Re: [Psidev-ms-dev] mzML base64binary conversion

[Eric D. <ede...@sy...>]

Hi Da Qi, there are many libraries out there for many languages that read
mzML, so you may not need to re-implement it yourself. If Python is a
language of choice, you might look at this recent paper:



http://www.mcponline.org/content/early/2018/12/18/mcp.RP118.001070?papetoc=







*From:* Shofstahl, Jim <jim...@th...>
*Sent:* Tuesday, January 8, 2019 6:50 AM
*To:* Mass spectrometry standard development <
psi...@li...>
*Subject:* Re: [Psidev-ms-dev] mzML base64binary conversion



The spectral data (and chromatogram data) is stored as a Base64 encoded
string.  Most of the programming languages will contain methods/functions
to convert to and from the

Base64 format.  In C# those methods are part of the Convert class.



https://docs.microsoft.com/en-us/dotnet/api/system.convert?view=netframework-4.7.2



The FromBase64String method takes a string value and converts it to a
byte[] array which can then be converted to another data type.  We tend to
convert it using

as a MemoryStream object but there are other ways to do the conversion:



        protected static float[] ConvertToFloat(byte[] array, int points)

        {

            var arrayValues = new float[points];



            using (var memStream = new MemoryStream(array))

            {

                using (var binReader = new BinaryReader(memStream))

                {

                    for (var i = 0; i < points; i++)

                    {

                        arrayValues[i] = binReader.ReadSingle();

                    }

                }

            }



            // Return the value(s)

            return arrayValues;

        }



*From:* 戚达(Da Qi) <qi...@ge...>
*Sent:* Monday, January 7, 2019 5:43 PM
*To:* psi...@li...
*Subject:* [Psidev-ms-dev] mzML base64binary conversion



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Hi,



Does anyone know how to decode the binary string to real data in mzML?



<binaryDataArrayList count="2">


<binaryDataArray encodedLength="268">


<cvParam cvRef="MS" accession="MS:1000514" name="m/z array" unitCvRef="MS"
unitAccession="MS:1000040" unitName="m/z"/>


<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>


<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>


<binary>O6+NQ43Hp0N978lDce3XQ6Zr5kORjf9DdUMLRCfJDEThihJEqO4SRGiZGERKzBpEKwcbRKjOKURoIS1EFJ4wRI1XMUQpvDdEIeA5RJjmQkQr70NERGNGRMeDR0RMh0hE2Y5JRG/KTEQncU5EHXJPRMupUETZ9lNEQiBURLS4VETjxVVEbTdYRMk2WkQ34VpEBhFbRN10W0Q5/FtExxteRAqvX0QSY2BEJZ5gRJ5HYUQ/jWFEEutkRGCNZURcx2VErg9vROF6fEQ=</binary>


</binaryDataArray>


<binaryDataArray encodedLength="268">


<cvParam cvRef="MS" accession="MS:1000515" name="intensity array"
unitCvRef="MS" unitAccession="MS:1000131" unitName="number of counts"/>


<cvParam cvRef="MS" accession="MS:1000576" name="no compression"/>


<cvParam cvRef="MS" accession="MS:1000521" name="32-bit float"/>


<binary>AEB6RADQakUAwOxEAGwGRgDgE0UAcDxFAMDIRABASEQA4N5EAMBWRAAAJ0UAIAZFADA+RQBgu0QAAB5EAMB+RQDAhUUAwLREANCpRQBwA0UAABFEAEAsRADgJkUAMAlFAOAbRQDAlEQAAKZEALBBRQAgpEQA4F1FAMDBRADAi0QAIDZFAIBFRQAAEEUAoHRFAKCMRACAL0QAINtEAGAKRQDAO0QAQONFAHAIRQD4gUUAgONDAGDaRADQLkUAAGJEAABNRAAA0EQ=</binary>


</binaryDataArray>

                                                </binaryDataArrayList>



Best,

Da Qi