SpectConnect protocols

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SpectConnect specifications


Unique identifier OMICS_13685
Name SpectConnect
Interface Application programming interface
Restrictions to use None
Input data GC/MS data
Computer skills Advanced
Version 1.0
Source code URL http://spectconnect.mit.edu/spectconnect-1.0.tar.bz2
Maintained Yes


  • person_outline Gregory Stephanopoulos <>

Publication for SpectConnect

SpectConnect in pipelines

PMCID: 5878833
PMID: 29628813
DOI: 10.1007/s11306-018-1352-x

[…] beginning for retention index calculation. all gc–ms data files were processed with amdis (version 2.71, national institute of standards and technology, gaithersburg, md, usa) and the web-based tool spectconnect (styczynski et al. ) to perform the peak picking, spectral deconvolution and compound identification. annotation of metabolites was performed according to the retention index deviation […]

PMCID: 2537566
PMID: 18793460
DOI: 10.1186/1471-2105-9-S9-S15

[…] at locations along the chromatogram lacking peaks. finally, two-way, one-run-at-a-time approaches such as amdis [], when applied serially to multiple runs, e.g., with the help of met-idea [] or spectconnect [], have been observed to produce an artifact where single chemical eluates are identified as multiple mass-chromatographic features [], again largely the result of misalignment. thus, […]

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SpectConnect in publications

PMCID: 5950193
PMID: 29785207
DOI: 10.1186/s13068-018-1135-7

[…] pre-processed in automated mass spectral deconvolution and identification system (amdis) software [] for peak detection and deconvolution of mass spectra. the pre-processed data were uploaded into spectconnect (http://spectconnect.mit.edu) [] for peak alignment and for generating the data matrix with golm metabolome database (gmd) mass spectral reference library []. the normalized abundance […]

PMCID: 5832874
PMID: 29497074
DOI: 10.1038/s41598-018-22073-7

[…] mass spectral deconvolution and identification system (amdis) was used for retention index calculation, peak identification, deconvolution and integration. a compound matrix was generated by spectconnect online tool with compounds found in more than 50% of the replicates and an 80% similarity threshold of mass spectra. we applied these rather loose settings purposely in order not to miss […]

PMCID: 5812932
PMID: 29269494
DOI: 10.1128/AEM.02200-17

[…] and converted to .elu format using amdis mass spectrometry software () with the sensitivity set to low, resolution to medium, and support threshold to high. chromatograms were aligned using spectconnect (spectconnect.mit.edu) () with the support threshold set to low. the integrated signal (is) matrix output was used for all further analysis. zeros were replaced with two-thirds […]

PMCID: 5618323
PMID: 28758940
DOI: 10.3390/metabo7030038

[…] custom visual basic program in microsoft excel that grouped peaks across samples based on identical metabolite annotation and rt proximity. peak alignment across samples was further confirmed using spectconnect [] to assess similarity in spectral fragmentation patterns and by manual curation. the raw, transformed, and sorted data used for each of the three comparisons in the metabolomic […]

PMCID: 5453443
PMID: 28570677
DOI: 10.1371/journal.pone.0177883

[…] of chromatograms were performed using amdis 2.71 (“automated mass spectral deconvolution and identification system” freely available from http://www.amdis.net) and the web-based platform “spectconnect” (http://spectconnect.mit.edu/) []., differential abundance of the metabolite data was analyzed using edger (v 3.14.0) []. data was normalized using the default trimmed mean of m-values […]

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SpectConnect institution(s)
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
SpectConnect funding source(s)
This work was supported by d the NSF Graduate Research Fellows Program and NIH Metabolomics Roadmap Initiative, DK070291.

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