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An in-house software was used to resolve ambiguities resulting from protein isoforms and multiple accession numbers [78].
For each protein in the combined list (or protein group with multiple accession numbers), the total number of MS/MS spectra, which were assigned to peptides was calculated.
At the beginning, for each protein (or protein group with multiple accession numbers) in the combined lists, the total number of MS/MS spectra that were assigned a peptide mapping to that protein was calculated.
Proteins identified in the two separate mass spectrometry runs (control vs. androgen treated) were combined into a single list, and ambiguities resulting from protein isoforms and multiple accession numbers [34] were resolved using in-house software.
A given protein as identified by the GeneID may have multiple accession numbers.
The datasets supporting the results of this article are deposited in the European Nucleotide Archive, with multiple accession numbers provided in the article (listed in Additional file 1: Table S1).
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The search can be made as following: by using a sophisticated text expression accepting wildcards and Booleans - this search applies to all fields of the whole database; by accession number (accepting wildcards) - one or multiple accession number(s) separated by a space can be searched at one time; by organism; by PFAM or CDD numbers; by date; by range of length of amino acids sequence.
Some of the sequences matched multiple GenBank accession numbers and the second or third ranked e-values could represent additional coding regions on the same fragment.
These data are publicly available on the online Gene Expression Omnibus (Gene Expression Profile of Multiple Myeloma, accession number GSE2658. http://www.ncbi.nlm.nih.gov/geo/).nih.gov/geo/
This can happen when multiple ESTs with different accession numbers are actually identical.
Compared with the existing methods for predicting eukaryotic protein subcellular localization, the new predictor is much more powerful and flexible, particularly in dealing with proteins with multiple locations and proteins without available accession numbers.
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