scholarly journals Automated Peak Harvesting of MALDI–MS spectra for high throughput proteomics

2003 ◽  
Vol 17 (2-3) ◽  
pp. 579-595 ◽  
Author(s):  
E. J. Breen ◽  
W. L. Holstein ◽  
F. G. Hopwood ◽  
P. E. Smith ◽  
M. L. Thomas ◽  
...  
Keyword(s):  
High Throughput ◽  
Mass Spectra ◽  
Software Tool ◽  
Complex Data ◽  
Two Dimensional Gel Electrophoresis ◽  
Maldi Tof ◽  
Peptide Mass ◽  
Low Concentrations ◽  
Recent Developments ◽  
Automated Software

High throughput proteomics is realized not only by the use of automated hardware but also by the application of efficient, automated software routines to complex data. In this paper, we present the recent developments of our software tool Peak Harvester for the automatic harvesting of monoisotopic peaks from MALDI-TOF mass spectra of peptides. Peak Harvester uses advanced mathematical morphology to convert mass spectra into stick representations. Poisson modeling of theoretical isotopic distributions is then applied to derive the monoisotopic peptide mass from an isotopically resolved group of peaks. The accuracy of Peak Harvester is demonstrated via the analysis of peptide spectra from low concentrations of bovine serum albumin blotted onto PVDF membranes and of tryptic digested platelet proteins derived from human blood following two-dimensional gel electrophoresis. The results demonstrate the power of this software as it can accurately assign monoisotopic masses, including those from overlapping isotopic distributions, and picks masses as accurately as an experienced human operator. We have further developed Peak Harvester to include peak harvesting from MALDI-TOF Post Source Decay (PSD) experiments. Here we demonstrate the versatility of the software by both the analysis of PSD data from 2DE and the analysis of peptide mass spectra collected directly from tryptic digests on a PVDF membrane.

Comparative proteomic analysis on human L-02 liver cells treated with varying concentrations of trichloroethylene

2007 ◽  
Vol 23 (2) ◽  
pp. 91-101 ◽  
Author(s):  
Jianjun Liu ◽  
Haiyan Huang ◽  
Xiumei Xing ◽  
Renrong Xi ◽  
Zhixiong Zhuang ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Underlying Mechanism ◽  
Liver Cells ◽  
Control Group ◽  
Two Dimensional Gel Electrophoresis ◽  
Comparative Proteomic Analysis ◽  
Maldi Tof ◽  
Flight Mass Spectrometry ◽  
Peptide Mass ◽  
Tof Ms

To determine the differential proteomic expressions in human L-02 liver cells induced by varying concentrations of trichloroethylene (TCE), comparative proteomic analysis was performed on human L-02 liver cells which were treated with varying concentrations of TCE. According to the result of MTT test, we designed four different groups, in which the cells were treated with 0 μM (control group), 3, 10 or 40 μM TCE for 24 h, respectively. Comparative analysis of approximately 800 spots resolved by two-dimensional gel electrophoresis (2DE) in the soluble proteomes of L-02 cells from the four different groups resulted in 10 differential proteins. To identify the differential spots, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS) was carried out; if the results from the tool were insufficient, tandem MS (MALDI-TOF-TOF-MS) was then performed. The raw data of peptide mass fingerprints (PMFs) and MS/MS spectra were searched against the IPI human data base for exact matches. Then western blot was employed to verify the result of proteomic analysis, the following result confirmed that the results of proteomic analysis were reliable. These results might provide an insight into the underlying mechanism of TCE intoxication and find biological markers for diagnosis and therapy of TCE-induced diseases.

scholarly journals Probability-Based Scoring Function as a Software Tool Used in the Genome-Based Identification of Proteins from Spirulina platensis

2009 ◽  
Vol 3 (1) ◽  
pp. 59-68 ◽  
Author(s):  
Thammasorn Wimada ◽  
Eadjongdee Korakot ◽  
Hongsthong Apiradee ◽  
Porkaew Kriengkrai ◽  
Cheevadhanarak Supapon
Keyword(s):  
Molecular Weight ◽  
High Throughput ◽  
In Silico ◽  
Spirulina Platensis ◽  
Protein Identification ◽  
Scoring Function ◽  
Software Tool ◽  
Peptide Mass Fingerprinting ◽  
Peptide Mass ◽  
Proteomic Research

One of the major goals of proteomic research is the identification of proteins, a goal that often requires various software tools and databases. These tools have to be able to handle large amounts of data, such as those generated by PMF (Peptide Mass Fingerprinting), a high throughput technique. A newly sequenced organism, Spirulina platensis, was recently used to generate an in silico database, and thus an in-house tool designed for compatibility with this database and its inputs (PMF) was constructed in the present study. With a probability based scoring function, this tool effectively ranked ambiguous protein identification results by using five criteria: score, number of matched peptides, % coverage, pI and molecular weight. As a result, the protein identification step of Spirulina proteomic studies can be achieved precisely. Moreover, a very useful function of this tool is its capability for batch processing, in which the system can handle proteinidentification searches of a hundred of proteins automatically, from a single user’s input. Therefore, the tool not only gives accurate protein identification results but also saves the user time in processing a large amount of data.

