VIPER: an advanced software package to support high-throughput LC-MS peptide identification

Monroe, Matthew E.; Tolić, Nikola; Jaitly, Navdeep; Shaw, Jason L.; Adkins, Joshua N.; Smith, Richard D.

doi:10.1093/bioinformatics/btm281

Cited by 178 publications

(190 citation statements)

References 10 publications

Supporting

Mentioning

188

Contrasting

Unclassified

Order By: Relevance

“…Peptide identifications filtered with an MS-generating function spectral probability score of Յ1 ϫ 10 Ϫ9 (26) were assembled into an A. fumigatus-specific AMT tag database. For identification, VIPER software (27) was used to correlate each AMT tag entry with a unique LC-MS feature relying on high mass measurement accuracy (MMA average Ϯ 0.683 ppm) and normalized elution time accuracy (NET average Ϯ 0.363%) (supplemental Tables S1-S4). Single peptides matching multiple proteins (typically protein isoforms) were removed.…”

Section: Lc-ms Measurement Of Abp-labeled Proteins-digestedmentioning

confidence: 99%

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum

Wiedner

Burnum

Pederson

et al. 2012

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background:A. fumigatus is an opportunistic pathogen responsible for pulmonary invasive aspergillosis. Results: Multiplexed ABPP revealed significant changes in A. fumigatus metabolism and stress response during culture with human serum over time. Conclusion: Changes in functional pathways indicate robust adaptation to environmental change. Significance: A. fumigatus grows under stress by altering metabolism, energy production, and protein biosynthesis, which is relevant for lung colonization.

show abstract

Section: Lc-ms Measurement Of Abp-labeled Proteins-digestedmentioning

confidence: 99%

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum

Wiedner

Burnum

Pederson

et al. 2012

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

show abstract

“…Decon2LS, VIPER [31]; freely available at http://ncrr.pnl.gov/software/) developed in-house. The first step involved deisotoping of the raw MS data to give the monoisotopic mass, charge state, and intensity of the major peaks in each mass spectrum.…”

Section: Processing Of Quantitative Lc-tof Ms Datasetsmentioning

confidence: 99%

Application of the accurate mass and time tag approach in studies of the human blood lipidome

Ding

Sørensen

Jaitly

et al. 2008

Journal of Chromatography B

Self Cite

View full text Add to dashboard Cite

We report a preliminary demonstration of the accurate mass and time (AMT) tag approach for lipidomics. Initial data-dependent LC-MS/MS analyses of human plasma, erythrocyte, and lymphocyte lipids were performed in order to identify lipid molecular species in conjunction with complementary accurate mass and isotopic distribution information. Identified lipids were used to populate initial lipid AMT tag databases containing 250 and 45 entries for those species detected in positive and negative electrospray ionization (ESI) modes, respectively. The positive ESI database was then utilized to identify human plasma, erythrocyte, and lymphocyte lipids in high-throughput LC-MS analyses based on the AMT tag approach. We were able to define the lipid profiles of human plasma, erythrocytes, and lymphocytes based on qualitative and quantitative differences in lipid abundance.

show abstract

“…DeconTools is a software package used to de-isotope mass spectra and detect features in MS dataset by using the isotopic signatures of expected components. Consequently, VIPER [92] is used to identify LC-MS peaks from MS peaks across elution time. Figure 4.12 shows the result of the raw dataset processed by VIPER, vertical axis represents the mass, and the horizontal axis is the retention time.…”

Section: Dataset Twomentioning

confidence: 99%

NBPMF: Novel network-based inference methods for peptide mass fingerprinting

Liang

Lajoie

Zhang

2017

2017 IEEE 16th International Conference on Cognitive Informatics &Amp; Cognitive Computing (ICCI*CC)

View full text Add to dashboard Cite

Proteins are large, complex molecules that perform a vast array of functions in every living cell. A proteome is a set of proteins produced in an organism, and proteomics is the large-scale study of proteomes. Several high-throughput technologies have been developed in proteomics, where the most commonly applied are mass spectrometry (MS) based approaches.MS is an analytical technique for determining the composition of a sample. Recently it has become a primary tool for protein identification, quantification, and post translational modification (PTM) characterization in proteomics research. There are usually two different ways to identify proteins: top-down and bottom-up. Top-down approaches are based on subjecting intact protein ions and large fragment ions to tandem MS directly, while bottom-up methods are based on mass spectrometric analysis of peptides derived from proteolytic digestion, usually with trypsin.In bottom-up techniques, peptide mass fingerprinting (PMF) is widely used to identify proteins from MS dataset. Conventional PMF representatives such as probabilistic MOWSE algorithm, is based on mass distribution of tryptic peptides. In this thesis, we developed a novel network-based inference software termed NBPMF. By analyzing peptide-protein bipartite network, we designed new peptide protein matching score functions. We present two methods: the static one, ProbS, is based on an independent probability framework; and the dynamic one, HeatS, depicts input dataset as dependent peptides. Moreover, we use linear regression to adjust the matching score according to the masses of proteins. In addition, we consider the order of retention time to further correct the score function. In the post processing, we design two algorithms: assignment of peaks, and protein filtration. The former restricts that a peak can only be assigned to one peptide in order to reduce random matches; and the latter assumes each peak can only be assigned to one protein. In the result validation, we propose two new target-decoy search strategies to estimate the false discovery rate (FDR). The experiments on simulated, authentic, and simulated authentic dataset demonstrate that our NBPMF approaches lead to significantly improved performance compared to several state-of-the-art methods.i

show abstract

VIPER: an advanced software package to support high-throughput LC-MS peptide identification

Abstract: VIPER may be downloaded free of charge at http://ncrr.pnl.gov/software/

Cited by 178 publications

References 10 publications

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum

Multiplexed Activity-based Protein Profiling of the Human Pathogen Aspergillus fumigatus Reveals Large Functional Changes upon Exposure to Human Serum

Application of the accurate mass and time tag approach in studies of the human blood lipidome

NBPMF: Novel network-based inference methods for peptide mass fingerprinting

Contact Info

Product

Resources

About