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linear trap quadrupole.
The standards and samples were analyzed on a Finnigan Surveyor high performance liquid chromatography (HPLC) system equipped with a Finnigan linear trap quadrupole (LTQ) mass spectrometer (Thermo Scientific, Germany).
The digested samples were separated on a WCX-HILIC capillary column packed in-house with PolyCAT A resin, coupled to a linear trap quadrupole Fourier transformation ion cyclotron resonance (LTQFT-ICR) instrument.
A total of 476 proteins, (corresponding to 170 unique identities) were identified using electrospray ionization linear trap quadrupole (ESI-LTQ) mass spectrometry (MS), 445 of them being present among the 1211 estimated spots.
In-gel digestion with trypsin and protein identification via a Nano liquid chromatography linear trap quadrupole mass spectrometry (NanoLC-LTQ MS/MS) analysis were performed as described previously [61].
The eluted peptides were analysed online in the linear trap quadrupole Velos.
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The effluent from the HPLC was directly electrosprayed into a linear trap quadrupole-Orbitrap XL mass spectrometer (Thermo Fisher Scientific).
The resulting peptides were desalted and analyzed by on-line HPLC on a Linear Trap Quadrupole-Orbitrap Elite (LTQ-Orbitrap Elite).
Data acquisition of oxidized PAPC species was performed by a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR-MS) (linear trap quadrupole-Fourier transform, LTQ-FT; Thermo Scientific) coupled to an UHPLC (Accela; Thermo Scientific) as described previously (Fauland et al, 2011).
The extracted peptides from each gel section were subjected to peptide fractionation using reversed-phase high performance liquid chromatography (Thermo Scientific, Waltham, MA, USA) and the gradient-eluted peptides were analyzed by a hyphenated LTQ-FTICR (linear trap quadrupole-Fourier Transform ion cyclotron resonance) mass spectrometer (Thermo Scientific).
LC-MS/MS was performed using an 1100 Series nanoflow high performance liquid chromatography system (Agilent Technologies) on-line coupled to a linear trapping quadrupole (LTQ -Fourier transform (FT) or a LTQ -Fourier (transformher ScientiFTc, Bremen, Germany).
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