scholarly journals Sensitive and specific spectral library searching with COSS and Percolator

2021 ◽  
Author(s):  
Genet Abay Shiferaw ◽  
Ralf Gabriels ◽  
Elien Vandermarliere ◽  
Lennart Martens ◽  
Pieter-Jan Volders
Keyword(s):  
Peptide Identification ◽  
High Sensitivity ◽  
Substantial Improvement ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Sequence Database ◽  
Post Processing ◽  
Spectral Library ◽  
False Discovery ◽  
Sequence Database Search

Maintaining high sensitivity while limiting false positives is a key challenge in peptide identification from mass spectrometry data. Here, we therefore investigate the effects of integrating the machine learning-based post-processor Percolator into our spectral library searching tool COSS. To evaluate the effects of this post-processing, we have used twenty data sets from two different projects and have matched these against the NIST spectral library. The matching is carried out using two performant spectral library search engines (COSS and MsPepSearch), both with and without Percolator post-processing, and using sequence database search engine MS-GF+ as a baseline comparator. The addition of the Percolator rescoring step was particularly effective for COSS, resulting in a substantial improvement in sensitivity and specificity of the identifications. Importantly, the false discovery rate was especially strongly affected, resulting in much more reliable results. COSS is freely available as open source under the permissive Apache2 license, and binaries and source code are found at https://github.com/compomics/COSS .

scholarly journals COSS: A fast and user-friendly tool for spectral library searching

2019 ◽  
Author(s):  
Genet Abay Shiferaw ◽  
Elien Vandermarliere ◽  
Niels Hulstaert ◽  
Ralf Gabriels ◽  
Lennart Martens ◽  
...  
Keyword(s):  
Scoring Functions ◽  
Sequence Database ◽  
Spectral Library ◽  
Data Formats ◽  
Large Databases ◽  
Search Tool ◽  
Spectral Searching ◽  
Spectral Libraries ◽  
User Friendly ◽  
Sequence Database Search

ABSTRACTSpectral similarity searching to identify peptide-derived MS/MS spectra is a promising technique, and different spectrum similarity search tools have therefore been developed. Each of these tools, however, comes with some limitations, mainly due to low processing speed and issues with handling large databases. Furthermore, the number of spectral data formats supported is typically limited, which also creates a threshold to adoption. We have therefore developed COSS (CompOmics Spectral Searching), a new and user-friendly spectral library search tool supporting two scoring functions. COSS also includes decoy spectra generation for result validation. We have benchmarked COSS on three different spectral libraries and compared the results with established spectral search and sequence database search tool. Our comparison showed that COSS more reliably identifies spectra and is faster than other spectral library searching tools. COSS binaries and source code can be freely downloaded from https://github.com/compomics/COSS.

Development and validation of a spectral library searching method for peptide identification from MS/MS

PROTEOMICS ◽  
2007 ◽  
Vol 7 (5) ◽  
pp. 655-667 ◽  
Author(s):  
Henry Lam ◽  
Eric W. Deutsch ◽  
James S. Eddes ◽  
Jimmy K. Eng ◽  
Nichole King ◽  
...  
Keyword(s):  
Peptide Identification ◽  
Spectral Library ◽  
Searching Method ◽  
Development And Validation

High field FT-ICR mass spectrometry data sets enlighten qualitative DOM alteration in lake sediment porewater profiles

2017 ◽  
Vol 108 ◽  
pp. 51-60 ◽  
Author(s):  
Peter Herzsprung ◽  
Wolf von Tümpling ◽  
Katrin Wendt-Potthoff ◽  
Norbert Hertkorn ◽  
Mourad Harir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Lake Sediment ◽  
High Field ◽  
Mass Spectrometry Data ◽  
Data Sets ◽  
Ft Icr

Detection of Ureteral Stones in Kidney Ureter Bladder Radiography: Usefulness of Digital Post-processing

2021 ◽  
Vol 17 ◽  
Author(s):  
Sang Lim Choi ◽  
Sung Bin Park ◽  
Seungwook Yang ◽  
Eun Sun Lee ◽  
Hyun Jeong Park ◽  
...  
Keyword(s):  
Detection Sensitivity ◽  
Ureteral Stones ◽  
Data Sets ◽  
Post Processing ◽  
Stone Size ◽  
Data Set ◽  
Detection Rates ◽  
Exact Test ◽  
Significant Difference ◽  
Exact Size

