Dataset Information

An improved peptide-spectral matching algorithm through distributed search over multiple cores and multiple CPUs.

ABSTRACT:

Background

A real-time peptide-spectrum matching (RT-PSM) algorithm is a database search method to interpret tandem mass spectra (MS/MS) with strict time constraints. Restricted by the hardware and architecture of individual workstation, previous RT-PSM algorithms either are not fast enough to satisfy all real-time system requirements or need to sacrifice the level of inference accuracy to provide the required processing speed.

Results

WE DEVELOP TWO PARALLELIZED ALGORITHMS FOR MS/MS DATA ANALYSIS: a multi-core RT-PSM (MC RT-PSM) algorithm which works on individual workstations and a distributed computing RT-PSM (DC RT-PSM) algorithm which works on a computer cluster. Two data sets are employed to evaulate the performance of our proposed algorithms. The simulation results show that our proposed algorithms can reach approximately 216.9-fold speedup on a sub-task process (similarity scoring module) and 84.78-fold speedup on the overall process compared with a single-thread process of the RT-PSM algorithm when 240 logical cores are employed.

Conclusions

The improved RT-PSM algorithms can achieve the processing speed requirement without sacrificing the level of inference accuracy. With some configuration adjustments, the proposed algorithm can support many peptide identification programs, such as X!Tandem, CUDA version RT-PSM, etc.

SUBMITTER: Sun J

PROVIDER: S-EPMC4021225 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Publications

An improved peptide-spectral matching algorithm through distributed search over multiple cores and multiple CPUs.

Sun Jian J Chen Bolin B Wu Fang-Xiang FX

Proteome science 20140411

<h4>Background</h4>A real-time peptide-spectrum matching (RT-PSM) algorithm is a database search method to interpret tandem mass spectra (MS/MS) with strict time constraints. Restricted by the hardware and architecture of individual workstation, previous RT-PSM algorithms either are not fast enough to satisfy all real-time system requirements or need to sacrifice the level of inference accuracy to provide the required processing speed.<h4>Results</h4>WE DEVELOP TWO PARALLELIZED ALGORITHMS FOR MS ...[more]

PMID: 24721686

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Project description:Glycoprotein changes occur in not only protein abundance but also the occupancy of each glycosylation site by different glycoforms during biological or pathological processes. Recent advances in mass spectrometry instrumentation and techniques have facilitated analysis of intact glycopeptides in complex biological samples by allowing the users to generate spectra of intact glycopeptides with glycans attached to each specific glycosylation site. However, assigning these spectra, leading to identification of the glycopeptides, is challenging. Here, we report an algorithm, named GPQuest, for site-specific identification of intact glycopeptides using higher-energy collisional dissociation (HCD) fragmentation of complex samples. In this algorithm, a spectral library of glycosite-containing peptides in the sample was built by analyzing the isolated glycosite-containing peptides using HCD LC-MS/MS. Spectra of intact glycopeptides were selected by using glycan oxonium ions as signature ions for glycopeptide spectra. These oxonium-ion-containing spectra were then compared with the spectral library generated from glycosite-containing peptides, resulting in assignment of each intact glycopeptide MS/MS spectrum to a specific glycosite-containing peptide. The glycan occupying each glycosite was determined by matching the mass difference between the precursor ion of intact glycopeptide and the glycosite-containing peptide to a glycan database. Using GPQuest, we analyzed LC-MS/MS spectra of protein extracts from prostate tumor LNCaP cells. Without enrichment of glycopeptides from global tryptic peptides and at a false discovery rate of 1%, 1008 glycan-containing MS/MS spectra were assigned to 769 unique intact N-linked glycopeptides, representing 344 N-linked glycosites with 57 different N-glycans. Spectral library matching using GPQuest assigns the HCD LC-MS/MS generated spectra of intact glycopeptides in an automated and high-throughput manner. Additionally, spectral library matching gives the user the possibility of identifying novel or modified glycans on specific glycosites that might be missing from the predetermined glycan databases.

Dataset Information

An improved peptide-spectral matching algorithm through distributed search over multiple cores and multiple CPUs.

Background

Results

Conclusions

Publications

An improved peptide-spectral matching algorithm through distributed search over multiple cores and multiple CPUs.

Similar Datasets

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