Xtract algorithm

Manufactured by Thermo Fisher Scientific

The Xtract algorithm is a data analysis tool developed by Thermo Fisher Scientific. Its core function is to extract relevant information from complex datasets, enabling users to identify patterns, trends, and insights. The Xtract algorithm is designed to process and analyze data in a structured and efficient manner.

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Lab products found in correlation

Xcalibur qual browser, by Thermo Fisher Scientific (2 mentions) Peaks studio, by Bioinformatics Solutions (1 mentions)

6 protocols using xtract algorithm

Mass Spectrometry Proteoform Quantification

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Mass spectra were processed using Xcalibur Qual Browser (v4.2 Thermo Fisher Scientific) and the Xtract algorithm (v3.0 Thermo Fisher Scientific) for deconvolution and deisotoping of spectras (mass mode MH+, mono isotopic masses extracted, 189-2000 mass range, signal to noise 3, fit factor 80%, Remainder 25%, averagine no sulfur, and max charge 17). The extracted deconvoluted spectra were then analyzed further using Xcalibur and the peak area of the extracted ion chromatogram (XIC) was determined for each proteoforms of interest (automatic processing, smoothing Gaussian 7 points, 500 mmu mass tolerance, mass precision 4 decimals). Proteoform quantification (XIC peak area) values were exported for further analysis in Microsoft Excel and GraphPad Prism.

Ordureau A., Paulo J.A., Zhang J., An H., Swatek K.N., Cannon J.R., Wan Q., Komander D, & Harper J.W. (2020). Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling. Molecular Cell, 77(5), 1124-1142.e10.

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Comprehensive MS/MS Fragment Ion Analysis

Cited 2 times

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Raw MS/MS spectra were deconvoluted using the Xtract algorithm (Thermo Fisher Scientific). The spectra were then compared against all possible b, y, c, and z^•-type fragment ions which could be formed from that protein. Modifications were allowed for fragment ions containing a cysteine involved in a disulfide bond to consider all possible cleavage positions of the disulfide bond (S-S and C-S cleavage) and for hydrogen rearrangement products. Cleavage of all disulfide bonds were allowed but only one peptide backbone bond cleavage was considered. Internal fragment ions were not considered because they have been shown to be significantly less prevalent than terminal fragment ions and would greatly increase the fragment ion search space, leading to the false identification of fragment ions^{55 (link)–57 (link)}. Fragment ions were matched within a mass tolerance of 10 parts per million.

Rush M.J., Riley N.M., Westphall M.S, & Coon J.J. (2018). Top-Down Characterization of Proteins with Intact Disulfide Bonds Using Activated-Ion Electron Transfer Dissociation. Analytical chemistry, 90(15), 8946-8953.

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Mass Spectrometry Fragmentation Analysis

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Raw files were deconvoluted and de-isotoped to the neutral monoisotopic masses using Xtract algorithm provided by Thermo Scientific Inc. Manual analysis of IRMPD, UVPD, and combined UVPD and IRMPD data was performed with the aid of ProSight Light software [30 (link)] and Protein Prospector v5.14.4. (http://prospector.ucsf.edu/prospector/mshome.htm). All major ion types (a, a + 1, a + 2, b – 1, b, b + 1, b + 2, c – 1, c, c + 1, x – 1, x, x + 1, x + 2, y, y – 1, y – 2, z – 1, z, z + 1) were considered. We observed a substantial number of secondary fragment ions, including d, v, and w, which were analyzed by Protein Prospector. H₂O and NH₃ losses from the fragment ions were also considered. Single protein mode with a fragment mass tolerance set to 15 ppm was used for all methods.

Halim M.A., Girod M., MacAleese L., Lemoine J., Antoine R, & Dugourd P. (2016). Combined Infrared Multiphoton Dissociation with Ultraviolet Photodissociation for Ubiquitin Characterization. Journal of the American Society for Mass Spectrometry, 27(9), 1435-1442.

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Mass Spectrometry Proteoform Analysis

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Mass spectra were processed using Xcalibur Qual Browser (v4.2 Thermo Fisher Scientific) and the Xtract algorithm (v3.0 Thermo Fisher Scientific) for deconvolution and deisotoping of spectras (mass mode MH+, mono isotopic masses extracted, 189–2000 mass range, signal to noise 3, fit factor 80%, Remainder 25%, averagine no sulfur, and max charge 17). The extracted deconvoluted spectra were then analyzed further using Xcalibur and the peak area of the extracted ion chromatogram (XIC) was determined for each proteoforms of interest (automatic processing, smoothing gaussian 7 points, 500 mmu mass tolerance, mass precision 4 decimals). Proteoform quantification (XIC peak area) values were exported for further analysis in Microsoft Excel and GraphPad Prism.

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Top-down Mass Spectrometry Analysis Protocol

Cited 1 time

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Data from top-down NSI-MS/MS was analyzed using MASH Suite (version 1.0.0.23928, UW-Madison, U.S.A.)68 (link) and further validated by manual inspection. Peak deconvolution for manual data analysis was performed using the Xtract algorithm (Thermo Scientific Inc.). Data from top-down LC-MS/MS was analyzed by ProSightPTM69 (link) and PEAKS studio (version 7.0, Bioinformatics Solutions, Waterloo, Canada)70 (link) against Glycine max 2S albumin pre-protein sequence. In all cases, 10 ppm MS and 0.05 Da MS/MS tolerances were used for data analysis. EA (Cys) was included as a fixed modification and additional EA was set as a variable modification to account for possible polymerization of the alkylating agent. For AGE product analysis, CML (Lys) and CEL (Lys) were added as variable modifications. A stringent false discovery rate of 0.1% was set for all searches. All sequences identified were further validated by manual inspection.

Serra A., Gallart-Palau X., See-Toh R.S., Hemu X., Tam J.P, & Sze S.K. (2016). Commercial processed soy-based food product contains glycated and glycoxidated lunasin proteoforms. Scientific Reports, 6, 26106.

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Histone H1 Proteoform Characterization

Cited 1 time

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Unprocessed MS1 and MS2 spectra were manually inspected using Qual Browser 4.0.27.10 (Thermo Scientific). Canonical human histone H1 sequences were obtained from Uniprot [36 (link)]. Histone H1 subtypes were identified from the MS1 spectra using predicted intact H1 isotopic distribution patterns (Predator Manual Validation Helper v2.8, National High Magnetic Field Laboratory) and manually validated from the MS2 spectra with the aid of an in-house fragment ion calculator. The targeted MS2 spectra were deconvolved using the Xtract algorithm (Thermo Scientific) [37 (link)] and manually annotated. Modification site assignments were cross-referenced with TopFD [38 (link)] annotations generated by MASH Native [39 (link)].

Siqueira E., Kim B.H., Reser L., Chow R., Delaney K., Esteller M., Ross M.M., Shabanowitz J., Hunt D.F., Guil S, & Ausió J. (2023). Analysis of the interplay between MeCP2 and histone H1 during in vitro differentiation of human ReNCell neural progenitor cells. Epigenetics, 18(1), 2276425.

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