PAXDBapplication/xmlhttp://pax-db.org/downloads/latest/datasets/bioprojects-abundance-files-v4.0.zipprimary200OK0000ProteomicsChristian von Mering10090https://pax-db.org/dataset/10090/2956507553mering@imls.uzh.chUniversity of ZurichPAXDBFor the rescaling, the datasets are first parsed or processed such that the data reflect proportional abundances of whole protein molecules (i.e. proportionality to counts of complete, individual protein molecules, not to molecular weights, protein volumes, or digested peptides). In the case of spectral counting data protein. The proportional abundances are rescaled linearly to add up to one million; this means the abundance of each protein of interest is finally expressed in (parts per million,) relative to all other proteins in a sample. For a given protein abundance dataset, we then compute the absolute log abundance ratios of all pairs of proteins annotated to be functionally linked. The median of these absolute log abundance ratios represents an indirect quality metric: the closer it is to zero, the better (i.e. the more there is consistency between abundance values and functional annotations such as protein complexes or pathways). We then compute a background expectation for this metric, by permuting the abundance values in a given dataset randomly, and recomputing the median log abundance ratios. The permutation is repeated several times, yielding a distribution of medians. The actually observed median is then expressed as a Z-score distance to the random distribution ofmedians—this distance is termed the interaction consistency score.An increasing number of studies involve integrative analysis of gene and protein expression data, taking advantage of new technologies such as next-generation transcriptome sequencing and highly sensitive mass spectrometry (MS) instrumentation. Recently, a strategy, termed ribosome profiling (or RIBO-seq), based on deep sequencing of ribosome-protected mRNA fragments, indirectly monitoring protein synthesis, has been described. We devised a proteogenomic approach constructing a custom protein sequence search space, built from both Swiss-Prot- and RIBO-seq-derived translation products, applicable for MS/MS spectrum identification. To record the impact of using the constructed deep proteome database, we performed two alternative MS-based proteomic strategies as follows: (i) a regular shotgun proteomic and (ii) an N-terminal combined fractional diagonal chromatography (COFRADIC) approach. Although the former technique gives an overall assessment on the protein and peptide level, the latter technique, specifically enabling the isolation of N-terminal peptides, is very appropriate in validating the RIBO-seq-derived (alternative) translation initiation site profile. We demonstrate that this proteogenomic approach increases the overall protein identification rate 2.5% (e.g. new protein products, new protein splice variants, single nucleotide polymorphism variant proteins, and N-terminally extended forms of known proteins) as compared with only searching UniProtKB-SwissProt. Furthermore, using this custom database, identification of N-terminal COFRADIC data resulted in detection of 16 alternative start sites giving rise to N-terminally extended protein variants besides the identification of four translated upstream ORFs. Notably, the characterization of these new translation products revealed the use of multiple near-cognate (non-AUG) start codons. As deep sequencing techniques are becoming more standard, less expensive, and widespread, we anticipate that mRNA sequencing and especially custom-tailored RIBO-seq will become indispensable in the MS-based protein or peptide identification process. The underlying mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000124.Deep proteome coverage based on ribosome profiling aids mass spectrometry-based protein and peptide discovery and provides evidence of alternative translation products and near-cognate translation initiation events.Menschaert Gerben G, Van Criekinge Wim W, Notelaers Tineke T, Koch Alexander A, Crappé Jeroen J, Gevaert Kris K, Van Damme Petra PAdd, 