Proportion of redundant peptides in decoy databases for simulated proteogenomic search. (DOCX 14Â kb
Distribution of CC according to Pfam database: A. Distribution of PCC and NCC according to Pfam data...
Complete results of the various database searches described in the text. (XLSX 101 kb
Descriptions of supplementary methods [1, 4, 14, 17, 24, 26, 37, 38]. (DOCX 96Â kb
Number of peptides with charge 3+ at 1% FDR identified from search against real proteogenomic databa...
Number of peptides with charge 2+ at 1% FDR identified from search against real proteogenomic databa...
Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb
Peptide (charge 3+) identification results from search against simulated proteogenomic databases for...
Peptide (charge 2+) identification results from search against simulated proteogenomic databases for...
Supplementary methods. Descriptions on the human MS/MS data set, RNA sequencing analysis, constructi...
Background: Proteogenomics is a promising approach for various tasks ranging from gene annotation to...
Tables S1. Peptide spectral counts by best ranked UniProt ID for 118 human breast tissues. (XLSX 768...
Table with identifications of MS/MS spectra of H. pylori E48 and H-13 in classical Mascot search aga...
Analysis simulated dataset 3. This simulated dataset models an input with incomplete annotation of c...
This compressed file contains a tab-delimited table listing the peptide evidence generated by proces...
Normalization simulated dataset 3. The file contains the simulated datasets used to model difference...
Distribution of CC according to Pfam database: A. Distribution of PCC and NCC according to Pfam data...
Complete results of the various database searches described in the text. (XLSX 101 kb
Descriptions of supplementary methods [1, 4, 14, 17, 24, 26, 37, 38]. (DOCX 96Â kb
Number of peptides with charge 3+ at 1% FDR identified from search against real proteogenomic databa...
Number of peptides with charge 2+ at 1% FDR identified from search against real proteogenomic databa...
Workflow for generating a simulated proteogenomic database for yeast. (DOCX 743Â kb
Peptide (charge 3+) identification results from search against simulated proteogenomic databases for...
Peptide (charge 2+) identification results from search against simulated proteogenomic databases for...
Supplementary methods. Descriptions on the human MS/MS data set, RNA sequencing analysis, constructi...
Background: Proteogenomics is a promising approach for various tasks ranging from gene annotation to...
Tables S1. Peptide spectral counts by best ranked UniProt ID for 118 human breast tissues. (XLSX 768...
Table with identifications of MS/MS spectra of H. pylori E48 and H-13 in classical Mascot search aga...
Analysis simulated dataset 3. This simulated dataset models an input with incomplete annotation of c...
This compressed file contains a tab-delimited table listing the peptide evidence generated by proces...
Normalization simulated dataset 3. The file contains the simulated datasets used to model difference...
Distribution of CC according to Pfam database: A. Distribution of PCC and NCC according to Pfam data...
Complete results of the various database searches described in the text. (XLSX 101 kb
Descriptions of supplementary methods [1, 4, 14, 17, 24, 26, 37, 38]. (DOCX 96Â kb
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