{"database":"PAXDB","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["http://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":{"citationCount":0,"reanalysisCount":0,"viewCount":0,"searchCount":0},"additional":{"omics_type":["Proteomics"],"submitter":["Christian von Mering"],"species":["85962"],"full_dataset_link":["https://pax-db.org/dataset/85962/3620106669"],"submitter_email":["mering@imls.uzh.ch"],"submitter_affiliation":["University of Zurich"],"sample_protocol":[""],"repository":["PAXDB"],"data_protocol":["For the rescaling, the\ndatasets are first parsed or processed such that the data reflect\nproportional abundances of whole protein molecules\n(i.e. proportionality to counts of complete, individual protein\nmolecules, not to molecular weights, protein volumes, or digested\npeptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up\nto one million; this means the abundance of each protein of\ninterest is finally expressed in (parts per million,) relative to\nall other proteins in a sample. \nFor a given protein abundance dataset, we then compute\nthe absolute log abundance ratios of all pairs of proteins\nannotated to be functionally linked. The median of these absolute\nlog abundance ratios represents an indirect quality\nmetric: the closer it is to zero, the better (i.e. the more there\nis consistency between abundance values and functional annotations\nsuch as protein complexes or pathways). We then\ncompute a background expectation for this metric, by permuting\nthe abundance values in a given dataset randomly,\nand recomputing the median log abundance ratios. The permutation\nis repeated several times, yielding a distribution of\nmedians. The actually observed median is then expressed as a\nZ-score distance to the random distribution ofmedians—this\ndistance is termed the interaction consistency score."],"pubmed_abstract":["Correct annotation of protein coding genes is the basis of conventional data analysis in proteomic studies. Nevertheless, most protein sequence databases almost exclusively rely on gene finding software and inevitably also miss protein annotations or possess errors. Proteogenomics tries to overcome these issues by matching MS data directly against a genome sequence database. Here we report an in-depth proteogenomics study of Helicobacter pylori strain 26695. MS data was searched against a combined database of the NCBI annotations and a six-frame translation of the genome. Database searches with Mascot and X! Tandem revealed 1115 proteins identified by at least two peptides with a peptide false discovery rate below 1%. This represents 71% of the predicted proteome. So far this is the most extensive proteome study of Helicobacter pylori. Our proteogenomic approach unambiguously identified four previously missed annotations and furthermore allowed us to correct sequences of six annotated proteins. Since secreted proteins are often involved in pathogenic processes we further investigated signal peptidase cleavage sites. By applying a database search that accommodates the identification of semi-specific cleaved peptides, 63 previously unknown signal peptides were detected. The motif LXA showed to be the predominant recognition sequence for signal peptidases.<h4>Biological significance</h4>The results of MS-based proteomic studies highly rely on correct annotation of protein coding genes which is the basis of conventional data analysis. However, the annotation of protein coding sequences in genomic data is usually based on gene finding software. These tools are limited in their prediction accuracy such as the problematic determination of exact gene boundaries. Thus, protein databases own partly erroneous or incomplete sequences. Additionally, some protein sequences might also be missing in the databases. Proteogenomics, a combination of proteomic and genomic data analyses, is well suited to detect previously not annotated proteins and to correct erroneous sequences. For this purpose, the existing database of the investigated species is typically supplemented with a six-frame translation of the