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SpecArray specifications


Unique identifier OMICS_02394
Name SpecArray
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data A set of LC-MS data.
Output data A peptide versus sample array that stores the relative abundance of thousands of peptide features matched in all samples.
Operating system Unix/Linux
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes
Wikipedia https://sourceforge.net/p/sashimi/wiki/Home/




No version available


  • person_outline Xiao-jun Li <>

Publication for SpecArray

SpecArray citations


A flexible statistical model for alignment of label free proteomics data – incorporating ion mobility and product ion information

PMCID: 3878627
PMID: 24341404
DOI: 10.1186/1471-2105-14-364

[…] data provides a higher degree of specificity when making matches []. the majority of existing alignment techniques utilize mass-to-charge ratio and retention time information. such methods include specarray [], amt tag approaches [], xalign [], mzmine [], msinspect [], xcms [], petal [], openms [,], aplcms [], and mzmine2 []. semi-supervised approaches such as pepper [] and a method by fischer […]


File Formats Commonly Used in Mass Spectrometry Proteomics*

PMCID: 3518119
PMID: 22956731
DOI: 10.1074/mcp.R112.019695

[…] the output of the mass spectrometer runs, including vendor proprietary formats and mzxml or mzml. these mass spectrometer files are then processed by any number of possible software packages such as specarray (), msinspect (), superhirn (), corra (), maxquant (), pepper (), and others. the output of most of these programs is some sort of tab-delimited text file, but several programs support […]


Label free peptide profiling of Orbitrap™ full mass spectra

PMCID: 3042405
PMID: 21272362
DOI: 10.1186/1756-0500-4-21

[…] in which spectral intensities and retention times of peptide masses from samples belonging to different groups are presented in various ways., some of these software packages, such as superhirn and specarray, did at the time of analysis not run on the windows operating system (os) but only on linux []. other applications required customized data input formats or connection to pre-filled […]


Bioinformatics tools for cancer metabolomics

PMCID: 3155682
PMID: 21949492
DOI: 10.1007/s11306-010-0270-3

[…] metabolomics application, several mass spectrometry data processing software packages that were developed for proteomics can also be used to process metabolomics data. these include, among others, specarray (li et al. , http://tools.proteomecenter.org/wiki/index.php?title=software:specarray), msight (palagi et al. , http://www.expasy.org/msight/), and mapquant (leptos et al. , […]


BPDA A Bayesian peptide detection algorithm for mass spectrometry

PMCID: 3098078
PMID: 20920238
DOI: 10.1186/1471-2105-11-490

[…] the detection results of bpda, openms, and decon2ls, which was applied in conjunction with viper [], are summarized in additional file : table s2 (we also considered the method implemented in the specarray package [], but found it to be inferior to bpda, openms, and decon2ls -- the results were then omitted for the sake of conciseness). the number of features with unique monoisotopic masses […]


Review of Peak Detection Algorithms in Liquid Chromatography Mass Spectrometry

PMCID: 2766790
PMID: 20190954
DOI: 10.2174/138920209789177638

[…] cluster features are then compared with the selected amt tag databases for peptide/protein identification., peplist [] is the peak detection algorithm in the lc/ms data processing software package specarray. the algorithm differentiates peptide and non-peptide peaks based on isotope matching, intensity of ms peaks, intensity of lc peaks, frequency content of elution, and ms peaks. […]

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SpecArray institution(s)
Institute for Systems Biology, Seattle, WA, USA; Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Institute for Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zurich, University of Zurich, Zurich, Switzerland; Faculty of Natural Sciences, University of Zurich, Zurich, Switzerland
SpecArray funding source(s)
Supported in part by the NHLBI, National Institutes of Health, under Contract N01-HV-28179, the NCI, National Institutes of Health, under Contract N01-CO-12400 and under Grant 1R21CA114852, and the NIEHS, National Institutes of Health, under Grant U01-ES-11045.

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