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Matthias Mann - One of the best experts on this subject based on the ideXlab platform.
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How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra
Journal of the American Society for Mass Spectrometry, 2008Co-Authors: Jürgen Cox, Nina C. Hubner, Matthias MannAbstract:Matching Peptide tandem mass spectra to their cognate amino acid Sequences in databases is a key step in proteomics. It is usually performed by assigning a score to a spectrum-Sequence combination. De novo sequencing or partial de novo sequencing is useful for organisms without Sequenced genome or for Peptides with unexpected modifications. Here we use a very large, high accuracy proteomic dataset to investigate how much Peptide Sequence information is present in tandem mass spectra generated in a linear ion trap (LTQ). More than 400,000 identified tandem mass spectra from a single human cancer cell line project were assigned to 26,896 distinct Peptide Sequences. The average absolute fragment mass accuracy is 0.102 Da. There are on average about four complementary b- and y-ions; both series are equally represented but y ions are 2- to 3-fold more intense up to mass 1000. Half of all spectra contain uninterrupted b- or y-ion series of at least six amino acids and combining b- and y-ion information yields on average seven amino acid Sequences. These Sequences are almost always unique in the human proteome, even without using any precursor or Peptide Sequence tag information. Thus, optimal de novo sequencing algorithms should be able to obtain substantial Sequence information in at least half of all cases.
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error tolerant identification of Peptides in Sequence databases by Peptide Sequence tags
Analytical Chemistry, 1994Co-Authors: Matthias Mann, Matthias WilmAbstract:We demonstrate a new approach to the identification of mass spectrometrically fragmented Peptides. A fragmentation spectrum usually contains a short, easily identifiable series of Sequence ions, which yields a partial Sequence. This partial Sequence divides the Peptide into three parts-regions 1, 2, and 3-characterized by the added mass m1 of region 1, the partial Sequence of region 2, and the added mass m3 of region 3. We call the construct, m1 partial Sequence m3, a "Peptide Sequence tag" and show that it is a highly specific identifier of the Peptide. An algorithm developed here that uses the Sequence tag to find the Peptide in a Sequence database is up to 1 million-fold more discriminating than the partial Sequence information alone. Peptides can be identified even in the presence of an unknown posttranslational modification or an amino acid substitution between an entry in the Sequence database and the measured Peptide. These concepts are demonstrated with model and practical examples of electrospray mass spectrometry/mass spectrometry of tryptic Peptides. Just two to three amino acid residues derived by fragmentation are enough to identify these Peptides. In Peptide mapping applications, even less information is necessary.
Shabaz Mohammed - One of the best experts on this subject based on the ideXlab platform.
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toward full Peptide Sequence coverage by dual fragmentation combining electron transfer and higher energy collision dissociation tandem mass spectrometry
Analytical Chemistry, 2012Co-Authors: Christian K Frese, A Maarten F Altelaar, Henk W P Van Den Toorn, Dirk Nolting, Jens Griepraming, Albert J R Heck, Shabaz MohammedAbstract:Increasing Peptide Sequence coverage by tandem mass spectrometry improves confidence in database search-based Peptide identification and facilitates mapping of post-translational modifications and de novo sequencing. Inducing 2-fold fragmentation by combining electron-transfer and higher-energy collision dissociation (EThcD) generates dual fragment ion series and facilitates extensive Peptide backbone fragmentation. After an initial electron-transfer dissociation step, all ions including the unreacted precursor ions are subjected to collision induced dissociation which yields b/y- and c/z-type fragment ions in a single spectrum. This new fragmentation scheme provides richer spectra and substantially increases the Peptide Sequence coverage and confidence in Peptide identification.
Solange Lavielle - One of the best experts on this subject based on the ideXlab platform.