Purpose: Kidney, ureter, and bladder radiography (KUB) has frequently been used in suspected urolithiasis, but its performance is known to be lower than that of computed tomography (CT). This study aimed to investigate the diagnostic performance of digitally post-processed kidney ureter bladder radiography (KUB) in the detection of ureteral stones. Materials And Methods: Thirty patients who underwent digital KUB and CT were included in this retrospective study. The original digital KUB underwent post-processing that involved noise estimation, reduction, and whitening to improve the visibility of ureteral stones. Thus, 60 digital original or post-processed KUB images were obtained and ordered randomly for blinded review. After a period, a second review was performed after unblinding stone laterality. The detection rates were evaluated at both initial and second review, using CT as reference standard. The objective (size) and subjective (visibility) parameters of ureteral stones were analyzed. Fisher’s exact test was used to compare the detection sensitivity between the original and post-processed KUB data set. Visibility analysis was assessed with a paired t-test. Correlation of stone size between CT and digital KUB data sets was assessed with Pearson’s correlation test. Results: The detection rate was higher for most reviewers once stone laterality was provided and was non-significantly better for the post-processed KUB images (p > 0.05). There was no significant difference in stone size among CT and digital KUB data sets. In all reviews, visibility grade was higher in the post-processed KUB images, irrespective of whether stone laterality was provided. Conclusion: Digital post-processing of KUB yielded higher visibility of ureteral stones and could improve stone detection, especially when stone laterality was available. Thus, digitally post-processed KUB can be an excellent modality for detecting ureteral stones and measuring their exact size.

scholarly journals N-Linked Glycopeptide Identification Based on Open Mass Spectral Library Search

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Zhiwu An ◽  
Qingbo Shu ◽  
Hao Lv ◽  
Lian Shu ◽  
Jifeng Wang ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Peptide Identification ◽  
High Energy ◽  
Mass Spectral Library ◽  
Spectral Library ◽  
Data Set ◽  
Library Search ◽  
Mass Spectral

Confident characterization of intact glycopeptides is a challenging task in mass spectrometry-based glycoproteomics due to microheterogeneity of glycosylation, complexity of glycans, and insufficient fragmentation of peptide bones. Open mass spectral library search is a promising computational approach to peptide identification, but its potential in the identification of glycopeptides has not been fully explored. Here we present pMatchGlyco, a new spectral library search tool for intact N-linked glycopeptide identification using high-energy collisional dissociation (HCD) tandem mass spectrometry (MS/MS) data. In pMatchGlyco, (1) MS/MS spectra of deglycopeptides are used to create spectral library, (2) MS/MS spectra of glycopeptides are matched to the spectra in library in an open (precursor tolerant) manner and the glycans are inferred, and (3) a false discovery rate is estimated for top-scored matches above a threshold. The efficiency and reliability of pMatchGlyco were demonstrated on a data set of mixture sample of six standard glycoproteins and a complex glycoprotein data set generated from human cancer cell line OVCAR3.

Utilities for Mass Spectrometry Analysis of Proteins (UMSAP): Fast post-processing of mass spectrometry data

2018 ◽  
Vol 32 (19) ◽  
pp. 1659-1667 ◽  
Author(s):  
Kenny Bravo-Rodriguez ◽  
Birte Hagemeier ◽  
Lea Drescher ◽  
Marian Lorenz ◽  
Juliana Rey ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrometry Data ◽  
Mass Spectrometry Analysis ◽  
Post Processing ◽  
Spectrometry Analysis

Application of Fourier-Domain Post-Processing Technique for Ultrasonic Imaging with Matrix Phased Arrays in Advanced Manufacturing of Details and Machines

2018 ◽  
Vol 938 ◽  
pp. 81-88 ◽  
Author(s):  
Dmitry Dolmatov ◽  
Yana Salchak ◽  
Dmitriy Sednev ◽  
Roman Pinchuk
Keyword(s):  
Phased Arrays ◽  
Experimental Testing ◽  
Ultrasonic Imaging ◽  
High Sensitivity ◽  
Processing Technique ◽  
Post Processing ◽  
Real Component ◽  
Suggested Technique ◽  
Immersion Testing ◽  
Control Procedures

Quality of the components in the mechanical engineering is of the utmost importance. Most of quality control procedures can be provided by advanced quality assurance methods that enable visualization of inner structure of a component within all of the occurring defects. This paper suggests an innovative post-processing technique for Full-Matrix ultrasonic imaging with Matrix phased arrays in the case of immersion testing. Evaluation of the reliability was performed by simulation via CIVA software as well as by experimental testing of a real component with given defects. The obtained results of the research demonstrated high sensitivity and accuracy of the suggested technique.

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