User: Laurent

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Laurent1.6k
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Posts by Laurent

<prev • 68 results • page 1 of 7 • next >
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Answer: A: What Software do you use to view mzML files ?
... Pick you language: java: jmzml - https://code.google.com/p/jmzml/ (there are more java libraries out there) C++: proteowizard - http://proteowizard.sourceforge.net/ R (based on proteowizard): mzR - http://bioconductor.org/packages/release/bioc/html/mzR.html python: pyteomics - http://packages. ...
written 3.8 years ago by Laurent1.6k
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Job: Research Data Technician, Cambridge, UK
... The Cambridge Centre for Proteomics (CCP) is currently looking to recruit a Research Data Technician within its core facility unit. The core facility offers proteomics services to users from the University of Cambridge and other worldwide academic and industrial groups. The successful candidate wil ...
proteomics mass spectrometry job written 4.3 years ago by Laurent1.6k
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Comment: C: Official specs and API's for proteomics data (like Adam, VCF, HTS-JDK) (both fil
... In terms of identification, mzIdenML (version 1.1) is widely used. I think pepXML is still in use in the TPP suite. OpenMS also has/had it's own XML based formats (at least internally), but nowadays supports the official ones. ...
written 4.4 years ago by Laurent1.6k
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Answer: A: Official specs and API's for proteomics data (like Adam, VCF, HTS-JDK) (both fil
... These formats are the official formats for proteomics data: mzML for raw data, mzIdentML for identification data and mzQuantML for quantitation data. The former is widerly accepted, although it's predecessor mzXML is still being used. mzIdentML is also widely used. The latter, which is more recent, ...
written 4.4 years ago by Laurent1.6k
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Comment: C: Searching for a good search engine that is linux friendly and works with HCD dat
... Indeed, the actual paper MSGF+ paper is not published yet (MS-GF+: Universal Database Search Tool for Mass Spectrometry, Sangtae Kim, Pavel A. Pevzner, submitted), but you can have a look at Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases, San ...
written 4.4 years ago by Laurent1.6k
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Answer: A: Searching for a good search engine that is linux friendly and works with HCD dat
... I would suggest to get a go with MSGF+; it's cross-platform (java) and quite fast. ...
written 4.4 years ago by Laurent1.6k
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Comment: C: Best way to calculate p-value for protein regulations
... It is difficult to answer that question without information about your experimental design, but I would say no. You would use a paired test when each replicate i of condition C1 matches replicate i of condition C2 - same samples at different time points, or same individuals before/after drug adminis ...
written 4.5 years ago by Laurent1.6k
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Answer: A: Predict tissue origin by protein expression
... The recently published Human Proteome Map (HPM) portal has protein expression data from "multiple organs/tissues and cell types from individuals with clinically defined healthy tissues. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues." Similar work has been made ava ...
written 4.5 years ago by Laurent1.6k
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Answer: A: Library To Generate Theoretical Tandem Mass Spectra From Arbitrary Peptide Seque
... Using MSnbase, you can > library("MSnbase") > data(itraqdata) > xx <- pickPeaks(itraqdata) > i <- 14 > s <- as.character(fData(xx)[14, "PeptideSequence"]) > calculateFragments(s) Modifications used: C=160.030649 mz ion type pos z seq 1 88.03931 b1 ...
written 4.5 years ago by Laurent1.6k
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Comment: C: Best way to calculate p-value for protein regulations
... Missing value imputation is a concern in general. In your case, I would check that the distribution of the values after imputation is still compatible with the assumptions of the test.   ...
written 4.5 years ago by Laurent1.6k

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Appreciated 3.8 years ago, created a post with more than 5 votes. For A: Quantiles Normalization On Massive Dataset
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Quantiles Normalization On Massive Dataset
Scholar 4.5 years ago, created an answer that has been accepted. For A: Is there any possible way to list files from different locations?
Appreciated 4.6 years ago, created a post with more than 5 votes. For A: Quantiles Normalization On Massive Dataset
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: From Where In The Mzml File Does Toppview Get The Retention Time?
Scholar 4.6 years ago, created an answer that has been accepted. For A: Is there any possible way to list files from different locations?
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Teacher 7.3 years ago, created an answer with at least 3 up-votes. For A: From Where In The Mzml File Does Toppview Get The Retention Time?
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