scholarly journals matchms - processing and similarity evaluation of mass spectrometry data

2020 ◽  
Author(s):  
Florian Huber ◽  
Stefan Verhoeven ◽  
Christiaan Meijer ◽  
Hanno Spreeuw ◽  
Efraín Manuel Villanueva Castilla ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Open Access ◽  
High Throughput ◽  
Life Sciences ◽  
Research Community ◽  
Significant Fraction ◽  
Mass Spectrometry Data ◽  
Joint Effort ◽  
Complex Datasets

SummaryMass spectrometry data is at the heart of numerable applications in the biomedical and life sciences. With growing use of high throughput techniques researchers need to analyse larger and more complex datasets. In particular through joint effort in the research community, fragmentation mass spectrometry datasets are growing in size and number. Platforms such as MassBank (Horai et al. 2010), GNPS (Wang et al. 2016) or MetaboLights (Haug et al. 2020) serve as an open-access hub for sharing of raw, processed, or annotated fragmentation mass spectrometry data (MS/MS). Without suitable tools, however, exploitation of such datasets remains overly challenging. In particular, large collected datasets contain data aquired using different instruments and measurement conditions, and can further contain a significant fraction of inconsistent, wrongly labeled, or incorrect metadata (annotations).

154: Integration of TPSA and High-Throughput Mass Spectrometry Data Improves Prostate Cancer Prediction

2007 ◽  
Vol 177 (4S) ◽  
pp. 52-53
Author(s):  
Stefano Ongarello ◽  
Eberhard Steiner ◽  
Regina Achleitner ◽  
Isabel Feuerstein ◽  
Birgit Stenzel ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Cancer Prediction

scholarly journals Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

2011 ◽  
Vol 11 (2) ◽  
pp. 1412-1419 ◽  
Author(s):  
Christopher R. Kinsinger ◽  
James Apffel ◽  
Mark Baker ◽  
Xiaopeng Bian ◽  
Christoph H. Borchers ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Open Access ◽  
Data Quality ◽  
Quality Metrics ◽  
Mass Spectrometry Data ◽  
Open Access Data ◽  
Data Quality Metrics ◽  
Access Data

NORMALIZATION REGARDING NON-RANDOM MISSING VALUES IN HIGH-THROUGHPUT MASS SPECTROMETRY DATA

2005 ◽  
Author(s):  
PEI WANG ◽  
HUA TANG ◽  
HEIDI ZHANG ◽  
JEFFREY WHITEAKER ◽  
AMANDA G PAULOVICH ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Missing Values ◽  
Mass Spectrometry Data

scholarly journals A recombineering pipeline to clone large and complex genes in Chlamydomonas

2021 ◽  
Author(s):  
Tom Z Emrich-Mills ◽  
Gary Yates ◽  
James Barrett ◽  
Philipp Girr ◽  
Irina Grouneva ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Bacterial Artificial Chromosome ◽  
Molecular Biology ◽  
Fluorescent Protein ◽  
Artificial Chromosome ◽  
Research Community ◽  
Mass Spectrometry Data ◽  
Parallel Cloning ◽  
Mutant Complementation ◽  
Biology Research

Abstract The ability to clone genes has greatly advanced cell and molecular biology research, enabling researchers to generate fluorescent protein fusions for localization and confirm genetic causation by mutant complementation. Most gene cloning is PCR or DNA synthesis dependent, which can become costly and technically challenging as genes increase in size, particularly if they contain complex regions. This has been a long-standing challenge for the Chlamydomonas reinhardtii research community, as this alga has a high percentage of genes containing complex sequence structures. Here we overcame these challenges by developing a recombineering pipeline for the rapid parallel cloning of genes from a Chlamydomonas bacterial artificial chromosome collection. To generate fluorescent protein fusions for localization, we applied the pipeline at both batch and high-throughput scales to 203 genes related to the Chlamydomonas CO2 concentrating mechanism (CCM), with an overall cloning success rate of 77%. Cloning success was independent of gene size and complexity, with cloned genes as large as 23 kilobases. Localization of a subset of CCM targets confirmed previous mass spectrometry data, identified new pyrenoid components, and enabled complementation of mutants. We provide vectors and detailed protocols to facilitate easy adoption of this technology, which we envision will open up new possibilities in algal and plant research.

scholarly journals Evaluation and validation of an analytical approach for high-throughput metabolomic fingerprinting using direct introduction–high-resolution mass spectrometry: Applicability to classification of urine of scrapie-infected ewes

2018 ◽  
Vol 25 (2) ◽  
pp. 251-258 ◽  
Author(s):  
Estelle Rathahao-Paris ◽  
Sandra Alves ◽  
Nawel Boussaid ◽  
Nicole Picard-Hagen ◽  
Véronique Gayrard ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
High Throughput ◽  
Biological Samples ◽  
Matrix Effects ◽  
Mass Measurement ◽  
Direct Injection ◽  
Mass Spectrometry Data ◽  
Direct Injection Mass Spectrometry

Direct injection–mass spectrometry can be used to perform high-throughput metabolomic fingerprinting. This work aims to evaluate a global analytical workflow in terms of sample preparation (urine sample dilution), high-resolution detection (quality of generated data based on criteria such as mass measurement accuracy and detection sensitivity) and data analysis using dedicated bioinformatics tools. Investigation was performed on a large number of biological samples collected from sheep infected or not with scrapie. Direct injection–mass spectrometry approach is usually affected by matrix effects, eventually hampering detection of some relevant biomarkers. Reference compounds were spiked in biological samples to help evaluate the quality of direct injection–mass spectrometry data produced by Fourier Transform mass spectrometry. Despite the potential of high-resolution detection, some drawbacks still remain. The most critical is the presence of matrix effects, which could be minimized by optimizing the sample dilution factor. The data quality in terms of mass measurement accuracy and reproducible intensity was evaluated. Good repeatability was obtained for the chosen dilution factor (i.e., 2000). More than 150 analyses were performed in less than 16 hours using the optimized direct injection–mass spectrometry approach. Discrimination of different status of sheeps in relation to scrapie infection (i.e., scrapie-affected, preclinical scrapie or healthy) was obtained from the application of Shrinkage Discriminant Analysis to the direct injection–mass spectrometry data. The most relevant variables related to this discrimination were selected and annotated. This study demonstrated that the choice of appropriated dilution faction is indispensable for producing quality and informative direct injection–mass spectrometry data. Successful application of direct injection–mass spectrometry approach for high throughput analysis of a large number of biological samples constitutes the proof of the concept.

scholarly journals Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles)

2011 ◽  
Vol 10 (12) ◽  
pp. O111.015446 ◽  
Author(s):  
Christopher R. Kinsinger ◽  
James Apffel ◽  
Mark Baker ◽  
Xiaopeng Bian ◽  
Christoph H. Borchers ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Open Access ◽  
Data Quality ◽  
Quality Metrics ◽  
Mass Spectrometry Data ◽  
Open Access Data ◽  
Data Quality Metrics ◽  
Access Data

Interpretation of mass spectrometry data for high-throughput proteomics

2003 ◽  
Vol 376 (7) ◽  
pp. 1014-1022 ◽  
Author(s):  
Daniel C. Chamrad ◽  
Gerhard Koerting ◽  
Johan Gobom ◽  
Herbert Thiele ◽  
Joachim Klose ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data
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