Data were searched using the Spectrum Mill MS Proteomics Workbench (Agilent, Rev B.06.00.201) and the SwissProt human proteome database. For data extraction, spectrum merging was enabled based on precursor selection purity, spectral similarity, retention time (2-minute window), and m/z. Search settings were as follows: instrument = Agilent ESI Q-TOF; precursor mass tolerance = +/- 10 ppm; product ion mass tolerance = +/- 20 ppm; digest = no enzyme. Matches were considered valid if the following thresholds were satisfied: score > 10, percentage scored peak intensity (SPI) > 70%, and rank 1 minus rank 2 (R1-R2) score > 2.5. Spectra that could not be confidently matched to unmodified peptides in the SwissProt database were subjected to a second round of searches using the settings listed above, except oxidized methionine and deamidated asparagine/glutamine were considered as variable modifications and digest was set to AspN (maximum of two missed cleavages). Spectra that remained unmatched according to the validation filters listed above were searched against a custom database containing hypothetical human HIPs (2 (link)) using the same settings as in the first search.
Esi q tof
Manufactured by Agilent Technologies
Sourced in United States
The ESI Q-TOF is a high-performance mass spectrometry instrument designed for accurate mass analysis and identification of chemical compounds. It combines electrospray ionization (ESI) with a quadrupole-time-of-flight (Q-TOF) mass analyzer, providing precise mass measurements and detailed structural information about molecules.
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Lab products found in correlation
3 protocols using esi q tof
1
Comprehensive Proteomic Data Analysis
2
Comprehensive HIP Peptide Database for Mass Spectrometry
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Data were analyzed using the Spectrum Mill software with the SwissProt mouse/human database as well as HIP-specific databases that were generated using an in-house computer algorithm. The mouse HIP database contained each possible C-terminal truncation of insulin C-peptide linked to predicted naturally occurring cleavage products of insulin (1&2), ChgA, IAPP, secretogranin 1, and neuropeptide Y, making a total of 3000 peptides. More detail of this database and our established set of confidence criteria is provided elsewhere (5 (link)). The human HIP database contained all 30 HIP sequences that can form between C-peptide fragments on the left side linked to intact C-peptide on the right side. Search settings were as follows: instrument = Agilent ESI Q-TOF; precursor mass tolerance = ±10 ppm; product ion mass tolerance = ±20 ppm; and digest = no enzyme. Matches were considered valid if the following thresholds were satisfied: score >10, percentage scored peak intensity >70%, and rank one minus rank 2 (R1–R2) score >2.5.
3
UPLC-HRMS Analysis of Free Fatty Acids
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This
method is measured on an Acquity UPLC binary solvent manager
8 pump (Waters) coupled to an Agilent 6530 electrospray ionization
quadrupole time-of-flight (ESI-Q-TOF, Agilent, Jose, CA, USA) high-resolution
mass spectrometer using reference mass correction. The chromatographic
separation was achieved on an Acquity HSS T3 column (1.2 × 100
mm, 1.8 μm) maintained at 40 °C. The negative apolar lipids
that constitute FFAs were separated with a flow of 0.4 mL/min over
a 15 min gradient. In negative mode, the aqueous mobile phase A consisted
of 5:95 (v/v) acetonitrile/H2O with 10 mM ammonium formate,
and the organic mobile phase B consisted of 99% (v/v) methanol with
10 mM ammonium formate.
method is measured on an Acquity UPLC binary solvent manager
8 pump (Waters) coupled to an Agilent 6530 electrospray ionization
quadrupole time-of-flight (ESI-Q-TOF, Agilent, Jose, CA, USA) high-resolution
mass spectrometer using reference mass correction. The chromatographic
separation was achieved on an Acquity HSS T3 column (1.2 × 100
mm, 1.8 μm) maintained at 40 °C. The negative apolar lipids
that constitute FFAs were separated with a flow of 0.4 mL/min over
a 15 min gradient. In negative mode, the aqueous mobile phase A consisted
of 5:95 (v/v) acetonitrile/H2O with 10 mM ammonium formate,
and the organic mobile phase B consisted of 99% (v/v) methanol with
10 mM ammonium formate.
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