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XTractor specifications

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Unique identifier OMICS_19039
Name XTractor
Restrictions to use License purchase required
Community driven No
Data access Browse
User data submission Not allowed
Maintained Yes

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  • person_outline NetPro Team

XTractor citations

 (7)
library_books

Role of the visual experience dependent nascent proteome in neuronal plasticity

2018
eLife
PMCID: 5815848
PMID: 29412139
DOI: 10.7554/eLife.33420.040

[…] Both MS1 and MS2 (tandem mass spectra) were extracted from the XCalibur data system format (.RAW) into MS1 and MS2 formats using in house software (RAW_Xtractor) (). Both binary and source codes are available at https://github.com/robinparky/rawconverter/ (; copy archived at https://github.com/elifesciences-publications/rawconverter). MS2 spectra rem […]

library_books

Decoding the Human Immunoglobulin G Glycan Repertoire Reveals a Spectrum of Fc Receptor and Complement Mediated Effector Activities

2017
Front Immunol
PMCID: 5539844
PMID: 28824618
DOI: 10.3389/fimmu.2017.00877

[…] e data files. The highest intensity of selected peaks (within an m/z window of ±0.2 and within a time window of ±15 s surrounding the retention time) was extracted using the in-house developed 3D Max Xtractor software tool. If above a signal:background ratio of 3, the background-subtracted area of the first three isotopic peaks of each glycopeptide in both 2+, 3+, and 4+ charge state were summed, […]

library_books

Multi level glyco engineering techniques to generate IgG with defined Fc glycans

2016
Sci Rep
PMCID: 5131652
PMID: 27872474
DOI: 10.1038/srep36964

[…] ta files. The highest intensity of selected peaks (within an m/z window of +/−0.2 and within a time window of +/−15 s surrounding the retention time) was extracted using the in-house developed 3D Max Xtractor software tool. A list of the glycopeptides which were extracted can be examined in . If above a signal:background ratio of 3, the background-subtracted area of the first 3 isotopic peaks of e […]

call_split

Pulsed Azidohomoalanine Labeling in Mammals (PALM) Detects Changes in Liver Specific LKB1 Knockout Mice

2015
J Proteome Res
PMCID: 4642245
PMID: 26445171
DOI: 10.1021/acs.jproteome.5b00653
call_split See protocol

[…] icates were combined before database searching. Both MS1 and MS2 (tandem mass spectra) were extracted from the XCalibur data system format (.RAW) into MS1 and MS2 formats using in house software (RAW_Xtractor). MS/MS spectra remaining after filtering were searched with the Prolucid Software against the UniProt_mouse_07-29-2013 concatenated to a decoy database in which the sequence for each entry i […]

library_books

Characterization of Functional Reprogramming during Osteoclast Development Using Quantitative Proteomics and mRNA Profiling*

2014
PMCID: 4188996
PMID: 25044017
DOI: 10.1074/mcp.M113.034371

[…] MS spectra were extracted from the raw data using Raw Xtractor (). Protein identification was performed by searching against the mouse UniProt database (downloaded on January 18, 2011, and containing 16,332 entries) using IP2 software (Integrated Proteom […]

library_books

Comparison of Phylogeny, Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex

2013
PLoS Negl Trop Dis
PMCID: 3772048
PMID: 24069493
DOI: 10.1371/journal.pntd.0002442

[…] or m/z 445.1200). For each spectrum, the 10 most intense ions were subjected to CID fragmentation, followed by MS2 acquisition on a linear trap analyzer. The tandem mass spectra were extracted by RAW Xtractor (version 1.9.9.2) . All of the MS/MS samples were analyzed using ProLuCID (version 1.3.1) . ProLuCID was set up to search a database (forward + reverse decoy) that was built from the protein […]


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XTractor institution(s)
Molecular Connections House, Bengaluru, India

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