Unrestrictive protein modification localization and quality control for open search of mass spectra

2018 ◽  
Author(s):  
Zhiwu An ◽  
Fuzhou Gong ◽  
Yan Fu
Keyword(s):  
Mass Spectrometry ◽  
Quality Control ◽  
Tandem Mass Spectrometry ◽  
Mass Spectra ◽  
Protein Modification ◽  
Software Tool ◽  
Tandem Mass ◽  
Simulation Data ◽  
Post Translational Modifications

We have developed PTMiner, a first software tool for automated, confident filtering, localization and annotation of protein post-translational modifications identified by open (mass-tolerant) search of large tandem mass spectrometry datasets. The performance of the software was validated on carefully designed simulation data. <br>

The Medicinal Chemistry of Therapeutic Peptides: Recent Developments in Synthesis and Design Optimizations

2019 ◽  
Vol 26 (13) ◽  
pp. 2330-2355 ◽  
Author(s):  
Anutthaman Parthasarathy ◽  
Sasikala K. Anandamma ◽  
Karunakaran A. Kalesh
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Therapeutic Potential ◽  
The Past ◽  
Recombinant Production ◽  
Tremendous Progress ◽  
Recent Developments ◽  
Therapeutic Peptides ◽  
Development Processes ◽  
Delivery Strategies

Peptide therapeutics has made tremendous progress in the past decade. Many of the inherent weaknesses of peptides which hampered their development as therapeutics are now more or less effectively tackled with recent scientific and technological advancements in integrated drug discovery settings. These include recent developments in synthetic organic chemistry, high-throughput recombinant production strategies, highresolution analytical methods, high-throughput screening options, ingenious drug delivery strategies and novel formulation preparations. Here, we will briefly describe the key methodologies and strategies used in the therapeutic peptide development processes with selected examples of the most recent developments in the field. The aim of this review is to highlight the viable options a medicinal chemist may consider in order to improve a specific pharmacological property of interest in a peptide lead entity and thereby rationally assess the therapeutic potential this class of molecules possesses while they are traditionally (and incorrectly) considered ‘undruggable’.

MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides

2021 ◽  
Author(s):  
Xiaoyu Yang ◽  
Pedatsur Neta ◽  
Yuri A. Mirokhin ◽  
Dmitrii V. Tchekhovskoi ◽  
Concepcion A. Remoroza ◽  
...  
Keyword(s):  
Mass Spectra ◽  
Software Tool ◽  
Tandem Mass ◽  
Tandem Mass Spectra

scholarly journals Network Analysis Based on Unique Spectral Features Enables an Efficient Selection of Genomically Diverse Operational Isolation Units

2021 ◽  
Vol 9 (2) ◽  
pp. 416
Author(s):  
Charles Dumolin ◽  
Charlotte Peeters ◽  
Evelien De Canck ◽  
Nico Boon ◽  
Peter Vandamme
Keyword(s):  
Network Analysis ◽  
Hierarchical Clustering ◽  
Mass Spectra ◽  
Spectral Features ◽  
Maldi Tof ◽  
Maldi Tof Mass Spectra ◽  
Diversity Studies ◽  
Technical Sample ◽  
Efficient Selection ◽  
Selection Of

Culturomics-based bacterial diversity studies benefit from the implementation of MALDI-TOF MS to remove genomically redundant isolates from isolate collections. We previously introduced SPeDE, a novel tool designed to dereplicate spectral datasets at an infraspecific level into operational isolation units (OIUs) based on unique spectral features. However, biological and technical variation may result in methodology-induced differences in MALDI-TOF mass spectra and hence provoke the detection of genomically redundant OIUs. In the present study, we used three datasets to analyze to which extent hierarchical clustering and network analysis allowed to eliminate redundant OIUs obtained through biological and technical sample variation and to describe the diversity within a set of spectra obtained from 134 unknown soil isolates. Overall, network analysis based on unique spectral features in MALDI-TOF mass spectra enabled a superior selection of genomically diverse OIUs compared to hierarchical clustering analysis and provided a better understanding of the inter-OIU relationships.

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