Get quick answers to your questions about the article from our AI researcher chatbot
{'id': 'https://openalex.org/W1995693931', 'doi': 'https://doi.org/10.1089/106652799318300', 'title': '<i>De Novo</i>Peptide Sequencing via Tandem Mass Spectrometry', 'display_name': '<i>De Novo</i>Peptide Sequencing via Tandem Mass Spectrometry', 'publication_year': 1999, 'publication_date': '1999-10-01', 'ids': {'openalex': 'https://openalex.org/W1995693931', 'doi': 'https://doi.org/10.1089/106652799318300', 'mag': '1995693931', 'pmid': 'https://pubmed.ncbi.nlm.nih.gov/10582570'}, 'language': 'en', 'primary_location': {'is_oa': False, 'landing_page_url': 'https://doi.org/10.1089/106652799318300', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S78571599', 'display_name': 'Journal of Computational Biology', 'issn_l': '1066-5277', 'issn': ['1066-5277', '1557-8666'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320443', 'host_organization_name': 'Mary Ann Liebert, Inc.', 'host_organization_lineage': ['https://openalex.org/P4310320443'], 'host_organization_lineage_names': ['Mary Ann Liebert, Inc.'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}, 'type': 'article', 'type_crossref': 'journal-article', 'indexed_in': ['crossref', 'pubmed'], 'open_access': {'is_oa': False, 'oa_status': 'closed', 'oa_url': None, 'any_repository_has_fulltext': False}, 'authorships': [{'author_position': 'first', 'author': {'id': 'https://openalex.org/A5015744482', 'display_name': 'Vlado Dančík', 'orcid': 'https://orcid.org/0000-0002-5970-6660'}, 'institutions': [{'id': 'https://openalex.org/I207624831', 'display_name': 'Slovak Academy of Sciences', 'ror': 'https://ror.org/03h7qq074', 'country_code': 'SK', 'type': 'government', 'lineage': ['https://openalex.org/I207624831']}, {'id': 'https://openalex.org/I4210120676', 'display_name': 'Mathematical Institute of the Slovak Academy of Sciences', 'ror': 'https://ror.org/02fhy7464', 'country_code': 'SK', 'type': 'facility', 'lineage': ['https://openalex.org/I207624831', 'https://openalex.org/I4210120676']}], 'countries': ['SK'], 'is_corresponding': False, 'raw_author_name': 'Vlado Dančík', 'raw_affiliation_strings': ['Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts and Mathematical Institute, Slovak Academy of Sciences, Grešákova 6, Košice, Slovakia.'], 'affiliations': [{'raw_affiliation_string': 'Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts and Mathematical Institute, Slovak Academy of Sciences, Grešákova 6, Košice, Slovakia.', 'institution_ids': ['https://openalex.org/I207624831', 'https://openalex.org/I4210120676']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5073279628', 'display_name': 'Theresa A. Addona', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I4210147799', 'display_name': 'Millennium Engineering and Integration (United States)', 'ror': 'https://ror.org/05qmdfk04', 'country_code': 'US', 'type': 'company', 'lineage': ['https://openalex.org/I4210147799']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Theresa A. Addona', 'raw_affiliation_strings': ['Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.'], 'affiliations': [{'raw_affiliation_string': 'Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.', 'institution_ids': ['https://openalex.org/I4210147799']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5006801972', 'display_name': 'Karl R. Clauser', 'orcid': 'https://orcid.org/0000-0002-1052-9456'}, 'institutions': [{'id': 'https://openalex.org/I4210147799', 'display_name': 'Millennium Engineering and Integration (United