XPRESS pipeline

XPRESS specifications


Unique identifier OMICS_02488
Alternative name TPP distribution
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Medium
Stability Stable
Maintained Yes


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  • person_outline Ruedi Aebersold <>

Publication for XPRESS

XPRESS IN pipelines

PMCID: 5620370
PMID: 28794267
DOI: 10.1091/mbc.E17-02-0093

[…] frame of 20 s following the fragmentation event. full-scan data were acquired in profile, and fragments were analyzed in centroid mode by xcalibur software. the lc unit was controlled by chromeleon xpress software., for data analysis, maxquant (cox and mann, 2008), perseus (tyanova et al., 2016), and excel (microsoft office 2013) were used. the enzyme specificity was set […]

PMCID: 4632068
PMID: 26392412
DOI: 10.1534/g3.115.021444

[…] 15.99). tandem mass spectra peptide and protein assignments were validated by the peptideprophet (keller et al. 2002) and proteinprophet (nesvizhskii et al. 2003) programs, available in the current tpp distribution (http://tools.proteomecenter.org/wiki/index.php?title=software:tpp). protein probabilities yielding a 0.05 false-discovery rate threshold were applied to the resulting protein lists […]

PMCID: 4632068
PMID: 26392412
DOI: 10.1534/g3.115.021444

[…] assessment of peptide and protein identifications by peptideprophet (keller et al. 2002) and proteinprophet (nesvizhskii et al. 2003), quantitative silac ratios for proteins were determined using xpress software (han et al. 2001). precursor ion elution profiles of heavy vs. light peptides were determined with a mass tolerance of 0.05 (>5 sec) and the area under the curve was used […]

PMCID: 3365017
PMID: 22693568
DOI: 10.1371/journal.pone.0037108

[…] peptide identification, we determined the ratio of medium to heavy isotope, which should reflect the change in production of the corresponding protein after 12 hours of imatinib treatment, using the xpress quantitation algorithm [105]. the quality of the peptide ratio data was ensured as follows: low-quality peptide quantitative ratios were algorithmically identified and removed from the dataset […]

XPRESS institution(s)
University of Connecticut Health Center, Farmington, CT, USA; Institute for Systems Biology, Seattle, WA, USA

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