genome. Here, we studied the proteome of the major human pathogen Helicobacter pylori that is responsible for many gastric diseases such as duodenal ulcers and gastric cancer. Our in-depth proteomic study highly reliably identified 1115 proteins (FDR<0.01%) by at least two peptides (FDR<1%) which represent 71% of the predicted proteome deposited at NCBI. The proteogenomic data analysis of our data set resulted in the unambiguous identification of four previously missed annotations, the correction of six annotated proteins as well as the detection of 63 previously unknown signal peptides. We have annotated proteins of particular biological interest like the ferrous iron transport protein A, the coiled-coil-rich protein HP0058 and the lipopolysaccharide biosynthesis protein HP0619. For instance, the protein HP0619 could be a drug target for the inhibition of the LPS synthesis pathway. Furthermore it has been proven that the motif \"LXA\" is the predominant recognition sequence for the signal peptidase I of H. pylori. Signal peptidases are essential enzymes for the viability of bacterial cells and are involved in pathogenesis. Therefore signal peptidases could be novel targets for antibiotics. The inclusion of the corrected and new annotated proteins as well as the information of signal peptide cleavage sites will help in the study of biological pathways involved in pathogenesis or drug response of H. pylori."],"pubmed_title":["Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics."],"pubmed_authors":["Müller Stephan A SA, Findeiß Sven S, Pernitzsch Sandy R SR, Wissenbach Dirk K DK, Stadler Peter F PF, Hofacker Ivo L IL, von Bergen Martin M, Kalkhof Stefan S"],"data_synonyms":["Add, DmelCG43443, ADD, ADD-87, Hts-RC, data, AU023367, Data Set, protein complex, supply, Proteins, Ovhts, Gene, HtsRC, CG9325, protein, neutral molecular compounds, protein-containing complex, Dmel_CG9325, Xt, Peptide, 1B1, add, Polypeptides, anon-EST:Posey9, protein polypeptide chains, native protein, peptido, htsRC, GLI3-190, natural protein, polypeptide chain, Add-hts, Protein, CG43443, Gene Products, l(2)k14523, Dmel_CG34197, l(2)00634, median, Ovhts-RC, background, supply and distribution, protein aggregate, all_pairs, molecule, Bph, molecula, Random selection by shearing, oligonucleotide random primer, proportion, HTS-R1, HTS, Hts, molecules, peptides, l(2)k06121, adducin, GLI3FL, distribution, AI854843, proportionality, add-like, HTS-RC, rate, proteins, Molekuel, Pdn, sample population, introduction, Protein Gene Products, Gene Proteins, Adducin, RANDOM, 10^[-6], ppm, sample, supply., quotient, Peptid, peptidos, Polypeptide, Attention Deficit Hyperactivity Disorder, l(2)01103, EST D, CG34197, HtsF, ratio"],"pubmed_title_synonyms":["Helicobacter pylori (strain 26695), Profiling, Proteinase, ZMPOMA1, Proteolytic Enzyme, protein complex, Researchs, 2010001O09Rik, Proteins, Helicobacter pylori strain 26695, cleavage, Proteogenomic Profiling, Gene, Coding, Protease, protein, protein-containing complex, Peptide, Esteroproteases, protein polypeptide chains, Hydrolase, native protein, natural protein, polypeptide chain, Protein, Gene Products, Peptidases, Helicobacter pylori KE26695, Proteogenomic Research, Proteases, peptidase, Peptide Hydrolase, Analysis, protein aggregate, Medical, Clinical, Research, Medical Coding, Helicobacter pylori str. 26695, YKR087C, proteins, Proteolytic, Proteogenomic Analysis., Proteinases, Protein Gene Products, Gene Proteins, Peptidase, Enzyme, Proteogenomic, Helicobacter pylori ATCC 700392, DAB1, MPRP-1, Proteolytic Enzymes"],"name_synonyms":["Peptidomics., organism, whole body, multi-cellular organism, whole organism, animal, body, Koerper"],"pubmed_abstract_synonyms":["AU043776, Materials, Product, Proteolytic Enzyme, antimicrobials, Compounds, Peptide Signal Sequence, antimicrobial agents, Progress Reports, PPS1, Stomach Neoplasms, malignant fundus of stomach neoplasm, DmelCG6383, Esteroproteases, Polypeptides, protein polypeptide chains, Lwr, microbicides, Anti Mycobacterial Agent, Summary Report, CG9063, Software