APEX Quantitative Proteomics Tool protocols

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APEX Quantitative Proteomics Tool specifications

Information


Unique identifier OMICS_02485
Name APEX Quantitative Proteomics Tool
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Stability Stable
Requirements
Trans-Proteomic Pipeline
Maintained Yes

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Publication for APEX Quantitative Proteomics Tool

APEX Quantitative Proteomics Tool in pipelines

 (4)
2017
PMCID: 5712127
PMID: 29197336
DOI: 10.1186/s12864-017-4293-2

[…] ptm locations were identified using ptmprophet in both the monarch data presented here and a comparable dataset in m. sexta []., relative compositional protein abundance was quantified using the apex quantitative proteomics tool []. the training dataset was constructed using fifty proteins with the highest number of uncorrected spectral counts (n i), and identification probabilities. all 35 […]

2013
PMCID: 3686733
PMID: 23840478
DOI: 10.1371/journal.pone.0066462

[…] conversion into the mzxml format, ms data were re-scored using the algorithms peptideprophet™ and proteinprophet™ , . prot.xml files were analysed using an in house-developed software tool termed apex quantitative proteomics tool v1.1 . using a pre-defined set of ms analysis parameters and 30 physicochemical properties provided by the apex tool (default settings), arff files for oi […]

2009
PMCID: 2716310
PMID: 19563668
DOI: 10.1186/1477-5956-7-22

[…] estimated by normalizing for the measured total protein concentration, as described in more detail for the apex quantitation of sd1 proteins., the apex quantitation of sd1 proteins using the apex quantitative proteomics tool consisted of three steps: building a sd1 training dataset, computing sd1 protein oi (expected number of unique proteotypic peptides for protein i) values, […]

2009
PMCID: 2716310
PMID: 19563668
DOI: 10.1186/1477-5956-7-22

[…] demonstrating that the corresponding genes were indeed expressed. the coverage of the genome-predicted sd1 proteome was ca. 26%. this dataset was subjected to protein quantitation using the apex quantitative proteomics tool (fig. ). the random forest classifier algorithm was trained on a high quality training dataset of 100 abundant proteins to predict protein oi values. the algorithm […]


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APEX Quantitative Proteomics Tool in publications

 (9)
PMCID: 5727318
PMID: 29234088
DOI: 10.1038/s41598-017-17536-2

[…] variable modification, peptide mass tolerance of 50 ppm, fragment mass tolerance of 0.1 da, and 1 missed cleavage., protein quantitation was performed using label-free spectral counting, employing apex quantitative proteomics tool v.1.1 as described previously. mascot output files were converted to the pepxml format using trans-proteomic pipeline software v. 3.2.2 (institute for systems […]

PMCID: 5435083
PMID: 28333336
DOI: 10.1093/molbev/msx084

[…] abundance estimates. we note that the second correction approach could not be applied to m. spicilegus as the genome is not yet sequenced., the quantitation of proteins was conducted using the apex quantitative proteomics tool (; ). 50 proteins with the highest numbers of spectral counts, and peptide and protein identification probabilities in the m. musculus sperm were utilized […]

PMCID: 5090203
PMID: 27804984
DOI: 10.1038/srep35864

[…] and the potential impact of this highly abundant protein on various quantitative approaches, a semi-quantitative spectral counting approach was employed. protein quantitation was conducted using the apex quantitative proteomics tool. fifty sfps previously identified using the same ms/ms methodology (data not shown) were utilized for the training dataset based on having the highest numbers […]

PMCID: 4366636
PMID: 25798057
DOI: 10.7150/ijbs.10666

[…] seattle, wa, usa) with a confidence level of 95%. protein identifications were accepted with a greater than 99% probability. the false discovery rate was less than 1%, which was calculated using the apex-quantitative proteomics tool (revision1.0.0, j. craig venter institute, rockville, md, usa)., the proteomics data of gcafs and giafs were normalized by mean normalization. the fold-change method […]

PMCID: 3686733
PMID: 23840478
DOI: 10.1371/journal.pone.0066462

[…] conversion into the mzxml format, ms data were re-scored using the algorithms peptideprophet™ and proteinprophet™ , . prot.xml files were analysed using an in house-developed software tool termed apex quantitative proteomics tool v1.1 . using a pre-defined set of ms analysis parameters and 30 physicochemical properties provided by the apex tool (default settings), arff files for oi […]


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APEX Quantitative Proteomics Tool institution(s)
Pathogen Functional Genomics Resource Center, J Craig Venter Institute, Chinakville, MD, USA

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