[THIS IS WORK IN PROGRESS]

this is just a comment to explain the format, this is not included in the original file or supported by Sirius

>compound someCompoundName    
>parentmass 563.3311157226562    
>ionization [M + ?]+

TODO: Support multiple ions (see cli parameter) and probabilities? Lets say:

>ionization [M+H]+ (0.75), [M+Na]+ (0.1), ...
>formula C35H46O6

optional, usually unknown.
TODO Multiple comma separated formulas should be possible to shrink search space (e.g. special DB).

>instrumentation Unknown (LCMS)    
>source file:/home/dir/my_input_file.mgf

hash signs are additional comments/information. Hence, not really important

#FILENAME 140221_ME_14_11.mzML    
#SCANS 3216

In the following, a number of parameters, which can also be specified via our CLI options. If not set, standard parameters are used. In the Sirius-openMS-Adapter you don’t have to consider all of them. But we might use them, if someone runs Sirius independent and computes trees on your cluster. currently not all of them are read from file, but we are working on it

>profile qtof    
>elements CHNOP[2]S[5]ClF    
>no-recalibration    
>candidates 100    
>ppm-max 10    
>ppm-max-ms2 20    
>compound-timeout 100     
>tree-timeout 10

this is a MS1 which only contains the “feature” or all peaks correlated with the precursor peak. Since this data is produced by combining multiple MS1 (over time or different LC/MS runs) the mz and intensities should be much more accurate. Hence, we will e.g. take the isotope pattern from this spectrum. in the future, you could add a third column (next to mz and intensity) to include peaks quality numbers

>ms1merged    
297.1846618652344 0.07590501788605114    
315.194580078125 0.12240909060368306    
503.275146484375 0.26376816754988824    
504.27923583984375 0.07011663016065559    
563.3311157226562 1.0    
564.3378295898438 0.35435312936512653    
587.2991943359375 0.13540076279467494

if you have a very clever way in openMS to merge multiple MS2 into a single one, you could provide us with a merged MS2 e.g. >ms2merged else, we’ll take all the given MS2 and merge on our own.

>ms2merged    
 ...    
 ...    
 ...

please, don’t apply a baseline but give to us all the peaks.

The following part will contain the ‘normal’ MS1 and MS2 spectra. Each >ms1 corresponds to the following >ms2 . Having these spectra additionally to the >ms1merged and >ms2merged is still important. We will use them to 1. flag chimeric spectra (we see multiple compound peaks in the MS1 isolation window), which seems to be happening quite frequent; 2. learn the proper isolation filter. For the moment, you can probably limit the number of spectra to the, let’s say, 5-10 most intense MS2 (and their corresponding MS1).

