waited for 24 hours to process mergeMS2spectra(mymzxml).

[pukhtoon786]

The function extractMS2spectra seem to work with the provided files on the package but does not process high-resolution DDA MS2 data. The function "extractMS2spectra" works and you can see the length of the list using the function list(mymzxml). But when you run mergeMS2spectra(mymzxml), the merging never completes on centroided DDA MS2 files in mzXML format.

[animesh]

It did complete for me after about 12 hours but merged spectra has all 0 intensity? Any ideas what is going on?

mzML2 <- extractMS2spectra(paste0("20200909_MKA_H12C_PeptidesDHB_DDA-(1).mzML"))
mzML2merge10ppm <- mergeMS2spectra(mzML2,mz_tolerance=1e-05,t_tolerance=15000) 
 mzML2merge10ppm[[1]]
An object of class "MS2spectrum" 
 id: M681.09T4152.53 
 annotation:  
 precursor: 681.0880 
 retention time: 4152.53 
 polarity: negative 
 MS2 spectrum with 5802 fragment peaks 
 neutral loss pattern with 5692 neutral losses
> mzML2merge10ppm[[1]]@spectrum
            [,1] [,2]
   [1,] 190.9167    0
   [2,] 191.2501    0
   [3,] 191.4167    0
   [4,] 191.5834    0
   [5,] 191.8334    0
   [6,] 192.1667    0
   [7,] 192.4167    0
   [8,] 192.5834    0
   [9,] 192.9168    0
  [10,] 193.0001    0
  [11,] 193.2501    0
  [12,] 193.3334    0
  [13,] 193.4168    0
  [14,] 193.5001    0
  [15,] 193.6668    0
  [16,] 193.7501    0
  [17,] 193.9168    0
  [18,] 194.0001    0
  [19,] 194.0834    0
  [20,] 194.2501    0
  [21,] 194.3334    0
  [22,] 194.4168    0
  [23,] 194.5001    0
  [24,] 194.5834    0
  [25,] 194.6668    0
  [26,] 194.7501    0
  [27,] 194.8334    0
  [28,] 194.9168    0
  [29,] 195.0001    0
  [30,] 195.0834    0
  [31,] 195.1668    0
  [32,] 195.2501    0
  [33,] 195.3334    0
  [34,] 195.4168    0
  [35,] 195.5001    0
  [36,] 195.5834    0
  [37,] 195.6668    0
  [38,] 195.7501    0
  [39,] 195.8334    0
  [40,] 195.9168    0
  [41,] 196.0834    0
  [42,] 196.1668    0
  [43,] 196.2501    0
  [44,] 196.3334    0
  [45,] 196.5001    0
  [46,] 196.5834    0
  [47,] 196.6668    0
  [48,] 196.7501    0
  [49,] 196.9168    0
  [50,] 197.0001    0
  [51,] 197.0834    0
  [52,] 197.1668    0
  [53,] 197.2501    0
  [54,] 197.3334    0
  [55,] 197.5001    0
  [56,] 197.6668    0
  [57,] 197.7501    0
  [58,] 197.9168    0
  [59,] 198.0834    0
  [60,] 198.2501    0
  [61,] 198.4168    0
  [62,] 198.5834    0
  [63,] 198.8334    0
  [64,] 199.0001    0
  [65,] 199.3334    0
  [66,] 199.5001    0
  [67,] 199.5834    0
  [68,] 199.7501    0
  [69,] 199.9168    0
  [70,] 200.0001    0
  [71,] 200.0835    0
  [72,] 200.2501    0
  [73,] 200.3335    0
  [74,] 200.4168    0
  [75,] 200.5835    0
  [76,] 200.6668    0
  [77,] 200.7501    0
  [78,] 200.8335    0
  [79,] 200.9168    0
  [80,] 201.0001    0
  [81,] 201.1668    0
  [82,] 201.2501    0
  [83,] 201.4168    0
  [84,] 201.5001    0
  [85,] 201.6668    0
  [86,] 201.8335    0
  [87,] 201.9168    0
  [88,] 202.0001    0
  [89,] 202.0835    0
  [90,] 202.2501    0
  [91,] 202.3335    0
  [92,] 202.4168    0
  [93,] 202.5001    0
  [94,] 202.5835    0
  [95,] 202.6668    0
  [96,] 202.8335    0
  [97,] 202.9168    0
  [98,] 203.0835    0
