Spectronaut pulsar x tm 12

To process
DDA library data, MaxQuant software (version 1.5.3.17) was used to
search the FASTA sequence database. The database was obtained from
the web site http://www.uniprot.org. The iRT peptides sequence, denoted as (>Biognosys|iRT-Kit|Sequence_fusion
LGGNEQVTRYILAGVENSKGTFIIDPGGVIRGTFIIDPAAVIRGAGSSEPVTGLDAKTPVISGGPYEYRVEATFGVDESNAKTPVITGAPYEYRDGLDAASYYAPVRADVTPADFSEWSKLFLQFGAQGSPFLK),
was added. The parameters were configured as follows: the enzyme was
specified as trypsin, the maximum allowed missed cleavages were set
to two, the fixed modification was carbamidomethyl (C), and the dynamic
modifications included oxidation (M) and acetyl (Protein N-term).
All reported data were based on protein identification with a confidence
level of 99%, determined using the false discovery rate (FDR = N(decoy) × 2/(N(decoy) N(target)) ≤ 1%). A spectral library was constructed by importing
the original raw files and the results of DDA searching into Spectronaut
Pulsar X TM_12.0.20491.4 (Biognosys).
For DIA data analysis,
Spectronaut Pulsar X was employed to search the constructed spectral
library. The main software parameters were as follows: retention time
prediction type was defined as dynamic iRT, interference on MS2 level
correction was enabled, and cross-run normalization was enabled. All
results were filtered based on a Q value cutoff of
0.01 (equivalent to FDR <1%).

For DDA library data, the FASTA sequence database was searched using Spectronaut Pulsar X TM_12.0.20491.4 (Biognosys). The database was downloaded from the Ensembl website (http://asia.ensembl.org/index.html). All reported data were based on 99% confidence for protein identification, as determined by a false discovery rate (FDR=N (decoy)∗2/(N (decoy)+ N (target))) ≤1%. The spectral library was constructed by importing the original raw files and DDA search results into the Spectronaut Pulsar X TM. The DIA data were analyzed with Spectronaut Pulsar X TM by searching the above constructed spectral library. All results were filtered by setting the Q value cutoff at 0.01, equivalent to FDR<1% [23 (link)]. The mass spectrometry proteomics data were deposited in the ProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the iProX partner repository [24 ]. The dataset was authorized using a PXD number: PXD025678.