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Protocols

LaCyTools specifications

Information


Unique identifier OMICS_15184
Name LaCyTools
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License Apache License version 2.0
Computer skills Advanced
Version 1.0.1
Stability Stable
Requirements
Python, Numpy, Scipy, Matplotlib, tkinter, pytables
Maintained Yes

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Documentation


Maintainer


  • person_outline Manfred Wuhrer

Publication for LaCyTools

LaCyTools citations

 (4)
library_books

Estrogen induces St6gal1 expression and increases IgG sialylation in mice and patients with rheumatoid arthritis: a potential explanation for the increased risk of rheumatoid arthritis in postmenopausal women

2018
PMCID: 5932893
PMID: 29720252
DOI: 10.1186/s13075-018-1586-z

[…] ptide cluster. Analyte curation was performed using the signal-to-noise ratio, isotopic pattern quality, and observed mass-to-charge ratio (m/z) deviation as obtained after data (pre-)processing with LacyTools []. Following extraction of tryptic glycopeptides by a C18 solid-phase extraction trap column (Dionex Acclaim PepMap 100; Thermo Fisher Scientific), separation was performed with a Supelco A […]

call_split

Fc Glycosylation in Human IgG1 and IgG3 Is Similar for Both Total and Anti Red Blood Cell Anti K Antibodies

2018
Front Immunol
PMCID: 5797742
PMID: 29445378
DOI: 10.3389/fimmu.2018.00129
call_split See protocol

[…] RSLCnano system (Dionex/Thermo Scientific, Breda, the Netherlands) coupled to a Maxis Impact QTOF-MS (Bruker Daltonics, Bremen, Germany) as described previously ().Data processing was performed using LaCyTools (). Separate analyte curation was performed for IgG1 and IgG3 for both serum and eluates. Tryptic IgG1 glycopeptides contained the peptide sequence EEQYNSTYR, while the peptide sequence for […]

library_books

Sialic acid linkage differentiation of glycopeptides using capillary electrophoresis – electrospray ionization – mass spectrometry

2017
Sci Rep
PMCID: 5473812
PMID: 28623326
DOI: 10.1038/s41598-017-03838-y

[…] tides no internal standard was needed as the sample was rich enough to ensure proper alignment without an internal standard. The alignment program is an in-house and open source program, based on the LaCyTools alignment tool. The alignment program is supplied with this manuscript and can be found in  of the Supplementary Information. Briefly, an alignment procedure referred to as “targeted alignme […]

library_books

The N Glycosylation of Mouse Immunoglobulin G (IgG) Fragment Crystallizable Differs Between IgG Subclasses and Strains

2017
Front Immunol
PMCID: 5449507
PMID: 28620376
DOI: 10.3389/fimmu.2017.00608

[…] For automated relative quantification of the glycopeptides by LaCyTools (version 1.0.1, build 8) (), the nanoLC-MS files were converted to mzXML files. Chromatograms were aligned based on at least six glycopeptide signals with a signal-to-noise ratio (S/N) above […]

Citations

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LaCyTools institution(s)
Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, Netherlands; Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia
LaCyTools funding source(s)
This work was supported by the Horizon Programme Zenith project funded by the Netherlands Genomic Initiative (project number: 93511033), the European Union (Seventh Framework Programs HighGlycan, grant number 278535 and IBD-BIOM, grant number 305479) and INTEGRA-LIFE (grant number 315997).

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