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by chinman (Monk)
on Mar 27, 2001 at 10:50 UTC ( #67442=user: print w/replies, xml ) Need Help??

I'm an analytical chemist and I work with a technique known as mass spectrometry (mass spec). My interests are directed at using Perl to automate various aspects of mass spectral data analysis. Mass spec is widely used in the pharmaceutical, biotechnology, chemical, and forensic industries. In recent years, mass spec has seen tremendous growth in the life scienes. In fact, its application is revolutionizing many aspects of drug discovery (e.g., proteomics). However, analysis of mass spectral data is becoming the rate limiting step in this endeavor.

Currently, I'm using Perl to automate "deconvolution" of biomolecule (protein, peptide, oligonucleotide) mass spectra. This allows for the unambiguous determination of molecular weights of large complex molecules. I've been pleasantly surprised with how fast Perl is at these tasks, despite the fact that it is an interpreted language. This is saving me time not having to worry about mucking around in C - at least for this initial phase. We've developed mass spectral deconvolution software - using Perl for the guts. <shameless plug> This product, called ProMass, is now shipping (hoo-aaah!). Check it out here. </shameless plug>

Here's some more information about what I do.

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[LanX]: before digging into deep debugging ... I have a strange UTF8 problem, probably it rings a bell:
[LanX]: two utf8 strings from different sources are base64 encoded, but after joining both the umlauts in teh second get deleted
[Corion]: LanX: You can't just join two base64 strings together
[LanX]: (not a high priority bug because I can use some HTML entities in the second string)
[Corion]: base64 is padded to a multiple of 4 chars (or something)
[LanX]: misunderstanding, I joined them before converting to base64
[Corion]: Also, I would be wary of encodings and try to make really sure that both input strings are UTF-8. Maybe join the input strings from one source together to see whether they decode as bad or not
[Corion]: LanX: Then the problem should persist without encoding to base64 too ;)

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