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LaCyTools: A Targeted Liquid Chromatography-Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides
- Source :
- Journal of Proteome Research, 15(7), 2198-2210. AMER CHEMICAL SOC
- Publication Year :
- 2016
-
Abstract
- Bottom-up glycoproteomics by liquid chromatography-mass spectrometry (LC-MS) is an established approach for assessing glycosylation in a protein- and site-specific manner. Consequently, tools are needed to automatically align, calibrate, and integrate LC-MS glycoproteomics data. We developed a modular software package designed to tackle the individual aspects of an LC-MS experiment, called LaCyTools. Targeted alignment is performed using user defined m/z and retention time (t(r)) combinations. Subsequently, sum spectra are created for each user defined analyte group. Quantitation is performed on the sum spectra, where each user defined analyte can have its own tr, minimum, and maximum charge states. Consequently, LaCyTobls deals with multiple charge states, which gives an output per charge state if desired, and offers various analyte and spectra quality criteria. We compared throughput and performance of LaCyTools to combinations of available tools that deal with individual processing steps. LaCyTools yielded relative quantitation of equal precision (relative standard deviation
- Subjects :
- 0301 basic medicine
Proteomics
Analyte
relative quantitation
alpha-1-antitrypsin
User defined
Mass spectrometry
01 natural sciences
Biochemistry
bioinformatics
glycoproteomics
immunoglobulin G
liquid chromatography
mass spectrometry
profiling
quality control
Mass Spectrometry
03 medical and health sciences
Software
Liquid chromatography–mass spectrometry
Data processing
Electronic Data Processing
Chromatography
Chemistry
business.industry
010401 analytical chemistry
Glycopeptides
General Chemistry
0104 chemical sciences
Glycoproteomics
030104 developmental biology
business
Modular software
Chromatography, Liquid
Subjects
Details
- ISSN :
- 15353907
- Volume :
- 15
- Issue :
- 7
- Database :
- OpenAIRE
- Journal :
- Journal of proteome research
- Accession number :
- edsair.doi.dedup.....fa7a30ac04509a67279ef66cf66cae01