Engineering, Proteases, Analysis, Bacteriocide, gastric neoplasm, C79691, antimicrobial, modification by symbiont of host biological process, stimulation by symbiont of host programmed cell death, Analyses, Genomes, Progress Report, anabolism, OFC6, Antibiotika, Leader Peptide, Helicobacter pylori str. 26695, crumb, Anti Bacterial Compound, proteins, SAP-1, SAP-2, Leader Signal Peptides, Staphylococcal, BcDNA:GH03694, Lccp, malignant neoplasm of body of stomach, Field Reports, Proteogenomic, medicine, cleft lip and/or palate with mucous cysts of lower lip, Antimycobacterial Agent, Homo sapiens disease, ferrous iron transport, Diagnostic Findings, protein biosynthetic process, anatomical protrusion, Data Set, GASC, Saposin-A, Parotid isoelectric focusing variant protein, VWS1, lipopolysaccharide anabolism, signal, predicted, STOMACH NEOPL, Software Tools, lipopolysaccharide formation, Computer Applications, Computer Applications Software, protein formation, Protein Sorting, Coilin, lipopolysaccharide synthesis, Anti Bacterial Agent, Bacteriocides, Anti-Mycobacterial Agent, Antimycobacterial, Stomach Cancer, l(2)05487, l(2)05486, Software Applications, gastric tumour, i56, Antibacterial, Source Software, BcDNAGH03694, Field, INSDC_feature:gene, MASCOT, whole genome, MISS, i105, human, 3L6, Ran/M1, Applications, Report, protein synthesis, Saposin-D, rich, Material, Saposin-C, Saposin-B, activation by symbiont of host programmed cell death, tumor of stomach, Sorting Signal, Protein Sorting Signal, Clinical Finding, ulcer, Proteolytic Enzymes, ulcers, p80-coilin, Computer Software Applications, Crbs, antibiotique, Researchs, Biocatalysts, Neoplasms, regulation by symbiont of host system process, Helicobacter pylori strain 26695, Proteogenomic Profiling, biosynthesis, protein-containing complex, Signals, Human, Agent, dip4, DmelCG8710, ferrous ion transport, Crumbs, induction by organism of non-apoptotic programmed cell death in other organism during symbiotic interaction, Gene Products, disease or disorder, Antibiotic, lip pit syndrome, Ubc 9, malignant tumor of fundus of stomach, Peptide Hydrolase, Medical, Man, Application, Open Source Softwares, CT19912, 0509/20, Clinical, Ly87, DmelCG3018, Software Application, Dispersin, Peptide Leader Sequences, Signal, Open Source Software, Gastric Cancer, man, Computer Software Application, synthesis, genomic profiling, mKIAA0989, Anti-Bacterial, Leader Signal, Enzyme, Component C, drugs, Tools, CLN80, Helicobacter pylori ATCC 700392, peptidos, DAB1, Antibiotics, species, LPS biosynthetic process, Investigative Reports, PIT, Cancer, Pharmaceuticals, Antibiotikum, Products, tumour of stomach, Stomach Neoplasm, disruption by symbiont of host cell, ferric iron transport, hemolysin activity, Peptide P-C, 2010001O09Rik, Proteins, C14orf32, disorders, 2310009E07Rik, CG8710, responsivity., Co-beta-glucosidase, motif, cancer of fundus of stomach, Cell, Tool, Stomach Cancers, polypeptide, Sequences, native protein, Research 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Pharmaceutic, Softwares, Genetic Material, l(2)02858, Rasl2-8, Helicobacter nemestrinae, Sphingolipid activator protein 1, stomach neoplasm (disease), Parotid proline-rich protein 1|2, Proteogenomic Analysis, YKR087C, Ulcer, induction by organism of programmed cell death in other organism during symbiotic interaction, modification by symbiont of host morphology or physiology, Antibacterial Agents, Stomach, data analysis, disease, Agents, spine, neoplasm of stomach, Biocatalyst, Cistron, Polypeptide, Db-F, Proteomes, l(3)S050920, ca greater curvature of stomach, other disease, human being, Campylobacter pyloridis, AW549739, Sorting Signals, Gene, Coding, Protease, far, Computer, Peptide Signal Sequences, Symptoms and Signs, protrusion, Db-s, iron ion import, Investigative, Ca fundus - stomach, polypeptide chain, Homo sapiens, stomach neoplasm, Parotid acidic protein, Signal Peptide, Bacteriocidal, Finding, antibiotics, stomach tumor, Drugs, study, reactivity, induction of non-apoptotic 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