>ms1peaks    
210.9044647216797 33143.015625    
217.73321533203125 21267.84375    
223.0562286376953 24709.314453125    
226.9507598876953 114752.65625    
234.39041137695312 25033.623046875    
238.4574432373047 21784.265625    
238.8363494873047 18646.724609375    
238.8405303955078 19625.076171875    
255.79945373535156 27974.916015625    
271.26239013671875 30973.611328125    
279.15899658203125 86259.5390625    
282.9114990234375 24559.986328125    
282.92767333984375 29071.580078125    
291.92254638671875 22666.2421875    
295.16827392578125 160342.859375    
296.1729736328125 29294.802734375    
297.18475341796875 86077.40625    
297.85760498046875 27014.646484375    
298.4665222167969 23304.326171875    
300.21990966796875 24263.029296875    
301.1399230957031 70695.1640625    
303.7633972167969 25118.896484375    
311.9073181152344 31817.705078125    
313.17877197265625 654827.125    
314.18218994140625 136606.78125    
315.19464111328125 119552.5859375    
318.92340087890625 26182.185546875    
325.4056701660156 25278.857421875    
331.1907958984375 107084.40625    
331.2841796875 52877.0703125    
343.73394775390625 22706.9375    
345.6029052734375 32553.095703125    
362.92547607421875 22855.052734375    
382.4386291503906 23381.513671875    
385.0718078613281 32560.037109375    
389.9631652832031 23730.673828125    
406.4020080566406 34586.609375    
423.36236572265625 157314.6875    
424.36474609375 63696.40625    
431.7023620605469 35758.3046875    
441.3719482421875 199359.84375    
442.375732421875 50911.4140625    
443.9761657714844 24911.638671875    
459.3815002441406 306836.09375    
460.3839111328125 60445.875    
467.44769287109375 23686.923828125    
481.29693603515625 47670.390625    
482.2959289550781 41347.9609375    
482.3999938964844 47474.7890625    
483.3783264160156 44766.9609375    
483.40240478515625 34157.28125    
484.3837890625 36754.96875    
487.35809326171875 31803.716796875    
497.3554992675781 43438.0390625    
498.8971862792969 29536.291015625    
500.4079895019531 52950.671875    
503.2752990722656 299657.96875    
504.2793273925781 85978.390625    
505.3293151855469 70367.0546875    
513.298583984375 66633.375    
515.3126831054688 51513.4296875    
523.3392333984375 114823.4765625    
525.32177734375 177986.53125    
526.3240966796875 115610.5    
533.3235473632812 126914.8125    
534.3302001953125 32763.646484375    
547.3026733398438 470361.5    
548.3054809570312 156665.40625    
549.32080078125 211828.515625    
550.3243408203125 62340.4765625    
551.3355102539062 144093.796875    
552.3396606445312 33408.28125    
554.6472778320312 22859.935546875    
563.3311157226562 1081881.5    
564.0441284179688 32525.919921875    
564.1807861328125 39462.7734375    
564.3378295898438 337545.625    
565.3167114257812 66542.90625    
565.3370361328125 40899.1953125    
571.3009643554688 765965.6875    
572.30322265625 242096.28125    
573.3185424804688 64867.3671875    
580.3117065429688 39356.25    
587.2938232421875 127508.78125    
588.3007202148438 50403.2109375    
593.8499755859375 26105.798828125    
603.2952880859375 24652.044921875    
605.3047485351562 45838.125    
631.3180541992188 78215.0859375    
676.5643310546875 25118.404296875    
699.3046264648438 27569.115234375    
720.930908203125 30136.619140625    
738.234375 26556.732421875    
739.6992797851562 23152.205078125    
768.2940673828125 25798.541015625    
770.0189208984375 23643.958984375    
773.2342529296875 23687.755859375    
817.3745727539062 157266.625    
818.382080078125 50265.109375    

>ms2peaks    
196.42184448242188 2633.143310546875    
196.46969604492188 3721.77685546875    
199.63748168945312 3072.041015625    
200.60662841796875 4375.54833984375    
207.979736328125 2448.370361328125    
228.31753540039062 2446.14599609375    
259.2853698730469 2712.002685546875    
261.7287902832031 3147.88623046875    
271.73095703125 2858.3544921875    
307.0590515136719 2613.810302734375    
311.93475341796875 4248.90380859375    
317.14508056640625 2837.740234375    
330.5431213378906 3470.46826171875    
335.16424560546875 6054.703125    
345.6324768066406 3867.29248046875    
351.215576171875 3102.68359375    
353.1735534667969 376849.71875    
353.2287292480469 3415.669921875    
371.09185791015625 3142.74755859375    
385.1008605957031 4099.6826171875    
402.4444580078125 2974.18603515625    
431.73681640625 4901.09228515625    
446.4543151855469 2866.7080078125    
448.62939453125 2588.66552734375    
479.7850341796875 4376.76220703125    
487.39532470703125 4969.8212890625    
515.5122680664062 2923.443115234375    
521.1932373046875 2760.1630859375    
521.22021484375 2806.689208984375    
545.3251342773438 33513.5078125    
564.0701293945312 4226.6923828125    

