{"id":"https://openalex.org/W2120412864","doi":"https://doi.org/10.1186/1471-2105-8-102","title":"SAMPI: Protein Identification with Mass Spectra Alignments","display_name":"SAMPI: Protein Identification with Mass Spectra Alignments","publication_year":2007,"publication_date":"2007-03-26","ids":{"openalex":"https://openalex.org/W2120412864","doi":"https://doi.org/10.1186/1471-2105-8-102","mag":"2120412864","pmid":"https://pubmed.ncbi.nlm.nih.gov/17386090"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-102","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-102","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-102","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056696475","display_name":"Hans\u2010Michael Kaltenbach","orcid":"https://orcid.org/0000-0003-2500-1221"},"institutions":[{"id":"https://openalex.org/I20121455","display_name":"Bielefeld University","ror":"https://ror.org/02hpadn98","country_code":"DE","type":"education","lineage":["https://openalex.org/I20121455"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Hans-Michael Kaltenbach","raw_affiliation_strings":["AG Genominformatik, Technische Fakult\u00e4t, Universit\u00e4t Bielefeld, Bielefeld, Germany. michael@cebitec.uni-bielefeld.de","AG Genominformatik, Technische Fakult\u00e4t, Universit\u00e4t Bielefeld, Bielefeld, Germany#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"AG Genominformatik, Technische Fakult\u00e4t, Universit\u00e4t Bielefeld, Bielefeld, Germany. michael@cebitec.uni-bielefeld.de","institution_ids":["https://openalex.org/I20121455"]},{"raw_affiliation_string":"AG Genominformatik, Technische Fakult\u00e4t, Universit\u00e4t Bielefeld, Bielefeld, Germany#TAB#","institution_ids":["https://openalex.org/I20121455"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027887614","display_name":"Andreas Wilke","orcid":"https://orcid.org/0000-0002-7699-2267"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andreas Wilke","raw_affiliation_strings":["Computation Institute, University of Chicago, Chicago, IL, 60637, USA","Computation Institute, University of Chicago, Chicago, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computation Institute, University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Computation Institute, University of Chicago, Chicago, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5033025664","display_name":"Sebastian B\u00f6cker","orcid":"https://orcid.org/0000-0002-9304-8091"},"institutions":[{"id":"https://openalex.org/I76198965","display_name":"Friedrich Schiller University Jena","ror":"https://ror.org/05qpz1x62","country_code":"DE","type":"education","lineage":["https://openalex.org/I76198965"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Sebastian B\u00f6cker","raw_affiliation_strings":["Lehrstuhl f\u00fcr Bioinformatik, Friedrich-Schiller-Universit\u00e4t Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany","Lehrstuhl f\u00fcr Bioinformatik, Friedrich-Schiller Universit\u00e4t Jena, Jena, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Lehrstuhl f\u00fcr Bioinformatik, Friedrich-Schiller-Universit\u00e4t Jena, Ernst-Abbe-Platz 2, 07743, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]},{"raw_affiliation_string":"Lehrstuhl f\u00fcr Bioinformatik, Friedrich-Schiller Universit\u00e4t Jena, Jena, Germany","institution_ids":["https://openalex.org/I76198965"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033025664","https://openalex.org/A5056696475"],"corresponding_institution_ids":["https://openalex.org/I20121455","https://openalex.org/I76198965"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4757,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.6225589,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"8","issue":"1","first_page":"102","last_page":"102"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9708999991416931,"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":0.9708999991416931,"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":0.008100000210106373,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.007600000128149986,"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/identification","display_name":"Identification (biology)","score":0.6987575888633728},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.657655656337738},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.534069836139679},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4017859101295471},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.36310815811157227},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3460698127746582},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31334447860717773},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08423447608947754},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.060805320739746094}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6987575888633728},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.657655656337738},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.534069836139679},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4017859101295471},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.36310815811157227},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3460698127746582},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31334447860717773},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08423447608947754},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.060805320739746094},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010449","descriptor_name":"Peptide Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010455","descriptor_name":"Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019032","descriptor_name":"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019032","descriptor_name":"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019032","descriptor_name":"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false},{"descriptor_ui":"D048230","descriptor_name":"Corynebacterium