Mass spectra were acquired using a Thermo Fisher Scientific Finnigan LTQ linear ion trap mass spectrometer (San Jose, CA, USA). Data collection and processing was achieved using Thermo Fisher Scientific Xcalibur 2.2 SP1 software. The paper substrate was positioned with its tip parallel to the mass spectrometer inlet using a copper alligator clip, which was connected to an external high-voltage supply, as illustrated in Figure 1 . MS parameters were as follows: ±30 V transfer capillary voltage; ±2 kV spray voltage; 3 microscans; 100 ms ion injection time; 3 mm distance from ion source to MS analyzer inlet for both positive- and negative-ion modes; 240°C transfer capillary temperature and 100 V capillary voltage for positive-ion mode; 250°C transfer capillary temperature and −120 V capillary voltage for negative-ion mode. Tandem MS with collision-induced dissociation (CID) was used for analyte identification and was optimized for each analyte.
Finnigan ltq linear
Manufactured by Thermo Fisher Scientific
Sourced in United States
The Finnigan LTQ linear is a mass spectrometer designed for analytical applications. It utilizes a linear ion trap to analyze and detect molecular ions. The core function of the Finnigan LTQ linear is to provide high-sensitivity and high-resolution mass analysis capabilities for researchers and analysts.
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3 protocols using finnigan ltq linear
1
Mass Spectrometry Analysis of Compounds
2
Standardized LC-MS/MS Protein Identification
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The standard LC-MS/MS and database searching were performed according to the protocol described previously (Sun et al., 2015 (link)). Briefly, LC-MS analysis was carried out using a Surveyor MS Pump Plus HPLC system coupled to a Thermo Fisher Finnigan LTQ linear ion trap mass spectrometer (Thermo Fisher Corporation, San Jose, CA, USA) using nano-electrospray ionization. Tryptic peptides were loaded onto a trap column (300SB-C18, 5 × 0.3 mm, 5 μm particle size; Agilent Technologies, Santa Clara, CA, USA) connected through a zero dead volume union to the self-packed analytical column (C18, 100 × 0.1 mm, 3 μm particle size; SunChrom, Germany). The peptides were then separated by linear gradient elution involving 0–45% B over 55 min followed by 45–100% B over 10 min (B is 80% acetonitrile, 0.1% formic acid) at a flow rate of 500 nL/min. MS data were analyzed using SEQUEST against the National Center for Biotechnology Information (NCBI) human protein database and the results filtered, sorted, and displayed using Bioworks 3.2. Returned protein lists were filtered using the parameters: Peptide Xcorr value >1.90 (for +1 charge), >2.75 (for +2 charge), >3.75 (for +3 charge); peptide Delt CN >0.1; protein probabilities <0.001. At least two unique peptides were required for each identified protein.
3
Proteomic Analysis of LINC01255 Interactors
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Finnigan LTQ linear ion trap mass spectrometer (Thermo Fisher Corporation, San Jose, CA) in line with a Thermo Finnigan Surveyor MS Pump Plus HPLC system.
The mass spectrometry analysis was carried out in a data-dependent mode with an automatic switch between a full MS and an MS/MS scan in the obitrap. Peptide sequences were searched using trypsin specificity and allowing a maximum of two missed cleavages. Sequest was searched with a peptide tolerance of 3.0 Da and a fragment ion tolerance of 1.0 Da. The results of peptide sequences information of LINC01255 interact proteins were offered in Supplemental Table 1.
The mass spectrometry analysis was carried out in a data-dependent mode with an automatic switch between a full MS and an MS/MS scan in the obitrap. Peptide sequences were searched using trypsin specificity and allowing a maximum of two missed cleavages. Sequest was searched with a peptide tolerance of 3.0 Da and a fragment ion tolerance of 1.0 Da. The results of peptide sequences information of LINC01255 interact proteins were offered in Supplemental Table 1.
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