States)', 'ror': 'https://ror.org/05qmdfk04', 'country_code': 'US', 'type': 'company', 'lineage': ['https://openalex.org/I4210147799']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Karl R. Clauser', 'raw_affiliation_strings': ['Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.'], 'affiliations': [{'raw_affiliation_string': 'Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.', 'institution_ids': ['https://openalex.org/I4210147799']}]}, {'author_position': 'middle', 'author': {'id': 'https://openalex.org/A5054751943', 'display_name': 'James E. Vath', 'orcid': None}, 'institutions': [{'id': 'https://openalex.org/I4210147799', 'display_name': 'Millennium Engineering and Integration (United States)', 'ror': 'https://ror.org/05qmdfk04', 'country_code': 'US', 'type': 'company', 'lineage': ['https://openalex.org/I4210147799']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'James E. Vath', 'raw_affiliation_strings': ['Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.'], 'affiliations': [{'raw_affiliation_string': 'Millennium Pharmaceuticals, 640 Memorial Drive, Cambridge, Massachusetts.', 'institution_ids': ['https://openalex.org/I4210147799']}]}, {'author_position': 'last', 'author': {'id': 'https://openalex.org/A5027480961', 'display_name': 'Pavel A. Pevzner', 'orcid': 'https://orcid.org/0000-0002-0418-165X'}, 'institutions': [{'id': 'https://openalex.org/I1174212', 'display_name': 'University of Southern California', 'ror': 'https://ror.org/03taz7m60', 'country_code': 'US', 'type': 'education', 'lineage': ['https://openalex.org/I1174212']}], 'countries': ['US'], 'is_corresponding': False, 'raw_author_name': 'Pavel A. Pevzner', 'raw_affiliation_strings': ['Departments of Mathematics, Computer Science and Molecular Biology, University of Southern California, Los Angeles, California.'], 'affiliations': [{'raw_affiliation_string': 'Departments of Mathematics, Computer Science and Molecular Biology, University of Southern California, Los Angeles, California.', 'institution_ids': ['https://openalex.org/I1174212']}]}], 'institution_assertions': [], 'countries_distinct_count': 2, 'institutions_distinct_count': 4, 'corresponding_author_ids': [], 'corresponding_institution_ids': [], 'apc_list': None, 'apc_paid': None, 'fwci': 6.885, 'has_fulltext': True, 'fulltext_origin': 'ngrams', 'cited_by_count': 600, 'citation_normalized_percentile': {'value': 0.982464, 'is_in_top_1_percent': False, 'is_in_top_10_percent': True}, 'cited_by_percentile_year': {'min': 99, 'max': 100}, 'biblio': {'volume': '6', 'issue': '3-4', 'first_page': '327', 'last_page': '342'}, 'is_retracted': False, 'is_paratext': False, 'primary_topic': {'id': 'https://openalex.org/T10519', 'display_name': 'Advanced Proteomics Techniques and Applications', 'score': 1.0, 'subfield': {'id': 'https://openalex.org/subfields/1607', 'display_name': 'Spectroscopy'}, 'field': {'id': 'https://openalex.org/fields/16', 'display_name': 'Chemistry'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, 'topics': [{'id': 'https://openalex.org/T10519', 'display_name': 'Advanced Proteomics Techniques and Applications', 'score': 1.0, 'subfield': {'id': 'https://openalex.org/subfields/1607', 'display_name': 'Spectroscopy'}, 'field': {'id': 'https://openalex.org/fields/16', 'display_name': 'Chemistry'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10683', 'display_name': 'Mass Spectrometry Techniques and Applications', 'score': 0.9999, 'subfield': {'id': 'https://openalex.org/subfields/1607', 'display_name': 'Spectroscopy'}, 'field': {'id': 