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, ratioTaf[[II]]250, Taf200, dTAF[[II]]230, TAF[[II]]250, d230, dTAF[[II]]250, TAF[[II]]230, TFIID TAF250, cel, cell, TAF200, l(3)84Ab, dTAFII250, Taf1p, TAF[II]250, BG:DS00004.13, TAFII-250, CG17603, TAF250/230, TAF[[II]], EfW1, Cell, dTAF230, dTAF250, dmTAF[[II]]230, TAFII250, DmelCG17603, TAF1., Taf250, dmTAF1, SR3-5, Taf230, p230, TAF[[II]]250/230, TFIID, TAF, TAF230, TAF250Translation Profiling, protein translation, Profiling, Acquired Immuno-Deficiency Syndrome, protein anabolism, Immunodeficiency Syndrome, protein biosynthetic process, biopolymerization, Footprintings, ARTSeq, protein complex, Capture, Ribosome Profilings, Proteins, total expressed protein, ribosome profiling, Gene, Acquired Immunodeficiency Syndrome, protein, Acquired Immunodeficiency, Spectrum Analyses, active mRNA translation sequencing, protein-containing complex, acquired immune deficiency syndrome, Spectrum Analysis, Immuno-Deficiency Syndromes, Peptide, Spectroscopy, Translation, polypeptide, peptide, Polypeptides, Translation Profilings, protein polypeptide chains, Ribosome-Bound tRNA, MS, native protein, peptido, AIDS, natural protein, polypeptide chain, Ribosome Footprinting, Ribo-Seq, Protein, acquired immunodeficiency syndrome, Mass, Gene Products, protein formation, Footprinting, Immuno-Deficiency Syndrome, protein biosynthesis, Profilings, Analysis, tRNA Captures, Ribosome Bound tRNA Capture, protein aggregate, Translating Ribosome Affinity Purification, Immunologic Deficiency Syndrome, translation initiation., Mass Spectrum Analyses, Mass Spectroscopy, Mass Spectrum Analysis, Mass Spectrum, Ribosome, Ribosome-Bound tRNA Captures, Acquired, Acquired immunodeficiency syndrome, Acquired Immunodeficiency Syndromes, peptides, Analyses, Acquired Immune Deficiency Syndrome, Spectrometry, Ribosome-Bound tRNA Capture, proteins, protein synthesis initiation, tRNA Capture, Ribosome-Bound, Ribosome Footprintings, Acquired Immuno Deficiency Syndrome, Protein Gene Products, biopolymerisation, Gene Proteins, Immunodeficiency Syndromes, Acquired Immuno-Deficiency Syndromes, Syndromes, protein synthesis, Acquired Immuno-Deficiency, Captures, Syndrome, ribosome footprinting, Peptid, peptidos, Polypeptide, Proteomesl(3)Ca, mCRY, titin, Cell Lines, 26S protease, l(3)62Ca, d-titin, 0020/01, threonine endopeptidase activity, Mbh1, SLS, Sls, Cell, ingensin, kettin, large multicatalytic protease, CFU-MC, HEL-S-66, Line, DmelCG1915, Titin, prosome, Crry, multicatalytic endopeptidase complex, anon-CREST, Ket, CFU-Mast, tricorn proteinase, D-titin, l(3)j1D7, Lines, AFCP, colony forming unit mast cell, muscle, D-Titin, CG18857, MIC10, ket, muscle element, sam, sal, TLX, l(3)dre8, lens neutral proteinase, CG1915, CT41299, musculus, multicatalytic proteinase (complex), proteasome endopeptidase complex., KZ, polyhedral organelle, l(3)S002001, l(3)rL182, CG18242, tricorn protease, AHUS2, TRA2.10, Mcp, MCP, alkaline protease, multicatalytic proteinase, CG18245protein translation, Forms, apparatus, Protein Structure Database, Materials, Nucleotide Sequencing, determination, Ribo-seq, Massively-Parallel, Gene Expression Profile, ribosomal RNA, Protein Sequence Database, Splice Variants, Nucleotide Polymorphisms, Initiator Codons, protein, Profiles, Protein Splice, Reading Frame, Protein Databases, peptide, Polypeptides, protein polypeptide chains, Personal, Techniques, devices, High-Throughput RNA Sequencing, peptido, Method, Ribosome Footprinting, Ribo-Seq, ORFs, Analysis, Profilings, protein aggregate, Unassigned, Non Polyadenylated, Unassigned Reading Frame, Deep Sequencing, Mass Spectrum Analysis, Unidentified Reading Frames, appliances, Protein Splice Variant, peptides, Analyses, Illumina Sequencing, Start Codons, Polyadenylated Messenger, Single Nucleotide, Open, Records as Topics, Ribosome-Bound tRNA Capture, proteins, purification, Protein Isoform, procedures, protein synthesis initiation, Signatures, Travel Documents, allergic reaction, isolation and purification, Protein Coding, High Throughput RNA Sequencing, Methodological Studies, Proteogenomic, Expression Signature, Transcriptomes, Sequence