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Incorporation of Cα-methyl amino acids by solid phase Peptide synthesis in a Peptide Sequence
Tetrahedron Letters, 1996Co-Authors: Alié Brunissen, Mimoun Ayoub, Solange LavielleAbstract:Abstract (S)-αMethylmethionine, (S)-αMethylleucine, 2-aminoisobutyric acid and (S)-αMethylphenylalanine have been incorporated by solid phase Peptide strategy in a Peptide Sequence. The coupling reactions of these Boc-αMe amino acids and of the following residue in the Sequence were readily achieved after silylation with chlorotrimethylsilane of the amine function on the resin.
Jürgen Cox - One of the best experts on this subject based on the ideXlab platform.
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How Much Peptide Sequence Information Is Contained in Ion Trap Tandem Mass Spectra
Journal of the American Society for Mass Spectrometry, 2008Co-Authors: Jürgen Cox, Nina C. Hubner, Matthias MannAbstract:Matching Peptide tandem mass spectra to their cognate amino acid Sequences in databases is a key step in proteomics. It is usually performed by assigning a score to a spectrum-Sequence combination. De novo sequencing or partial de novo sequencing is useful for organisms without Sequenced genome or for Peptides with unexpected modifications. Here we use a very large, high accuracy proteomic dataset to investigate how much Peptide Sequence information is present in tandem mass spectra generated in a linear ion trap (LTQ). More than 400,000 identified tandem mass spectra from a single human cancer cell line project were assigned to 26,896 distinct Peptide Sequences. The average absolute fragment mass accuracy is 0.102 Da. There are on average about four complementary b- and y-ions; both series are equally represented but y ions are 2- to 3-fold more intense up to mass 1000. Half of all spectra contain uninterrupted b- or y-ion series of at least six amino acids and combining b- and y-ion information yields on average seven amino acid Sequences. These Sequences are almost always unique in the human proteome, even without using any precursor or Peptide Sequence tag information. Thus, optimal de novo sequencing algorithms should be able to obtain substantial Sequence information in at least half of all cases.
Irving Listowsky - One of the best experts on this subject based on the ideXlab platform.
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subunit diversity and tissue distribution of human glutathione s transferases interpretations based on electrospray ionization ms and Peptide Sequence specific antisera
Biochemical Journal, 1997Co-Authors: Jonathan Rowe, Edward Nieves, Irving ListowskyAbstract:Uncertainties about the composition and identities of glutathione S-transferases (GSTs) in human tissue have impeded studies on their biological functions. A rigorous protocol has therefore been developed to characterize the human proteins. Cytosolic GST subunits were resolved by reverse-phase HPLC methods, individual components were assigned to Alpha, Mu and Pi classes on the basis of their immunoreactivities, and Peptide-Sequence-specific antisera were used to distinguish among five different Mu-class subunits (GSTM1-GSTM5). Each subunit type was characterized and identified unambiguously by electrospray ionization-MS. Acetylation of N-terminal residues in the GSTA1, GSTA2, GSTM3 and GSTM4 subunits were the only natural post-translational modifications detected. The unique structure of GSTM3, with N- and C-terminal Peptide extensions predicted from cDNA Sequences, was confirmed. Only testis and brain were rich sources of GSTM3 subunits. Subunit profiles were distinct and characteristic of the particular tissue type, and this tissue specificity in GST expression was evident even in organs from different individuals. For instance, livers had relatively simple GST compositions, consisting of a preponderance of Alpha-class subunits and GSTM1 (when present). By contrast, representation of most subunit types was a characteristic feature of testis, which had the highest levels of GSTs. GSTM4 and GSTM5 subunits, here identified for the first time in human tissue extracts, were minor components, with GSTM5 found only in brain, lung and testis. Specimens devoid of GSTM1 subunits, particularly those from null-genotype individuals, were readily discerned at the protein level. Liver was the only rich source of the GSTM1 subunit (although it also constituted a major fraction of adrenal GSTs), and so the functional conSequences of the GSTM1 gene deletion are likely to vary in extrahepatic tissues.