glutamicum","qualifier_ui":"Q000302","qualifier_name":"isolation & purification","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-8-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-102","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-102","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17386090","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17386090","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c47997b792ee4113a7d80233f794e0e7","is_oa":true,"landing_page_url":"https://doaj.org/article/c47997b792ee4113a7d80233f794e0e7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 102 (2007)","raw_type":"article"},{"id":"pmh:oai:pub.librecat.org:1783712","is_oa":true,"landing_page_url":"https://pub.uni-bielefeld.de/record/1783712","pdf_url":null,"source":{"id":"https://openalex.org/S4306401671","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Kaltenbach H-M, Wilke A, B\u00f6cker S. SAMPI: protein identification with mass spectra alignments. &lt;em&gt;BMC Bioinformatics&lt;/em&gt;. 2007;8(1):102.","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1851022","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1851022","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-102","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-102","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-102","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2120412864.pdf","grobid_xml":"https://content.openalex.org/works/W2120412864.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W938539187","https://openalex.org/W1527640254","https://openalex.org/W1554256846","https://openalex.org/W1561803476","https://openalex.org/W1865803280","https://openalex.org/W1972101418","https://openalex.org/W1974830441","https://openalex.org/W1979692315","https://openalex.org/W1981593008","https://openalex.org/W1985560593","https://openalex.org/W1999291689","https://openalex.org/W2016701426","https://openalex.org/W2023096047","https://openalex.org/W2040703580","https://openalex.org/W2053757278","https://openalex.org/W2055043387","https://openalex.org/W2079497005","https://openalex.org/W2085393537","https://openalex.org/W2092523771","https://openalex.org/W2112143438","https://openalex.org/W2121904553","https://openalex.org/W2150746288","https://openalex.org/W2151397064","https://openalex.org/W2155997603","https://openalex.org/W2503093402","https://openalex.org/W2610179052"],"related_works":["https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W3107784576","https://openalex.org/W623104033","https://openalex.org/W1972473893","https://openalex.org/W2118505788"],"abstract_inverted_index":{"BACKGROUND:":[0],"Mass":[1,76,177],"spectrometry":[2,159],"based":[3,93],"peptide":[4],"mass":[5,27,90,158],"fingerprints":[6],"(PMFs)":[7],"offer":[8],"a":[9,38,80,95,137,200],"fast,":[10],"efficient,":[11],"and":[12,25,59,64,105,109,146,161],"robust":[13],"method":[14,115,131],"for":[15,34,43,73,102,132,174],"protein":[16,19,35,138],"identification.":[17],"A":[18],"is":[20,29,92,116],"digested":[21],"(usually":[22],"by":[23,203,208],"trypsin)":[24],"its":[26],"spectrum":[28],"compared":[30],"to":[31,118,165,182,195],"simulated":[32],"spectra":[33,91],"sequences":[36],"in":[37],"database.":[39,148],"However,":[40],"existing":[41,85],"tools":[42],"analyzing":[44,74,175],"PMFs":[45],"often":[46],"suffer":[47],"from":[48],"missing":[49,63,108],"or":[50],"heuristic":[51],"analysis":[52],"of":[53,56,62,82,89,136,141,153],"the":[54,134,142,151,166,205],"significance":[55,135],"search":[57],"results":[58,164],"insufficient":[60],"handling":[61],"additional":[65,110],"peaks.":[66],"RESULTS:":[67],"We":[68,149],"present":[69,127],"an":[70,128],"unified":[71],"framework":[72,173],"Peptide":[75,176],"Fingerprints":[77,178],"that":[78,98],"offers":[79],"number":[81],"advantages":[83],"over":[84],"methods:":[86],"First,":[87],"comparison":[88],"on":[94,184],"scoring":[96,123,144,209],"function":[97,145],"can":[99],"be":[100],"custom-designed":[101],"certain":[103],"applications":[104],"explicitly":[106],"takes":[107],"peaks":[111],"into":[112],"account.":[113],"The":[114,171],"able":[117,194],"simulate":[119],"almost":[120],"every":[121],"additive":[122],"scheme.":[124],"Second,":[125],"we":[126,192],"efficient":[129],"deterministic":[130],"assessing":[133],"hit,":[139],"independent":[140],"underlying":[143],"sequence":[147],"prove":[150],"applicability":[152],"our":[154,163],"approach":[155],"using":[156,204],"biological":[157],"data":[160],"compare":[162],"standard":[167],"software":[168],"Mascot.":[169],"CONCLUSION:":[170],"proposed":[172],"shows":[179],"performance":[180],"comparable":[181],"Mascot":[183],"small":[185],"peak":[186],"lists.":[187],"Introducing":[188],"more":[189],"noise":[190],"peaks,":[191],"are":[193],"keep":[196],"identification":[197],"rates":[198],"at":[199],"similar":[201],"level":[202],"flexibility":[206],"introduced":[207],"schemes.":[210]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
