thyroxine modification, not recognized as a normal peptide pattern. Four hormonogenic sites were detected. Two donor sites were identified through the detection of a pyruvic acid residue in place of the initial tyrosine. Evidence for polypeptide cleavages sites due to the action of cathepsins and dipeptidyl proteases in the thyroid were also detected. This work shows that semi-quantitation of Tg iodination states is feasible for human biopsies and should be of significant medical interest for further characterization of human thyroid pathologies.Thyroglobulin (Tg) 3 is one of the most abundant proteins produced by the thyroid gland and comprises two identical subunits of ϳ330 kDa. This prohormonal glycoprotein is secreted by thyroid epithelial cells. It is stored in the lumen of thyroid follicles in a highly condensed and covalently crosslinked form with numerous disulfide bridges. There, Tg is used as a scaffold for thyroid hormonogenesis and as an iodine reservoir. Many post-translational modifications are known to occur on this protein such as glycosylation, sulfation, and iodination (1). A signal peptide is processed during its export to the lumen. The most specific Tg post-translational modification is certainly its iodination and 3,5,3Ј-triiodothyronine (T3) and thyroxine (T4) thyroid hormone synthesis. Indeed, through the combined action of NADPH oxidase and thyroperoxidase on the outer surface of the thyrocyte apical membrane, iodide ions that are also transported to the follicular lumen are covalently linked to some Tg tyrosyl residues to form mono-or diiodotyrosines (MIT or DIT, respectively). Coupling of two of these DIT residues then leads to the formation of T4 at an acceptor site, whereas coupling one MIT and one DIT moiety essentially forms T3 (2). In this reaction, the release of an iodotyrosyl moiety at the donor site leaves an "empty" side chain and the fate of this unusual residue is controversial. Some authors claim that a dehydroalanine is left instead of the tyrosine, whereas others observed pyruvic acid associated with cleavage of the polypeptide chain (3-7). Finally, the protein is proteolytically processed in the lumen, followed by endocytosis in lysosomes, to release the hormones. The principal proteases involved inclu...

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A model-based method for the prediction of the isotopic distribution of peptides

Cited by 46 publications

References 6 publications

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

An Efficient Method to Calculate the Aggregated Isotopic Distribution and Exact Center-Masses

Matrix‐assisted laser desorption/ionization imaging protocol for in situ characterization of tryptic peptide identity and distribution in formalin‐fixed tissue

Revisiting Iodination Sites in Thyroglobulin with an Organ-oriented Shotgun Strategy

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