'https://openalex.org/fields/16', 'display_name': 'Chemistry'}, 'domain': {'id': 'https://openalex.org/domains/3', 'display_name': 'Physical Sciences'}}, {'id': 'https://openalex.org/T10015', 'display_name': 'Genomics and Phylogenetic Studies', 'score': 0.9967, 'subfield': {'id': 'https://openalex.org/subfields/1312', 'display_name': 'Molecular Biology'}, 'field': {'id': 'https://openalex.org/fields/13', 'display_name': 'Biochemistry, Genetics and Molecular Biology'}, 'domain': {'id': 'https://openalex.org/domains/1', 'display_name': 'Life Sciences'}}], 'keywords': [{'id': 'https://openalex.org/keywords/database-search-engine', 'display_name': 'Database search engine', 'score': 0.45035088}, {'id': 'https://openalex.org/keywords/peptide-mass-fingerprinting', 'display_name': 'Peptide mass fingerprinting', 'score': 0.42356676}], 'concepts': [{'id': 'https://openalex.org/C31827203', 'wikidata': 'https://www.wikidata.org/wiki/Q874296', 'display_name': 'Tandem mass spectrometry', 'level': 3, 'score': 0.64599514}, {'id': 'https://openalex.org/C70721500', 'wikidata': 'https://www.wikidata.org/wiki/Q177005', 'display_name': 'Computational biology', 'level': 1, 'score': 0.5655717}, {'id': 'https://openalex.org/C162356407', 'wikidata': 'https://www.wikidata.org/wiki/Q180809', 'display_name': 'Mass spectrometry', 'level': 2, 'score': 0.5097384}, {'id': 'https://openalex.org/C46111723', 'wikidata': 'https://www.wikidata.org/wiki/Q471857', 'display_name': 'Proteomics', 'level': 3, 'score': 0.4988947}, {'id': 'https://openalex.org/C41008148', 'wikidata': 'https://www.wikidata.org/wiki/Q21198', 'display_name': 'Computer science', 'level': 0, 'score': 0.4920525}, {'id': 'https://openalex.org/C48000682', 'wikidata': 'https://www.wikidata.org/wiki/Q5227411', 'display_name': 'Database search engine', 'level': 3, 'score': 0.45035088}, {'id': 'https://openalex.org/C51679486', 'wikidata': 'https://www.wikidata.org/wiki/Q380546', 'display_name': 'DNA sequencing', 'level': 3, 'score': 0.42671442}, {'id': 'https://openalex.org/C27420735', 'wikidata': 'https://www.wikidata.org/wiki/Q5968721', 'display_name': 'Peptide mass fingerprinting', 'level': 4, 'score': 0.42356676}, {'id': 'https://openalex.org/C2779281246', 'wikidata': 'https://www.wikidata.org/wiki/Q172847', 'display_name': 'Peptide', 'level': 2, 'score': 0.4158903}, {'id': 'https://openalex.org/C185592680', 'wikidata': 'https://www.wikidata.org/wiki/Q2329', 'display_name': 'Chemistry', 'level': 0, 'score': 0.32298377}, {'id': 'https://openalex.org/C86803240', 'wikidata': 'https://www.wikidata.org/wiki/Q420', 'display_name': 'Biology', 'level': 0, 'score': 0.25862336}, {'id': 'https://openalex.org/C54355233', 'wikidata': 'https://www.wikidata.org/wiki/Q7162', 'display_name': 'Genetics', 'level': 1, 'score': 0.17183039}, {'id': 'https://openalex.org/C104317684', 'wikidata': 'https://www.wikidata.org/wiki/Q7187', 'display_name': 'Gene', 'level': 2, 'score': 0.16559193}, {'id': 'https://openalex.org/C23123220', 'wikidata': 'https://www.wikidata.org/wiki/Q816826', 'display_name': 'Information retrieval', 'level': 1, 'score': 0.14389595}, {'id': 'https://openalex.org/C97854310', 'wikidata': 'https://www.wikidata.org/wiki/Q19541', 'display_name': 'Search engine', 'level': 2, 'score': 0.1303111}, {'id': 'https://openalex.org/C43617362', 'wikidata': 'https://www.wikidata.org/wiki/Q170050', 'display_name': 'Chromatography', 'level': 1, 'score': 0.11293903}, {'id': 'https://openalex.org/C55493867', 'wikidata': 'https://www.wikidata.org/wiki/Q7094', 'display_name': 