International Coordination of Long-Term Ocean Biology Time Series Derived from Satellite Ocean Color Data

[ABSTRACT] In this paper, we will describe plans to coordinate the initial development of long-term ocean biology time series derived from global ocean color observations acquired by the United States, Japan and Europe, Specifically, we have been commissioned by the International Ocean Color Coordinating Group (IOCCG) to coordinate the development of merged products derived from the OCTS, SeaWiFS, MODIS, MERIS and GLI imagers. Each of these missions will have been launched by the year 2002 and will have produced global ocean color data products. Our goal is to develop and document the procedures to be used by each space agency (NASA, NASDA, and ESA) to merge chlorophyll, primary productivity, and other products from these missions. This coordination is required to initiate the production of long-term ocean biology time series which will be continued operationally beyond 2002. The purpose of the time series is to monitor interannual to decadal-scale variability in oceanic primary productivity and to study the effects of environmental change on upper ocean biogeochemical processes

DeNovoGUI: An Open Source Graphical User Interface for <i>de Novo</i> Sequencing of Tandem Mass Spectra

<i>De novo</i> sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of <i>de novo</i> sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available <i>de novo</i> sequencing software PepNovo+, greatly simplifying the use of <i>de novo</i> sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com

MPA Portable: A Stand-Alone Software Package for Analyzing Metaproteome Samples on the Go

Metaproteomics, the mass spectrometry-based analysis of proteins from multispecies samples faces severe challenges concerning data analysis and results interpretation. To overcome these shortcomings, we here introduce the MetaProteomeAnalyzer (MPA) Portable software. In contrast to the original server-based MPA application, this newly developed tool no longer requires computational expertise for installation and is now independent of any relational database system. In addition, MPA Portable now supports state-of-the-art database search engines and a convenient command line interface for high-performance data processing tasks. While search engine results can easily be combined to increase the protein identification yield, an additional two-step workflow is implemented to provide sufficient analysis resolution for further postprocessing steps, such as protein grouping as well as taxonomic and functional annotation. Our new application has been developed with a focus on intuitive usability, adherence to data standards, and adaptation to Web-based workflow platforms. The open source software package can be found at https://github.com/compomics/meta-proteome-analyzer

Glycoproteomic Analysis of Human Fibrinogen Reveals Novel Regions of O‑Glycosylation

Human fibrinogen is a 340 kDa, soluble plasma glycoprotein composed of paired sets of three subunits (α, β, γ). The protein plays a crucial role in protecting the vascular network against the loss of blood after tissue injury. The beta and gamma subunits each contain one N-glycosylation site, each of which is occupied by a biantennary N-glycan. So far O-linked oligosaccharides have rarely been described. Here, we make use of tryptic- and proteinase K-generated fibrinogen glycopeptides for the detailed analysis of the protein’s O-glycosylation by combining information obtained from both one- and two-dimensional nanoLC–ESI-ion trap (IT)–MS approaches. Glycopeptides were analyzed by ion trap-MS/MS which displayed fragmentations of glycosidic linkages and some peptide backbone cleavages. MS³ spectra of the generated O-glycopeptides showed cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N-glycan attachment sites of human fibrinogen could be confirmed. Moreover, we describe seven novel O-glycosylation regions in human fibrinogen, all occupied by a monosialylated T-antigen. Our findings may help to improve the general understanding of human fibrinogen in the blood clotting process

Glycoproteomic Analysis of Human Fibrinogen Reveals Novel Regions of O‑Glycosylation

Human fibrinogen is a 340 kDa, soluble plasma glycoprotein composed of paired sets of three subunits (α, β, γ). The protein plays a crucial role in protecting the vascular network against the loss of blood after tissue injury. The beta and gamma subunits each contain one N-glycosylation site, each of which is occupied by a biantennary N-glycan. So far O-linked oligosaccharides have rarely been described. Here, we make use of tryptic- and proteinase K-generated fibrinogen glycopeptides for the detailed analysis of the protein’s O-glycosylation by combining information obtained from both one- and two-dimensional nanoLC–ESI-ion trap (IT)–MS approaches. Glycopeptides were analyzed by ion trap-MS/MS which displayed fragmentations of glycosidic linkages and some peptide backbone cleavages. MS³ spectra of the generated O-glycopeptides showed cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N-glycan attachment sites of human fibrinogen could be confirmed. Moreover, we describe seven novel O-glycosylation regions in human fibrinogen, all occupied by a monosialylated T-antigen. Our findings may help to improve the general understanding of human fibrinogen in the blood clotting process

Glycoproteomic Analysis of Human Fibrinogen Reveals Novel Regions of O‑Glycosylation

