Comparison of search engine contributions in protein mass fingerprinting for protein identification

2007 ◽  
Vol 12 (2) ◽  
pp. 125-130 ◽  
Author(s):  
Won-A Joo ◽  
Jeong-Bok Lee ◽  
Mira Park ◽  
Jae-Won Lee ◽  
Hyun-Jung Kim ◽  
...  
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
Protein Mass

scholarly journals A comprehensive and scalable database search system for metaproteomics

2016 ◽  
Author(s):  
Sandip Chatterjee ◽  
Gregory S. Stupp ◽  
Sung Kyu (Robin) Park ◽  
Jean-Christophe Ducom ◽  
John R. Yates ◽  
...  
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
High Throughput Sequencing ◽  
Shotgun Proteomics ◽  
Identification Accuracy ◽  
Sequencing Data ◽  
Protein Database ◽  
Healthy Human ◽  
Genomic Libraries ◽  
Sequence Databases

AbstractBackgroundMass spectrometry-based shotgun proteomics experiments rely on accurate matching of experimental spectra against a database of protein sequences. Existing computational analysis methods are limited in the size of their sequence databases, which severely restricts the proteomic sequencing depth and functional analysis of highly complex samples. The growing amount of public high-throughput sequencing data will only exacerbate this problem. We designed a broadly applicable metaproteomic analysis method (ComPIL) that addresses protein database size limitations.ResultsOur approach to overcome this significant limitation in metaproteomics was to design a scalable set of sequence databases assembled for optimal library querying speeds. ComPIL was integrated with a modified version of the search engine ProLuCID (termed “Blazmass”) to permit rapid matching of experimental spectra. Proof-of-principle analysis of human HEK293 lysate with a ComPIL database derived from high-quality genomic libraries was able to detect nearly all of the same peptides as a search with a human database (~500x fewer peptides in the database), with a small reduction in sensitivity. We were also able to detect proteins from the adenovirus used to immortalize these cells. We applied our method to a set of healthy human gut microbiome proteomic samples and showed a substantial increase in the number of identified peptides and proteins compared to previous metaproteomic analyses, while retaining a high degree of protein identification accuracy, and allowing for a more in-depth characterization of the functional landscape of the samples.ConclusionsThe combination of ComPIL with Blazmass allows proteomic searches to be performed with database sizes much larger than previously possible. These large database searches can be applied to complex meta-samples with unknown composition or proteomic samples where unexpected proteins may be identified. The protein database, proteomics search engine, and the proteomic data files for the 5 microbiome samples characterized and discussed herein are open source and available for use and additional analysis.

Parallel FPGA Search Engine for Protein Identification

2010 ◽  
pp. 313-335
Author(s):  
Daniel Coca ◽  
Istvan Bogdan ◽  
Robert Beynon
Keyword(s):  
Search Engine ◽  
Protein Identification

pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification

2016 ◽  
Vol 88 (6) ◽  
pp. 3082-3090 ◽  
Author(s):  
Rui-Xiang Sun ◽  
Lan Luo ◽  
Long Wu ◽  
Rui-Min Wang ◽  
Wen-Feng Zeng ◽  
...  
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
High Efficiency ◽  
High Accuracy ◽  
Intact Protein

scholarly journals PepTiger: Search Engine for Error-Tolerant Protein Identification from de Novo Sequences

2007 ◽  
Vol 1 (1) ◽  
pp. 1-8
Author(s):  
Irina Fedulova ◽  
Zheng Ouyang ◽  
Charles Buck ◽  
Xiang Zhang
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
De Novo

scholarly journals Protein structure characterization with mass spectrometry

2004 ◽  
Vol 18 (1) ◽  
pp. 37-47 ◽  
Author(s):  
Richard Kriwacki ◽  
Nichole Reisdorph ◽  
Gary Siuzdak
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Chemical Modification ◽  
Protein Identification ◽  
Higher Order ◽  
Order Structure ◽  
Mass Analysis ◽  
Analysis Techniques ◽  
Protein Mass ◽  
Mass Mapping

Mass spectrometry is now commonly being used to determine both the primary and higher order structures of proteins. The basis for these investigations lies in the ability of mass analysis techniques to detect changes in protein conformation under differing conditions. These experiments can be conducted on proteins alone (with no modifying substance present) or in combination with proteolytic digestion or chemical modification. In addition to primary structure determination, proteases and chemical modification have long been used as probes of higher order structure, an approach that has been recently rejuvenated with the emergence of highly sensitive and accurate mass analysis techniques. Here, we review the application of proteases as probes of native structure and illustrate key concepts in the combined use of proteolysis, chemical modification, and mass spectrometry. For example, protein mass maps have been used to probe the structure of a protein/protein complex in solution (cell cycle regulatory proteins, p21 and Cdk2). This approach was also used to study the protein/protein complexes that comprise viral capsids, including those of the common cold virus where, in addition to structural information, protein mass mapping revealed mobile features of the viral proteins. Protein mass mapping clearly has broad utility in protein identification and profiling, yet its accuracy and sensitivity is also allowing for further exploration of protein structure and even structural dynamics.

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics

2018 ◽  
Vol 17 (7) ◽  
pp. 2249-2255 ◽  
Author(s):  
Lev I. Levitsky ◽  
Mark V. Ivanov ◽  
Anna A. Lobas ◽  
Julia A. Bubis ◽  
Irina A. Tarasova ◽  
...  
Keyword(s):  
Search Engine ◽  
Protein Identification ◽  
Shotgun Proteomics
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