'Biochemistry', 'level': 1, 'score': 0.07643178}], 'mesh': [{'descriptor_ui': 'D000465', 'descriptor_name': 'Algorithms', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': True}, {'descriptor_ui': 'D013058', 'descriptor_name': 'Mass Spectrometry', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D010455', 'descriptor_name': 'Peptides', 'qualifier_ui': 'Q000737', 'qualifier_name': 'chemistry', 'is_major_topic': True}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': 'Q000379', 'qualifier_name': 'methods', 'is_major_topic': True}, {'descriptor_ui': 'D000595', 'descriptor_name': 'Amino Acid Sequence', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D016208', 'descriptor_name': 'Databases, Factual', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D005069', 'descriptor_name': 'Evaluation Studies as Topic', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D013058', 'descriptor_name': 'Mass Spectrometry', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D013058', 'descriptor_name': 'Mass Spectrometry', 'qualifier_ui': 'Q000706', 'qualifier_name': 'statistics & numerical data', 'is_major_topic': False}, {'descriptor_ui': 'D010455', 'descriptor_name': 'Peptides', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': '', 'qualifier_name': None, 'is_major_topic': False}, {'descriptor_ui': 'D017421', 'descriptor_name': 'Sequence Analysis', 'qualifier_ui': 'Q000706', 'qualifier_name': 'statistics & numerical data', 'is_major_topic': False}], 'locations_count': 2, 'locations': [{'is_oa': False, 'landing_page_url': 'https://doi.org/10.1089/106652799318300', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S78571599', 'display_name': 'Journal of Computational Biology', 'issn_l': '1066-5277', 'issn': ['1066-5277', '1557-8666'], 'is_oa': False, 'is_in_doaj': False, 'is_core': True, 'host_organization': 'https://openalex.org/P4310320443', 'host_organization_name': 'Mary Ann Liebert, Inc.', 'host_organization_lineage': ['https://openalex.org/P4310320443'], 'host_organization_lineage_names': ['Mary Ann Liebert, Inc.'], 'type': 'journal'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}, {'is_oa': False, 'landing_page_url': 'https://pubmed.ncbi.nlm.nih.gov/10582570', 'pdf_url': None, 'source': {'id': 'https://openalex.org/S4306525036', 'display_name': 'PubMed', 'issn_l': None, 'issn': None, 'is_oa': False, 'is_in_doaj': False, 'is_core': False, 'host_organization': 'https://openalex.org/I1299303238', 'host_organization_name': 'National Institutes of Health', 'host_organization_lineage': ['https://openalex.org/I1299303238'], 'host_organization_lineage_names': ['National Institutes of Health'], 'type': 'repository'}, 'license': None, 'license_id': None, 'version': None, 'is_accepted': False, 'is_published': False}], 'best_oa_location': None, 'sustainable_development_goals': [], 'grants': [], 'datasets': [], 'versions': [], 'referenced_works_count': 32, 'referenced_works': ['https://openalex.org/W125558696', 'https://openalex.org/W1565550208', 'https://openalex.org/W1578163958', 'https://openalex.org/W1964443249', 'https://openalex.org/W1968898518', 'https://openalex.org/W1981978551', 'https://openalex.org/W1988587727', 'https://openalex.org/W1992345938', 'https://openalex.org/W1994985444', 'https://openalex.org/W1996310600', 'https://openalex.org/W2001848433', 'https://openalex.org/W2004561527', 'https://openalex.org/W2011039300', 'https://openalex.org/W2024307631', 'https://openalex.org/W2026465178', 'https://openalex.org/W2028249095', 'https://openalex.org/W2038396508', 