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Protocols

ms_lims specifications

Information


Unique identifier OMICS_02547
Name ms_lims
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Database management system MySQL
Computer skills Medium
Version 7.7.7
Stability Stable
Maintained Yes

Versioning


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Documentation


Publication for ms_lims

ms_lims citations

 (16)
call_split

Cell Intrinsic Control of Interneuron Migration Drives Cortical Morphogenesis

2018
Cell
PMCID: 5847171
PMID: 29474907
DOI: 10.1016/j.cell.2018.01.031
call_split See protocol

[…] Identified peptides were quantified using Mascot Distiller Tool, version 2.4.3.3 (Matrix Science in the precursor mode. All data management was done in ms-lims and data integration was performed using R (http://www.R-project.org) embedded in KNIME. The results of analyses are shown as the peptide ratio of the light (L)-labeled (CCP1cKO mice) versus t […]

library_books

Selective Glucocorticoid Receptor Properties of GSK866 Analogs with Cysteine Reactive Warheads

2017
Front Immunol
PMCID: 5672024
PMID: 29163463
DOI: 10.3389/fimmu.2017.01324

[…] idence were withheld. Spectra identified as peptides modified with GSK866, UAMC-1158, -1159, -1217, -1218, or Dex were manually validated to ensure correct assignment. All data management was done by ms_lims (). […]

call_split

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

2016
Sci Rep
PMCID: 4893672
PMID: 27264994
DOI: 10.1038/srep27220
call_split See protocol

[…] ndard as a source for P. furiosus proteins using a classical shotgun approach. The exact experimental details can be found in the .Identification data from the P. furiosus proteome was retrieved from ms_lims and used to compute metrics for the selection of optimal SRM peptides. For every identified peptide, the average matched intensity was computed in each of the three discovery experiments as fo […]

library_books

Exploring the potential of public proteomics data

2015
Proteomics
PMCID: 4738454
PMID: 26449181
DOI: 10.1002/pmic.201500295

[…] r submitters to provide additional information, or to annotate this information automatically in the standard file formats. This work has already started, notable in LIMS systems such as MASPECTRAS , ms_lims , and Proteios , but it will still take some time before it is straightforward to capture all the desired information.A related challenge is the provision of easy access to public data while c […]

library_books

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt acetylation defects

2014
Hum Mol Genet
PMCID: 4355026
PMID: 25489052
DOI: 10.1093/hmg/ddu611

[…] previously (). In all cases, two isotopic envelopes could clearly be distinguished [i.e. those of the in vivo acetylated (Ac) and in vitro acetylated forms (13C2D3)]. All data management were done in ms_lims (). The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository with the dataset i […]

call_split

Proteome Changes Induced by Imatinib and Novel Imatinib Derivatives in K562 Human Chronic Myeloid Leukemia Cells

2014
Proteomes
PMCID: 5302748
PMID: 28250386
DOI: 10.3390/proteomes2030363
call_split See protocol

[…] was set to 1. Only peptides that were ranked one and had an ion score at least equal to the corresponding identity threshold at 99% confidence were withheld and further data handling was done in the ms_lims database []. Peptide quantifications were carried out using the Mascot Distiller Quantitation Toolbox (version 2.2.1). The quantification method details were as follows: constrain search, yes; […]

Citations

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ms_lims institution(s)
Department of Medical Protein Research, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium; Department of Informatics, University of Bergen, Norway; ISAS – Institute for Analytical Sciences, Dortmund, Germany; Lehrstuhl fuer Bioinformatik, Institut fuer Informatik, Friedrich-Schiller-Universitaet Jena, Jena, Germany; European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Hinxton, Cambridge, UK
ms_lims funding source(s)
Institute for the Promotion of Innovation through Science and Technology in Flanders (IWT-Vlaanderen); Fund for Scientific Research – Flanders (Belgium). Grant Numbers: G.0077.06, G.0042.07; Concerted Research Actions. Grant Number: BOF07/GOA/012; Ghent University; Inter University Attraction Poles. Grant Number: IUAP06

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