{"database":"PeptideAtlas","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Other":["ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_Search_Results_429_201104201859.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_Search_Results_429_201104201859.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_prot_429_201104201901.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_mzXML_201104201852.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_RAW_201104201856.tar.gz","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_prot_429_201104201901.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_mzXML_201104201852.properties","ftp://ftp.peptideatlas.org/pub/PeptideAtlas/Repository/Yeast/PAe000145/PAe000145_README"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"submitter":["Steven Gygi et al. (Harvard)"],"disease":[""],"software":["TPP"],"full_dataset_link":["'https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ManageTable.cgi?TABLE_NAME=AT_sample&sample_id=156'"],"synonyms":[""],"submitter_email":["","edeutsch@systemsbiology.org"],"repository":["PeptideAtlas"],"sample_protocol":[""],"data_protocol":[""],"omics_type":["Proteomics"],"pubmed":[""],"instrument_platform":["LCQ DECA"],"project_tag":[""],"species":["Saccharomyces Cerevisiae"],"publication":[""],"pubmed_abstract":["Highly complex protein mixtures can be directly analyzed after proteolysis by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). In this paper, we have utilized the combination of strong cation exchange (SCX) and reversed-phase (RP) chromatography to achieve two-dimensional separation prior to MS/MS. One milligram of whole yeast protein was proteolyzed and separated by SCX chromatography (2.1 mm i.d.) with fraction collection every minute during an 80-min elution. Eighty fractions were reduced in volume and then re-injected via an autosampler in an automated fashion using a vented-column (100 microm i.d.) approach for RP-LC-MS/MS analysis. More than 162,000 MS/MS spectra were collected with 26,815 matched to yeast peptides (7,537 unique peptides). A total of 1,504 yeast proteins were unambiguously identified in this single analysis. We present a comparison of this experiment with a previously published yeast proteome analysis by Yates and colleagues (Washburn, M. P.; Wolters, D.; Yates, J. R., III. Nat. Biotechnol. 2001, 19, 242-7). In addition, we report an in-depth analysis of the false-positive rates associated with peptide identification using the Sequest algorithm and a reversed yeast protein database. New criteria are proposed to decrease false-positives to less than 1% and to greatly reduce the need for manual interpretation while permitting more proteins to be identified."],"pubmed_title":["Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome."],"pubmed_authors":["Peng Junmin J, Elias Joshua E JE, Thoreen Carson C CC, Licklider Larry J LJ, Gygi Steven P 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