Abstract：
:Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications in mass spectrometry-based proteomics. Most notably such predictions are used to weed out incorrect peptide-spectrum matches, and to design targeted proteomics experiments. In this study, we describe a RT predictor, ELUDE, which can be employed in both applications. ELUDE's predictions are based on 60 features derived from the peptide's amino acid composition and optimally combined using kernel regression. When sufficient data is available, ELUDE derives a retention time index for the condition at hand making it fully portable to new chromatographic conditions. In cases when little training data is available, as often is the case in targeted proteomics experiments, ELUDE selects and calibrates a model from a library of pretrained predictors. Both model selection and calibration are carried out via robust statistical methods and thus ELUDE can handle situations where the calibration data contains erroneous data points. We benchmarked our method against two state-of-the-art predictors and showed that ELUDE outperforms these methods and tracked up to 34% more peptides in a theoretical SRM method creation experiment. ELUDE is freely available under Apache License from http://per-colator.com.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Moruz L,Tomazela D,Käll Ldoi
10.1021/pr1005058subject
Has Abstractpub_date
2010-10-01 00:00:00pages
5209-16issue
10eissn
1535-3893issn
1535-3907journal_volume
9pub_type
杂志文章abstract：:Normozoospermic infertility has become a common and important health problem worldwide. We designed this metabolomic case-control study to investigate the possible mechanism and urinary biomarkers of normozoospermic infertility. Normozoospermic infertile cases (n = 71) and fertile controls (n = 47) were recruited. A u...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5003142
更新日期：2014-06-06 00:00:00
abstract：:Complicating proteomic analysis of whole tissues is the obvious problem of cell heterogeneity in tissues, which often results in misleading or confusing molecular findings. Thus, the coupling of tissue microdissection for tumor cell enrichment with capillary isotachophoresis-based selective analyte concentration not o...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300303t
更新日期：2012-08-03 00:00:00
abstract：:Rheumatoid arthritis is a progressive, highly debilitating disease where early diagnosis, enabling rapid clinical intervention, would provide obvious benefits to patients, healthcare systems, and society. Novel biomarkers that enable noninvasive early diagnosis of the onset and progression of the disease provide one r...
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
doi：10.1021/pr100651w
更新日期：2010-11-05 00:00:00
abstract：:Glycoproteins influence numerous indispensable biological functions, and changes in protein glycosylation have been observed in various diseases. The identification and characterization of glycoprotein and glycosylation sites by mass spectrometry (MS) remain challenging tasks, and great efforts have been devoted to th...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00772
更新日期：2016-11-04 00:00:00
abstract：:Advancements in studies on the evolutionary mechanisms underlying bacterial antibiotic resistance are unclear. This study aimed to investigate the evolutionary mechanism underlying bacterial antibiotic resistance using isobaric tags for relative and absolute quantitation-based quantitative proteomics along with functi...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00410
更新日期：2019-11-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500756u
更新日期：2015-01-02 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr901040u
更新日期：2010-03-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101095t
更新日期：2011-05-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01035
更新日期：2016-10-07 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100989c
更新日期：2011-02-04 00:00:00
abstract：:Dysregulated protein phosphorylation is a primary culprit in multiple physiopathological states. Hence, although analysis of signaling cascades on a proteome-wide scale would provide significant insight into both normal and aberrant cellular function, such studies are simultaneously limited by sheer biological complex...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0602803
更新日期：2006-10-01 00:00:00
abstract：:A well-described animal model was used to understand the molecular mechanisms of carcinogenesis and metastasis of gastric cancer at the protein level. Gastric cancer was induced in 12 Wistar rats by oral administration of N-methyl-N'-Nitro-N-Nitrosoguanidine (MNNG). The protein expression patterns of normal gastric ti...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049916l
更新日期：2004-09-01 00:00:00
abstract：:Neutrophilic granulocytes play a major role in the initiation and resolution of the inflammatory response, and demonstrate significant transcriptional and translational activity. Although much was known about neutrophils prior to the introduction of proteomics, the use of MS-based methodologies has provided an unprece...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1000253
更新日期：2010-04-05 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060671h
更新日期：2007-06-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00128
更新日期：2017-10-06 00:00:00
abstract：:Urine is an ideal material to study the cancer-related protein biomarkers in bladder, whereas exploration to these candidates is confronting technique challenges. Herein, we propose a comprehensive strategy of searching the urine proteins related with bladder cancer. The strategy consists of three core combinations, s...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00106
更新日期：2016-07-01 00:00:00
abstract：:Protein oxidation and nitration have been described during spinal cord injury (SCI) in animal models. Herein, mass spectrometry unambiguously identified GDP-dissociation inhibitor-2 (GDI-2) in SCI with post-translational modifications of 3-aminotyrosine (8 h post-injury) and an acrolein adduct of GDI-2 (72 h post-inju...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060620k
更新日期：2007-04-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101245u
更新日期：2011-05-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00396
更新日期：2016-05-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100554m
更新日期：2010-10-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4008078
更新日期：2014-02-07 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：2016-01-01 00:00:00
abstract：:Enzyme-mediated 18O/16O differential labeling of proteome samples often suffers from incomplete exchange of the carboxy-terminus oxygen atoms, resulting in ambiguity in the measurable abundance differences. In this study, an 18O/16O labeling strategy was optimized for and applied to the solution-based comparative anal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049790s
更新日期：2005-03-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060514i
更新日期：2007-02-01 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.0c00385
更新日期：2020-11-06 00:00:00
abstract：:This report demonstrates the application of a capillary LC-LTQ-orbitrap system to provide automated middle-down analysis of proteolytic peptides in the mass range 3000 to 10,000 Da. The novel workflow combines an underutilized method in the orbitrap-high resolution, mass-accurate product ion measurements-with software...
journal_title：Journal of proteome research
pub_type： 杂志文章
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更新日期：2010-08-06 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr500491r
更新日期：2014-10-03 00:00:00
abstract：:In the analysis of proteins in complex samples, pre-fractionation is imperative to obtain the necessary depth in the number of reliable protein identifications by mass spectrometry. Here we explore isoelectric focusing of peptides (peptide IEF) as an effective fractionation step that at the same time provides the adde...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0601180
更新日期：2006-07-01 00:00:00