Human fibrinogen is a 340 kDa, soluble plasma glycoprotein composed of paired sets of three subunits (α, β, γ). The protein plays a crucial role in protecting the vascular network against the loss of blood after tissue injury. The beta and gamma subunits each contain one N-glycosylation site, each of which is occupied by a biantennary N-glycan. So far O-linked oligosaccharides have rarely been described. Here, we make use of tryptic- and proteinase K-generated fibrinogen glycopeptides for the detailed analysis of the protein’s O-glycosylation by combining information obtained from both one- and two-dimensional nanoLC–ESI-ion trap (IT)–MS approaches. Glycopeptides were analyzed by ion trap-MS/MS which displayed fragmentations of glycosidic linkages and some peptide backbone cleavages. MS³ spectra of the generated O-glycopeptides showed cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N-glycan attachment sites of human fibrinogen could be confirmed. Moreover, we describe seven novel O-glycosylation regions in human fibrinogen, all occupied by a monosialylated T-antigen. Our findings may help to improve the general understanding of human fibrinogen in the blood clotting process

Glycoproteomic Analysis of Human Fibrinogen Reveals Novel Regions of O‑Glycosylation

Human fibrinogen is a 340 kDa, soluble plasma glycoprotein composed of paired sets of three subunits (α, β, γ). The protein plays a crucial role in protecting the vascular network against the loss of blood after tissue injury. The beta and gamma subunits each contain one N-glycosylation site, each of which is occupied by a biantennary N-glycan. So far O-linked oligosaccharides have rarely been described. Here, we make use of tryptic- and proteinase K-generated fibrinogen glycopeptides for the detailed analysis of the protein’s O-glycosylation by combining information obtained from both one- and two-dimensional nanoLC–ESI-ion trap (IT)–MS approaches. Glycopeptides were analyzed by ion trap-MS/MS which displayed fragmentations of glycosidic linkages and some peptide backbone cleavages. MS³ spectra of the generated O-glycopeptides showed cleavages of the peptide backbone and provided essential information on the peptide sequence. The previously reported N-glycan attachment sites of human fibrinogen could be confirmed. Moreover, we describe seven novel O-glycosylation regions in human fibrinogen, all occupied by a monosialylated T-antigen. Our findings may help to improve the general understanding of human fibrinogen in the blood clotting process

Additional file 1: Figure S1. of The impact of sequence database choice on metaproteomic results in gut microbiota studies

(A) The influence of the ORF finding approach on metagenomic databases. Venn diagrams indicate overlap among non-redundant peptide identifications obtained using ORFs found by FragGeneScan (FGS) or six-frame translation (6FT) as sequence databases. Percentage increase related to the use of a 6FT database in addition to the corresponding FGS database is shown on the bottom-right of each Venn diagram. Metagenomic databases derive from a 6-Mbps metagenome. Peptide identifications were obtained at 5 % FDR, using three different bioinformatic platforms (left, MetaProteomeAnalyzer; middle, MaxQuant; right, Proteome Discoverer) with the corresponding (and above indicated) search engines and peptide validation tools. (B) Comparison between reads- and contigs-based metagenomic databases at different sequencing depths. Venn diagrams indicate overlap among non-redundant peptide identifications obtained using reads (R) or assembled contigs (C) as sequence databases. ORFs from both reads and contigs were found by FragGeneScan (F). Metagenome sequencing depth was 18 (top), 6 (middle), or 3 (bottom) Mbps. Percentage increase related to the use of contigs-based database in addition to the corresponding reads-based database is shown in red on the bottom-right of each Venn diagram, while percentage increase related to the use of reads-based database in addition to the corresponding contigs-based database is shown in blue on the bottom-left of each Venn diagram. Peptide identifications were obtained at 5 % FDR, using three different bioinformatic platforms (left, MetaProteomeAnalyzer; middle, MaxQuant; right, Proteome Discoverer) with the corresponding (and above indicated) search engines and peptide validation tools. (TIF 2050 KB

Additional file 3: Figure S3. of The impact of sequence database choice on metaproteomic results in gut microbiota studies

Complementarity between reads-based database and other database types. Venn diagrams indicate overlap among non-redundant peptide identifications obtained using different sequence databases (see Additional file 1: Figure S1 and Additional file 2: Figure S2 for further details). Percentage increase related to the use of a given database in addition to the counterpart is shown on the bottom, on the same side and in the same color. Peptide identifications were obtained at 5 % FDR, using three different bioinformatic platforms (left, MetaProteomeAnalyzer; middle, MaxQuant; right, Proteome Discoverer) with the corresponding (and above indicated) search engines and peptide validation tools. (TIF 1780 KB

Additional file 5: Figure S5. of The impact of sequence database choice on metaproteomic results in gut microbiota studies

Histograms illustrating the number of taxa identified with the three DBs in human (left) and mouse (right) samples, distinguishing qualitatively differential (black), quantitatively differential (white) and non-differential (grey) taxa. (TIF 648 KB