  [99,] 203.2501    0
 [100,] 203.4168    0
 [101,] 203.5835    0
 [102,] 203.6668    0
 [103,] 203.8335    0
 [104,] 203.9168    0
 [105,] 204.0001    0
 [106,] 204.0835    0
 [107,] 204.1668    0
 [108,] 204.3335    0
 [109,] 204.4168    0
 [110,] 204.5001    0
 [111,] 204.5835    0
 [112,] 204.7501    0
 [113,] 204.8335    0
 [114,] 204.9168    0
 [115,] 205.0001    0
 [116,] 205.1668    0
 [117,] 205.3335    0
 [118,] 205.4168    0
 [119,] 205.5001    0
 [120,] 205.5835    0
 [121,] 205.6668    0
 [122,] 205.7501    0
 [123,] 205.8335    0
 [124,] 205.9168    0
 [125,] 206.0001    0
 [126,] 206.0835    0
 [127,] 206.1668    0
 [128,] 206.2501    0
 [129,] 206.3335    0
 [130,] 206.4168    0
 [131,] 206.5001    0
 [132,] 206.5835    0
 [133,] 206.7501    0
 [134,] 206.8335    0
 [135,] 206.9168    0
 [136,] 207.0001    0
 [137,] 207.0835    0
 [138,] 207.1668    0
 [139,] 207.2502    0
 [140,] 207.3335    0
 [141,] 207.4168    0
 [142,] 207.5002    0
 [143,] 207.5835    0
 [144,] 207.6668    0
 [145,] 207.7502    0
 [146,] 207.8335    0
 [147,] 207.9168    0
 [148,] 208.0002    0
 [149,] 208.0835    0
 [150,] 208.1668    0
 [151,] 208.3335    0
 [152,] 208.4168    0
 [153,] 208.5002    0
 [154,] 208.5835    0
 [155,] 208.6668    0
 [156,] 208.8335    0
 [157,] 208.9168    0
 [158,] 209.0002    0
 [159,] 209.0835    0
 [160,] 209.1668    0
 [161,] 209.2502    0
 [162,] 209.3335    0
 [163,] 209.4168    0
 [164,] 209.5002    0
 [165,] 209.5835    0
 [166,] 209.6668    0
 [167,] 209.7502    0
 [168,] 209.8335    0
 [169,] 209.9168    0
 [170,] 210.0002    0
 [171,] 210.0835    0
 [172,] 210.1668    0
 [173,] 210.3335    0
 [174,] 210.4168    0
 [175,] 210.5002    0
 [176,] 210.5835    0
 [177,] 210.6668    0
 [178,] 210.7502    0
 [179,] 210.8335    0
 [180,] 210.9168    0
 [181,] 211.0002    0
 [182,] 211.0835    0
 [183,] 211.1668    0
 [184,] 211.2502    0
 [185,] 211.3335    0
 [186,] 211.4168    0
 [187,] 211.5002    0
 [188,] 211.5835    0
 [189,] 211.6668    0
 [190,] 211.7502    0
 [191,] 211.8335    0
 [192,] 211.9168    0
 [193,] 212.0002    0
 [194,] 212.0835    0
 [195,] 212.1668    0
 [196,] 212.2502    0
 [197,] 212.3335    0
 [198,] 212.4168    0
 [199,] 212.5002    0
 [200,] 212.5835    0
 [201,] 212.6668    0
 [202,] 212.7502    0
 [203,] 212.8335    0
 [204,] 212.9168    0
 [205,] 213.0002    0
 [206,] 213.0835    0
 [207,] 213.1668    0
 [208,] 213.2502    0
 [209,] 213.3335    0
 [210,] 213.4168    0
 [211,] 213.5002    0
 [212,] 213.5835    0
 [213,] 213.6668    0
 [214,] 213.7502    0
 [215,] 213.8335    0
 [216,] 213.9168    0
 [217,] 214.0002    0
 [218,] 214.0835    0
 [219,] 214.1668    0
 [220,] 214.2502    0
 [221,] 214.3335    0
 [222,] 214.4169    0
 [223,] 214.5002    0
 [224,] 214.5835    0
 [225,] 214.6669    0
 [226,] 214.7502    0
 [227,] 214.8335    0
 [228,] 214.9169    0
 [229,] 215.0002    0
 [230,] 215.0835    0
 [231,] 215.1669    0
 [232,] 215.2502    0
 [233,] 215.3335    0
 [234,] 215.4169    0
 [235,] 215.5002    0
 [236,] 215.5835    0
 [237,] 215.6669    0
 [238,] 215.7502    0
 [239,] 215.8335    0
 [240,] 215.9169    0
 [241,] 216.2502    0
 [242,] 216.5835    0
 [243,] 216.7502    0
