The PIR-International Protein Sequence Database

Barker, Winona C.; Garavelli, John S.; McGarvey, Peter B.; Marzec, Christopher R.; Orcutt, Bruce C.; Srinivasarao, Geetha Y.; Yeh, Lai-Su L.; Ledley, Robert S.; Mewes, Hans‐Werner; Pfeiffer, Friedhelm; Tsugita, Akira; Wu, Cathy H.

doi:10.1093/nar/27.1.39

Cited by 150 publications

(47 citation statements)

References 8 publications

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“…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). Such an Averagine contains the normal isotope variants of carbon (C), hydrogen (H), nitrogen (N), oxygen (O), and sulfur (S).…”

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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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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“…By 1992, the PSD had shown steady growth, with increasing contributions from European and Asian protein sequence centres -most notably, from MIPS (Martinsried, Germany) and from JIPID (Tokyo, Japan). Accordingly, a tripartite collaboration was established, termed PIR-International, to formalise these relationships and establish and disseminate a comprehensive set of protein sequences (Barker et al, 1992). By this time, charging for access to the resource was no longer mentioned, possibly both as a consequence of this more formal distribution arrangement and the advent of browsers like Mosaic, which had suddenly and dramatically changed the way that information could be broadcast and received over the World Wide Web (or, simply, the Web).…”

Section: The Pir-psdmentioning

confidence: 99%

Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective

Attwood¹,

Gisel²,

Eriksson³

et al. 2011

Bioinformatics - Trends and Methodologies

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“…To test for the remote possibility of contamination of the samples, MS/MS spectra that resulted from the analyses of the eight 14028 S. typhimurium C-18 SPE samples were searched using SEQUEST against a non-redundant, multiorganism database from the Protein Information Resource (283,416 protein sequences, PIR-PSD release 78.00, Georgetown University, pir.georgetown.edu/) (19). The resulting data were filtered using the above optimal XCorr_Cutoff and ⌬Cn_Cutoff value pairs, and although 207 new peptides were identified, they seemingly randomly corresponded to 127 apparently unrelated proteins.…”

Section: Lc-ms/msmentioning

confidence: 99%

Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics

Manes

Gustin

Rue

et al. 2007

Molecular & Cellular Proteomics

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The pathogen Salmonella enterica is known to cause both food poisoning and typhoid fever. Because of the emergence of antibiotic-resistant isolates and the threat of bioterrorism (e.g. contamination of the food supply), there is a growing need to study this bacterium. In this investigation, comparative peptidomics was used to study S. enterica serovar Typhimurium cultured in either a rich medium or in an acidic, low magnesium, and minimal nutrient medium designed to roughly mimic the macrophage phagosomal environment (within which Salmonella are known to survive). Native peptides from cleared cell lysates were enriched by using isopropanol extraction and analyzed by using both LC-MS/MS and LC-FTICR-MS. We identified and quantified 5,163 peptides originating from 682 proteins, and the data clearly indicated that compared with Salmonella cultured in the rich medium, cells cultured in the phagosome-mimicking medium had dramatically higher abundances of a wide variety of protein degradation products, especially from ribosomal proteins. Salmonella from the same cultures were also analyzed using traditional, bottom-up proteomic methods, and when the peptidomics and proteomics data were analyzed together, two clusters of proteins targeted for proteolysis were tentatively identified. Possible roles of targeted proteolysis by phagocytosed Salmonella are discussed.

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The PIR-International Protein Sequence Database

Cited by 150 publications

References 8 publications

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

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

Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective

Targeted Protein Degradation by Salmonella under Phagosome-mimicking Culture Conditions Investigated Using Comparative Peptidomics

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