User: Julian

gravatar for Julian
Julian200
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200
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Location:
Manchester, UK
Last seen:
7 years, 4 months ago
Joined:
9 years, 2 months ago
Email:
j*******@manchester.ac.uk

I am a bioinformatician working at the University of Manchester. I focus principally on data related to protein mass spectrometry and proteomics.

Posts by Julian

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Mapping Uniprot To Ensembl Genes
... As well as the above pieces of software, or going into the flat file, is a tool called PICR (Protein Identifier Cross-Reference Service; http://www.ebi.ac.uk/Tools/picr/search.do). This was done a few years back to assist in issues like this, but was originally written to help cross-mapping of data ...
written 7.4 years ago by Julian200
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Answer: A: Bash $@ (Dollar At Variable) Loses Quote Characters
... Could you not call it in the following manner? This way you "escape" the quotes (this is probably the Google search term you wanted). $ ./time_it /xxx/blastp -outfmt \"6 std score\" -query x.faa -db nr -task blastp -out x.tsv Thereby you program is correct, just the way you use bash to call a bash ...
written 7.7 years ago by Julian200
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Answer: A: What Human Protein Fasta Files Are You Using When Searching Tandem Mass Spectra
... I have to be honest, we are still using the last IPI_human. However, in the very near future we will move to UniProt. We have a policy of updating our databases every 6 months with regard to searching tandem mass spectra, since some groups require the latest sequences and others require the same ver ...
written 7.8 years ago by Julian200
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Answer: A: What Are The Proteomics Data Repositories?
... Another one to consider is GPMDB. Data is submitted by running a public X!Tandem against the GPM database and selecting to add the data to the GPM. The GPM is split into species based sections (e.g., searching Human: http://human.thegpm.org/tandem/thegpm_tandem.html). The Peptide Atlas repository e ...
written 8.1 years ago by Julian200
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Statistical Analysis Of Proteomic Spectral Count Data
... How do people process spectral count data from protein mass spectrometry / proteomics data? The number of zero's in the data (most of which, due to the way the data is produced, you can't reliably define as zero). A standard t-test / anova doesn't seem appropriate as the data isn't normally distribu ...
proteomics statistics written 8.1 years ago by Julian200 • updated 8.1 years ago by Ahill1.6k
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Answer: A: Does Mzml(Converted From Raw), Wiff, Mgf, Dta, And Pepxml Contains "Mono-Isotopi
... Firstly, as @julieN stated, "monoisotopic" mass is just simply a mass that is of pure C12 (no C13). Most of the latest mass-spec's provide a monoisotopic mass, but some of the earlier models didn't have the resolution to be able to identify whether a peak was C12 pure, and hence they would provide a ...
written 8.2 years ago by Julian200
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Answer: A: How To Calculate Fold Change And Its Significance In Quantitative Proteomics
... In addition to what Laurent has answered, I would say that "common" statistical methods are only just beginning to be applied in Proteomics. One of the key areas I look to for statistical methodology is the Microarray field, although you have to have a bit of care with assumptions when dealing with ...
written 8.5 years ago by Julian200
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Answer: A: Open Source Mass Spec Search Engines?
... As well as what has been mentioned above, there are numerous other tools out there - all with slightly different approaches/algorithms (including spectral library approaches). You might want to take a look at http://www.ms-utils.org/wiki/pmwiki.php/Main/SoftwareList which contains a list of proteomi ...
written 9.0 years ago by Julian200 • updated 11 weeks ago by RamRS24k
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Comment: C: Why There Are No Proteomics Questions In Biostar?
... I'm not sure it is a lack of shared data! I don't even think it is a reluctance to share data, but rather is more about what data do we share? From that aspect, the nucleotide side of things is way ahead of the proteomics field. ...
written 9.0 years ago by Julian200

Latest awards to Julian

Autobiographer 7.4 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 8.1 years ago, created a post with more than 5 votes. For A: What Are The Proteomics Data Repositories?
Good Answer 8.1 years ago, created an answer that was upvoted at least 5 times. For A: What Are The Proteomics Data Repositories?
Teacher 8.1 years ago, created an answer with at least 3 up-votes. For A: What Are The Proteomics Data Repositories?
Popular Question 8.1 years ago, created a question with more than 1,000 views. For Statistical Analysis Of Proteomic Spectral Count Data
Teacher 8.5 years ago, created an answer with at least 3 up-votes. For A: How To Calculate Fold Change And Its Significance In Quantitative Proteomics

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