Abstract：
:A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each proteoform: (i) the accurate proteoform intact-mass, measured by liquid chromatography/mass spectrometry (LC-MS), and (ii) the number of lysine residues in each proteoform, determined using an isotopic labeling approach. These measured properties are then compared with those extracted from a catalog of theoretical proteoforms containing protein sequences and localized post-translational modifications (PTMs) for the organism under study. A match between the measured properties and those in the catalog constitutes an identification of the proteoform. In the present study, this strategy is extended by utilizing a global PTM discovery database and is applied to the widely studied model organism Escherichia coli, providing the most comprehensive elucidation of E. coli proteoforms and proteoform families to date.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Dai Y,Shortreed MR,Scalf M,Frey BL,Cesnik AJ,Solntsev S,Schaffer LV,Smith LMdoi
10.1021/acs.jproteome.7b00516subject
Has Abstractpub_date
2017-11-03 00:00:00pages
4156-4165issue
11eissn
1535-3893issn
1535-3907journal_volume
16pub_type
杂志文章abstract：:Controlled ovarian hyperstimulation is performed to assist with generation of multiple mature oocytes for use in in vitro fertilization (IVF). The goal of our study was to evaluate differences in protein and steroid profiles in ovarian follicular fluid (hFF) samples obtained during oocyte retrieval from women undergoi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300535g
更新日期：2012-10-05 00:00:00
abstract：:Due to the increasing prevalence of nosocomial and community-acquired antibiotic resistant Staphylococcus aureus (SA), understanding the determinants of SA nasal carriage has become a major imperative. Previous research has revealed many host and bacterial factors that contribute to SA nasal carriage. To assess bacter...
journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2011-04-01 00:00:00
abstract：:The International Mouse Phenotyping Consortium program has been established to ascribe biological functions to systematically knocked-out (KO) genes by in vivo and ex vivo phenotyping. The plasma clinical chemistry screen includes an assessment of liver, kidney, and bone function and provides a basic lipid profile and...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr501039k
更新日期：2015-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2009-10-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200092z
更新日期：2011-08-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00014
更新日期：2018-04-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00654
更新日期：2016-12-02 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2009-06-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200527z
更新日期：2011-09-02 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr8003024
更新日期：2008-10-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2014-11-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr301054n
更新日期：2013-01-04 00:00:00
abstract：:Activation of AMP-activated protein kinase (AMPK) upon energy depletion stimulates energy production and limits energy utilization. Erythrocytes lacking AMPK are susceptible to suicidal cell death (eryptosis). A hallmark of eryptosis is cell membrane scrambling with phosphatidylserine exposure at the erythrocyte surfa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101004j
更新日期：2011-04-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr2006457
更新日期：2011-11-04 00:00:00
abstract：:Nanobacteria may cause peripheral neuropathy by adhesion to the perineurium. This hypothesis receives support from five independent observations: (1) identification of perineurial apatite in diabetic patients with peripheral neuropathy, (2) massive presence of nanobacteria in a diabetic patient, (3) beneficial effect ...
journal_title：Journal of proteome research
pub_type： 信件
doi：10.1021/pr049935v
更新日期：2004-09-01 00:00:00
abstract：:High-resolution proton nuclear magnetic resonance (NMR) spectrometry of biofluids has been increasingly used in laboratory diagnosis of various diseases. In this study, we extended the use of (1)H NMR spectroscopy for laboratory diagnosis of exudative pleural effusions using pleural fluids. We compared this new NMR-ba...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5004856
更新日期：2014-09-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00428
更新日期：2018-01-05 00:00:00
abstract：:We report a hybrid search method combining database and spectral library searches that allows for a straightforward approach to characterizing the error rates from the combined data. Using these methods, we demonstrate significantly increased sensitivity and specificity in matching peptides to tandem mass spectra. The...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101130b
更新日期：2011-05-06 00:00:00
abstract：:Quantitative comparison of protein expression levels in 2D gels is complicated by the variables associated with protein separation and mass spectrometric responses. Metabolic labeling allows cells from different experiments to be mixed prior to analysis. This approach has been reported for prokaryotic cells. Here, we ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr025523f
更新日期：2002-07-01 00:00:00
abstract：:Cooperia oncophora is one of the most common intestinal parasitic nematodes in cattle worldwide. To date, C. oncophora infections are treated using broad-spectrum anthelmintics. However, during the past decade, reports of anthelmintic resistance in this parasite species have emerged worldwide, necessitating new avenue...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400114y
更新日期：2013-09-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2009-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2010-05-07 00:00:00
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journal_title：Journal of proteome research
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更新日期：2008-08-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章,评审
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更新日期：2004-09-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00601
更新日期：2020-03-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00239
更新日期：2020-08-07 00:00:00
abstract：:We report here using a novel technology-electrospray-assisted laser desorption ionization (ELDI)/mass spectrometry-for the rapid and sensitive detection of the major proteins that exist in dried biological fluids (e.g., blood, tears, saliva, serum), bacterial cultures, and tissues (e.g., porcine liver and heart) under...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050442f
更新日期：2006-05-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr070491n
更新日期：2008-01-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2021-01-01 00:00:00
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更新日期：2008-05-01 00:00:00
