MScDB: A Mass Spectrometry-centric Protein Sequence Database for Proteomics

2013 ◽  
Vol 12 (6) ◽  
pp. 2386-2398 ◽  
Author(s):  
Harald Marx ◽  
Simone Lemeer ◽  
Susan Klaeger ◽  
Thomas Rattei ◽  
Bernhard Kuster
Keyword(s):  
Mass Spectrometry ◽  
Protein Sequence ◽  
Sequence Database ◽  
Protein Sequence Database

scholarly journals A sectioning and database enrichment approach for improved peptide spectrum matching in large, genome-guided protein sequence databases

2019 ◽  
Author(s):  
Praveen Kumar ◽  
James E. Johnson ◽  
Caleb Easterly ◽  
Subina Mehta ◽  
Ray Sajulga ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Protein Sequence ◽  
Sequence Database ◽  
Sequencing Data ◽  
Proteomics Data ◽  
Step Method ◽  
Protein Sequence Database ◽  
Sectioning Method ◽  
Wide Range ◽  
Sequence Databases

AbstractMulti-omics approaches focused on mass-spectrometry (MS)-based data, such as metaproteomics, utilize genomic and/or transcriptomic sequencing data to generate a comprehensive protein sequence database. These databases can be very large, containing millions of sequences, which reduces the sensitivity of matching tandem mass spectrometry (MS/MS) data to sequences to generate peptide spectrum matches (PSMs). Here, we describe a sectioning method for generating an enriched database for those protein sequences that are most likely present in the sample. Our evaluation demonstrates how this method helps to increase the sensitivity of PSMs while maintaining acceptable false discovery rate statistics. We demonstrate increased true positive PSM identifications using the sectioning method when compared to the traditional large database searching method, whereas it helped in reducing the false PSM identifications when compared to a previously described two-step method for reducing database size. The sectioning method for large sequence databases enables generation of an enriched protein sequence database and promotes increased sensitivity in identifying PSMs, while maintaining acceptable and manageable FDR. Furthermore, implementation in the Galaxy platform provides access to a usable and automated workflow for carrying out the method. Our results show the utility of this methodology for a wide-range of applications where genome-guided, large sequence databases are required for MS-based proteomics data analysis.

Protein Sequence Database Methods

2004 ◽  
pp. 13-17
Author(s):  
Maria Jesus Martin ◽  
Claire O’Donovan ◽  
Rolf Apweiler
Keyword(s):  
Protein Sequence ◽  
Sequence Database ◽  
Protein Sequence Database

scholarly journals The PIR-International Protein Sequence Database

1992 ◽  
Vol 20 (suppl) ◽  
pp. 2023-2026 ◽  
Author(s):  
W. C. Barker ◽  
D. G. George ◽  
H.-W. Mewes ◽  
A. Tsugita
Keyword(s):  
Protein Sequence ◽  
Sequence Database ◽  
Protein Sequence Database
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