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Protocols

IDEAL-Q specifications

Information


Unique identifier OMICS_02382
Name IDEAL-Q
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for IDEAL-Q

IDEAL-Q citations

 (23)
library_books

Combining membrane proteomics and computational three way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs

2017
Sci Rep
PMCID: 5678157
PMID: 29118436
DOI: 10.1038/s41598-017-15347-z

[…] to estimate how close our hipsc cell lines to hesc cell lines at protein expression level (fig. ); the hipsc cell lines were expected to be very similar to the hesc cell lines. since the output of ideal-q, the software we used to quantify proteins, is not absolute expression level but relative expression ratio, we can only compare protein profiles using ratios with respect to the same base […]

library_books

Role of S Palmitoylation by ZDHHC13 in Mitochondrial function and Metabolism in Liver

2017
Sci Rep
PMCID: 5438363
PMID: 28526873
DOI: 10.1038/s41598-017-02159-4

[…] respectively. all ms raw data were processed with proteome discover version 2.1 (thermo fisher scientific). for label-free quantification of palmitoylated peptides, data analysis was performed using ideal-q software [34]. membrane proteomic quantitation was performed by proteome discover version 2.1. full experimental procedures are available in the supplementary data., for subcellular […]

library_books

Phosphoproteomics Reveals HMGA1, a CK2 Substrate, as a Drug Resistant Target in Non Small Cell Lung Cancer

2017
Sci Rep
PMCID: 5349541
PMID: 28290473
DOI: 10.1038/srep44021

[…] partner repository with the dataset identifier pxd000375 and doi 10.6019/pxd000375., the quantitation of phosphoproteomics and proteomics were performed by the semi label free algorithm by using ideal-q software. firstly, readw (xcalibur, thermo finnigan) program was used to convert the raw data files acquired from the ltq-orbitrap into mzxml file format for peptide peak reconstruction. […]

library_books

Increased liver specific proteins in circulating extracellular vesicles as potential biomarkers for drug and alcohol induced liver injury

2017
PLoS One
PMCID: 5321292
PMID: 28225807
DOI: 10.1371/journal.pone.0172463

[…] identification, raw data files from ms/ms data were converted into peak lists using mascot distiller (matrix science; version 2.3.2) using the default parameters. for protein quantification, we used ideal-q software (version 1.0.1.1) to analyze the lc-ms/ms data., total rna was extracted from each mouse liver using trizol and an rneasy mini kit (qiagen), by following the manufacturer’s […]

library_books

Direct derivation of maize plant and crop height from low cost time of flight camera measurements

2016
Plant Methods
PMCID: 5127001
PMID: 27933095
DOI: 10.1186/s13007-016-0150-6

[…] peak around the mean value, at the same time having heavy tails due to blunders. the q–q plots indicate a normal distribution including blunders which lead to a deviation from the linear shape of an ideal q–q plot. the distributions show a tendency towards a negative skew, with large chm differences occurring in the left tail pointing at a crop height underestimation in the chms derived from k2 […]

library_books

Temporal regulation of Lsp1 O GlcNAcylation and phosphorylation during apoptosis of activated B cells

2016
Nat Commun
PMCID: 4999498
PMID: 27555448
DOI: 10.1038/ncomms12526

[…] (condition a) (). the quantitative phosphoproteomic approach used in this study combined our previously developed automatic ph/acid-controlled imac procedure for phosphopeptide enrichment and the ideal-q algorithm for label-free quantification (see workflow in )., a total of 3,752 non-redundant phosphopeptides that mapped to 3,079 unique phosphorylation sites originating from 1,266 proteins […]


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