Databases, Protein Coding Regions, Translation Profiling, High-Throughput RNA, Initiator Codon, Data Set., protein anabolism, Start, protein biosynthetic process, anatomical protrusion, biopolymerization, ARTSeq, Polyadenylated, statistics and numerical data, Ribosome Profilings, Expression Profiles, High-Throughput DNA Sequencing, Initiator, active mRNA translation sequencing, Procedure, Isoform, Spectrum Analysis, Spectroscopy, Gene Expression, Sequence Database, Ribosome-Bound tRNA, Ion Torrent Sequencing, Expression Signatures, Massively-Parallel Sequencing, Next-Generation, protein formation, Genetic Materials, ribosomal profiling, numerical data, Ion Torrent, tRNA Captures, Translating Ribosome Affinity Purification, Region, Expression Profile, Genetic Material, region, Codons, Transcriptome Profiles, Polyadenylated Messenger RNA, ORF, Non Polyadenylated mRNA, protein_coding_transcript, translation initiation, MS/MS, Proteogenomic Analysis, Spectrometry, Codon, INSDC_feature:gene, Records as Topic, Methodological, Methodological Study, Ribosome Footprintings, Non-Polyadenylated mRNA, High Throughput Sequencing, Protein Sequence, protein synthesis, Identification Systems, Material, spine, Captures, Protein Database, ribosome footprinting, Personal Identification System, Travel, Cistron, Polypeptide, Ribo-seq assay, E430016J11Rik, Poly(A) RNA, Proteomes, High Throughput DNA Sequencing, Footprintings, Procedures, Transcriptome Profile, Open Reading Frame, Researchs, Capture, Proteogenomic Profiling, instruments, Gene, High-Throughput DNA, Spectrum Analyses, Database, protein-containing complex, Protein Structure Databases, Ximpact, Illumina, Next-Generation Sequencing, protrusion, Protein Sequence Databases, Translation, Unidentified Reading, Translation Profilings, method, polypeptide chain, Single Nucleotide Polymorphisms, isolation, utilization, sensitive, Messenger, Deep, method used in an experiment, Gene Products, Mass, Studies, Variant, Unassigned Reading Frames, Massively Parallel Sequencing, Documents, Isoforms, sensitivity, Technique, Mass Spectroscopy, Splice Variant, Frame, Ribosome-Bound tRNA Captures, sORF, Ion Proton Sequencing, Genetic, Research, MS2, Profile, Initiation Codon, Coding Region, messenger RNA, SWISS PROT, Protein Splice Variants, Pyrosequencing, tRNA Capture, Sequencing, Initiation Codons, Unidentified Reading Frame, Study, biopolymerisation, template RNA, Protein Structure, Polymorphisms, Structure Database, High-Throughput, RNA Sequencing, site, peptidos, Chromatographies, SWISS-PROT, Profiling, Protein Coding Region, data, RNA, lumen, use, Transcriptome, Nucleotide Polymorphism, protein complex, space, SwissProt, Proteins, ribosome profiling, Messenger RNA, total expressed protein, Personal Identification Systems, SNPs, Cistrons, impact-a, Peptide, Initiation, whole transcriptome, Amino Acid Sequence, polypeptide, MS, native protein, natural protein, equipment, Start Codon, Poly(A)+ mRNA, DNA Sequencing, chemical analysis, Protein, Gene Expression Signatures, Footprinting, INSDC_feature:mRNA, sequence, protein biosynthesis, Proteogenomic Research, Gene Expression Signature, Polyadenylated RNA, Small Open Reading Frames, techniques, Ribosome Bound tRNA Capture, anatomical spaces, Amino Acid Sequence Databases, membrane bound ribosome, Mass Spectrum Analyses, tandem MS, Data Base, Next Generation Sequencing, free ribosome, Mass Spectrum, Ribosome, lumen space, Poly(A)+ RNA, mRNA, Poly(A) Tail, Non-Polyadenylated, Databases, Record, Ribosome-Bound, primary structure of sequence macromolecule, Unidentified, Protein Gene Products, plan specification, Gene Proteins, Single Nucleotide Polymorphism, High-Throughput Sequencing, Gene Expression Profiles, Variants, High Throughput Nucleotide Sequencing, Small Open Reading Frame, Peptid, assay, Single, Signature, Polyadenylated mRNA, Structure Databases, Ion Proton, RWDD5, High-Throughput Nucleotide, methodology0falseM.musculus - Cell line, Cell line, SC (Menschaert,mcp,2013)abundance based on Spectral counting, cell_line, Interaction consistency score: 3.6, Coverage: 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