'https://openalex.org/W2051192900', 'https://openalex.org/W2058135122', 'https://openalex.org/W2058923971', 'https://openalex.org/W2083911564', 'https://openalex.org/W2089755851', 'https://openalex.org/W2093712725', 'https://openalex.org/W2095013942', 'https://openalex.org/W2095540453', 'https://openalex.org/W2097717077', 'https://openalex.org/W2103718154', 'https://openalex.org/W2141242603', 'https://openalex.org/W2146852491', 'https://openalex.org/W2148721874', 'https://openalex.org/W2313498935', 'https://openalex.org/W2752885492'], 'related_works': ['https://openalex.org/W649532618', 'https://openalex.org/W560807715', 'https://openalex.org/W2495414251', 'https://openalex.org/W2335684874', 'https://openalex.org/W2116007721', 'https://openalex.org/W2099218842', 'https://openalex.org/W2041461813', 'https://openalex.org/W2025005085', 'https://openalex.org/W2004515150', 'https://openalex.org/W1538266555'], 'abstract_inverted_index': {'Peptide': [0], 'sequencing': [1], 'via': [2], 'tandem': [3], 'mass': [4, 54, 87], 'spectrometry': [5], '(MS/MS)': [6], 'is': [7, 119], 'one': [8], 'of': [9, 31, 79, 86, 103, 109, 125, 136], 'the': [10, 26, 100, 134], 'most': [11, 120], 'powerful': [12], 'tools': [13], 'in': [14, 29, 99, 140], 'proteomics': [15], 'for': [16, 63, 122, 132], 'identifying': [17], 'proteins.': [18], 'Because': [19], 'complete': [20], 'genome': [21], 'sequences': [22, 124], 'are': [23, 92], 'accumulating': [24], 'rapidly,': [25], 'recent': [27], 'trend': [28], 'interpretation': [30, 43, 51, 66], 'MS/MS': [32, 41, 104], 'spectra': [33, 81], 'has': [34], 'been': [35], 'database': [36, 137], 'search.': [37], 'However,': [38], 'de': [39, 64], 'novo': [40, 65], 'spectral': [42], 'remains': [44], 'an': [45], 'open': [46], 'problem': [47], 'typically': [48], 'involving': [49], 'manual': [50], 'by': [52], 'expert': [53], 'spectrometrists.': [55], 'We': [56], 'have': [57], 'developed': [58], 'a': [59, 77], 'new': [60], 'algorithm,': [61], 'SHERENGA,': [62], 'that': [67], 'automatically': [68], 'learns': [69], 'fragment': [70], 'ion': [71], 'types': [72], 'and': [73, 131], 'intensity': [74], 'thresholds': [75], 'from': [76, 83, 128], 'collection': [78], 'test': [80, 90], 'generated': [82], 'any': [84], 'type': [85], 'spectrometer.': [88], 'The': [89], 'data': [91], 'used': [93], 'to': [94, 114], 'construct': [95], 'optimal': [96], 'path': [97], 'scoring': [98, 111], 'graph': [101], 'representations': [102], 'spectra.': [105], 'A': [106], 'ranked': [107], 'list': [108], 'high': [110], 'paths': [112], 'corresponds': [113], 'potential': [115], 'peptide': [116, 144], 'sequences.': [117], 'SHERENGA': [118], 'useful': [121], 'interpreting': [123], 'peptides': [126], 'resulting': [127], 'unknown': [129], 'proteins': [130], 'validating': [133], 'results': [135], 'search': [138], 'algorithms': [139], 'fully': [141], 'automated,': [142], 'high-throughput': [143], 'sequencing.': [145]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W1995693931', 'counts_by_year': [{'year': 2024, 'cited_by_count': 12}, {'year': 2023, 'cited_by_count': 9}, {'year': 2022, 'cited_by_count': 10}, {'year': 2021, 'cited_by_count': 17}, {'year': 2020, 'cited_by_count': 16}, {'year': 2019, 'cited_by_count': 19}, {'year': 2018, 'cited_by_count': 12}, {'year': 2017, 'cited_by_count': 12}, {'year': 2016, 'cited_by_count': 27}, {'year': 2015, 'cited_by_count': 29}, {'year': 2014, 'cited_by_count': 22}, {'year': 2013, 'cited_by_count': 21}, {'year': 2012, 'cited_by_count': 20}], 'updated_date': '2024-12-09T01:48:54.358926', 'created_date': '2016-06-24'}