>ms1peaks    
203.6443634033203 21207.671875    
211.57615661621094 23593.67578125    
212.39366149902344 23243.3125    
219.06863403320312 22669.3125    
219.4059295654297 21470.33984375    
221.67303466796875 23252.69140625    
226.2869110107422 22997.4765625    
226.9507598876953 111919.2734375    
239.45538330078125 25472.55078125    
246.59339904785156 23084.71875    
252.2428436279297 20578.375    
254.65011596679688 21194.88671875    
255.79945373535156 24727.41015625    
271.26239013671875 35629.85546875    
274.2220458984375 21732.515625    
278.351806640625 23880.49609375    
279.15899658203125 75531.78125    
282.924072265625 30162.78515625    
283.2624206542969 36006.2578125    
284.205078125 27979.2265625    
288.023193359375 22986.17578125    
294.9403991699219 24582.76171875    
295.16827392578125 105765.0078125    
301.1399230957031 49448.92578125    
304.95111083984375 21793.7578125    
307.2539367675781 21489.7265625    
311.93853759765625 27434.1953125    
313.17877197265625 219152.734375    
315.19464111328125 32484.83984375    
329.1731872558594 37874.328125    
349.00714111328125 23916.07421875    
354.2841796875 24503.66015625    
362.92547607421875 36167.98046875    
369.239990234375 23166.69140625    
372.54345703125 25292.8671875    
374.37872314453125 22038.27734375    
381.6007080078125 24489.46875    
383.21978759765625 770773.4375    
384.2252197265625 213345.875    
385.1117858886719 26615.94921875    
391.2846374511719 39629.44921875    
398.09283447265625 26565.28125    
399.2176513671875 112028.3515625    
401.2325439453125 306352.3125    
401.2781066894531 23536.6953125    
402.2335205078125 106904.859375    
415.2105407714844 31431.5390625    
417.2254638671875 27534.99609375    
419.0799865722656 26912.23046875    
431.7261047363281 38279.41796875    
431.7532043457031 36252.71484375    
435.57843017578125 21580.74609375    
439.35723876953125 24387.6171875    
441.1092834472656 23107.57421875    
443.2418518066406 37649.08984375    
469.8589782714844 26722.72265625    
474.2067565917969 23548.00390625    
481.29296875 55347.359375    
503.2752990722656 34898.95703125    
557.366943359375 27796.91796875    
563.3311157226562 316900.46875    
564.0896606445312 56509.16796875    
564.3378295898438 89707.15625    
565.3167114257812 105334.7421875    
566.318603515625 43092.62109375    
569.3453369140625 89883.7890625    
572.8727416992188 21768.87890625    
587.2938232421875 228949.625    
588.3007202148438 60727.19140625    
589.315673828125 109665.3671875    
590.3170166015625 74206.375    
591.3262939453125 562672.125    
592.332763671875 242901.390625    
592.3599853515625 27803.28515625    
593.3308715820312 36163.71484375    
603.2784423828125 42447.0546875    
605.3103637695312 182168.578125    
606.3076171875 64855.61328125    
616.047119140625 24419.0390625    
621.3034057617188 53112.83203125    
656.8258666992188 24863.0625    
659.3455810546875 27734.90625    
673.337646484375 23823.3515625    
677.3696899414062 24782.94140625    
700.0458984375 23455.75    
736.328125 24608.2421875    
765.3093872070312 26962.89453125    
802.4219360351562 27930.0390625

ms2 spectra can also be annotated with their collision energy, instead of using >ms2. currently we don’t use this information, but might use it in the future.

>collision 40     
159.13766479492188 2457.8427734375    
160.96311950683594 2961.9052734375    
167.03253173828125 2686.4912109375    
175.4770965576172 2873.95849609375    
180.2447509765625 2609.83544921875    
191.27447509765625 3180.7255859375    
191.43650817871094 2621.916015625    
196.46762084960938 5208.54150390625    
200.60662841796875 3882.55908203125    
216.607666015625 3176.0556640625    
218.4820098876953 2590.58203125    
231.7875518798828 3156.556640625    
236.14419555664062 2723.1845703125    
244.18988037109375 3146.20263671875    
246.77377319335938 2384.4736328125    
256.1680908203125 2539.77001953125    
257.7774963378906 3090.896484375    
274.1297607421875 2925.37939453125    
311.9139404296875 4201.83935546875    
335.16424560546875 4103.80908203125    
338.3162841796875 3183.5166015625    
353.1735534667969 141271.28125    
384.3594970703125 2898.94287109375    
385.0722961425781 3523.513671875    
431.709716796875 3407.46435546875    
442.24273681640625 2633.66357421875    
529.0499877929688 2718.86328125    
529.8140869140625 2511.12353515625    
545.3251342773438 12954.4140625    
553.6473999023438 2947.15966796875    
555.1171264648438 3227.5224609375    
563.97900390625 4174.8251953125