Proteome Discoverer

[…] state or charge state 1 were excluded. an underfill ratio of 1% was used., the ms raw files were searched using sequest and the output was further refined by percolator on the software platform proteome discoverer 1.4 (thermo) against the human uniprot database (90440 entries, including 23204 isoforms) and filtered to a 1% fdr cut off. a precursor ion mass tolerance of 10 ppm, and product […]

[…] were split when the program detected stop codons (*), undefined amino acids (x) or gaps (-). the search of ms/ms raw files against these databases was conducted using the sequest algorithm (proteome discoverer 1.3; thermo scientific) with the constraints previously described []. for peptide validation, the proteome discoverer 1.3 software was used by filtering based on the q-value […]

[…] selection for ms/ms was enabled to allow for detection of as many precursors as possible., raw data from the ms analysis was searched against ncbi s. aureus mssa476 using the sequest algorithm in proteome discoverer version 2.1 (). data were filtered to a 1% peptide and protein level false positive rate using a reverse database approach (). the area under the curve (auc)-based label free […]

[…] toggled automatically between ms and ms/ms acquisition. ms/ms data acquisition and processing were performed by xcalibur™ software (thermofisher scientific, ma)., proteins were identified through proteome discoverer software (ver. 2.1, thermo fisher scientific) and a mouse (mus musculus) uniprot protein sequence database (75568 sequences, and 32232886 residues). the reviewed protein sequences […]

[…] 2.0 kv; capillary temperature, 250 °c and isolation windows 4 m/z. all ms files (.raw) are accessible from the jpost repository at url: http://jpostdb.org/., all ms and ms/ms data were analyzed by proteome discoverer tm (v2.1, thermo) for protein and peptide identification with sequest ht algorithms. the data were queried against a uniprot/swiss-prot database (v2015-08; homo sapiens 20,203 […]

[…] 0.1% tfa solution prior to loading into an orbitrap fusion mass spectrometer. bioinformatic searches from swiss-prot were used to identify peptides, and a label-free precursor ion detection method (proteome discoverer, version 1.3; thermo scientific) was used for accurate mass measurements on proteins/peptides with specific retention times on precursors/fragments., standard deviations (s.d.) […]

[…] (scx) chromatography and analyzed on a ltq orbitrap velos mass spectrometer (thermo scientific). ms/ms spectra were searched against the refseq 40 database using mascot (matrix science) through proteome discoverer software (version 1.3, thermo scientific) to quantify proteins with respect to the within-itraq medians of log2 transformed and normalized reporter ion intensities derived […]

[…] precursor ions. multiple charged peptides were chosen for ms/ms experiments due to their good fragmentation characteristics. ms/ms spectra were interpreted, and peak lists were generated by proteome discoverer 1.4.1.14 (thermo fisher scientific). searches were performed using the sequest ht (thermo fisher scientific) against the latest uniprot database for whole human proteome (homo […]

[…] energy of 34 v. dynamic exclusion of precursor ions was set to 35 s and the fixed first mass was set to m/z 110 to match the itraq reporter ions (m/z 114–117)., thermo raw files were processed by proteome discoverer 1.4 (thermo). ms/ms spectra were searched against the aspgd protein database of a. fumigatus af293 […]

[…] rslc c18 column (2 μm particles, 100 å pore size; thermo scientific). the ms/ms spectra from each nano-lc-ms/ms fraction were searched against a selected rat tissue database (swissprot) using the proteome discoverer 2.1 software (thermo scientific). the search criteria were as follows: tryptic digestion, one missed cleavage, carbamidomethylation (c) and tmt plex (k and n-terminal) were fixed […]