 [244,] 216.9169    0
 [245,] 217.0002    0
 [246,] 217.0835    0
 [247,] 217.1669    0
 [248,] 217.2502    0
 [249,] 217.3335    0
 [250,] 217.4169    0
 [251,] 217.5002    0
 [252,] 217.5835    0
 [253,] 217.6669    0
 [254,] 217.7502    0
 [255,] 217.8335    0
 [256,] 217.9169    0
 [257,] 218.0002    0
 [258,] 218.0835    0
 [259,] 218.3335    0
 [260,] 218.4169    0
 [261,] 218.5835    0
 [262,] 218.7502    0
 [263,] 218.8335    0
 [264,] 218.9169    0
 [265,] 219.0002    0
 [266,] 219.1669    0
 [267,] 219.2502    0
 [268,] 219.3335    0
 [269,] 219.4169    0
 [270,] 219.5002    0
 [271,] 219.5835    0
 [272,] 219.6669    0
 [273,] 219.7502    0
 [274,] 219.8335    0
 [275,] 219.9169    0
 [276,] 220.0002    0
 [277,] 220.0835    0
 [278,] 220.2502    0
 [279,] 220.3335    0
 [280,] 220.4169    0
 [281,] 220.5002    0
 [282,] 220.5835    0
 [283,] 220.6669    0
 [284,] 220.7502    0
 [285,] 220.9169    0
 [286,] 221.0002    0
 [287,] 221.0835    0
 [288,] 221.1669    0
 [289,] 221.2502    0
 [290,] 221.3336    0
 [291,] 221.4169    0
 [292,] 221.5002    0
 [293,] 221.5836    0
 [294,] 221.6669    0
 [295,] 221.7502    0
 [296,] 221.8336    0
 [297,] 221.9169    0
 [298,] 222.0002    0
 [299,] 222.0836    0
 [300,] 222.2502    0
 [301,] 222.3336    0
 [302,] 222.4169    0
 [303,] 222.5002    0
 [304,] 222.5836    0
 [305,] 222.6669    0
 [306,] 222.7502    0
 [307,] 222.8336    0
 [308,] 222.9169    0
 [309,] 223.0002    0
 [310,] 223.1669    0
 [311,] 223.2502    0
 [312,] 223.3336    0
 [313,] 223.4169    0
 [314,] 223.5836    0
 [315,] 223.6669    0
 [316,] 223.7502    0
 [317,] 223.8336    0
 [318,] 223.9169    0
 [319,] 224.0002    0
 [320,] 224.0836    0
 [321,] 224.1669    0
 [322,] 224.2502    0
 [323,] 224.3336    0
 [324,] 224.4169    0
 [325,] 224.5002    0
 [326,] 224.5836    0
 [327,] 224.6669    0
 [328,] 224.7502    0
 [329,] 224.8336    0
 [330,] 224.9169    0
 [331,] 225.0002    0
 [332,] 225.0836    0
 [333,] 225.2502    0
 [334,] 225.3336    0
 [335,] 225.4169    0
 [336,] 225.5002    0
 [337,] 225.5836    0
 [338,] 225.6669    0
 [339,] 225.7502    0
 [340,] 225.8336    0
 [341,] 225.9169    0
 [342,] 226.0002    0
 [343,] 226.0836    0
 [344,] 226.1669    0
 [345,] 226.2502    0
 [346,] 226.3336    0
 [347,] 226.4169    0
 [348,] 226.5002    0
 [349,] 226.5836    0
 [350,] 226.6669    0
 [351,] 226.7502    0
 [352,] 226.8336    0
 [353,] 226.9169    0
 [354,] 227.0002    0
 [355,] 227.0836    0
 [356,] 227.1669    0
 [357,] 227.2502    0
 [358,] 227.3336    0
 [359,] 227.4169    0
 [360,] 227.5002    0
 [361,] 227.5836    0
 [362,] 227.6669    0
 [363,] 227.7502    0
 [364,] 227.8336    0
 [365,] 227.9169    0
 [366,] 228.0002    0
 [367,] 228.0836    0
 [368,] 228.1669    0
 [369,] 228.2502    0
 [370,] 228.3336    0
 [371,] 228.4169    0
 [372,] 228.5003    0
 [373,] 228.5836    0
 [374,] 228.6669    0
 [375,] 228.7503    0
 [376,] 228.8336    0
 [377,] 228.9169    0
 [378,] 229.0003    0
 [379,] 229.0836    0
 [380,] 229.1669    0
 [381,] 229.2503    0
 [382,] 229.3336    0
 [383,] 229.4169    0
 [384,] 229.5003    0
 [385,] 229.5836    0
 [386,] 229.6669    0
 [387,] 229.7503    0
 [388,] 229.8336    0
 [389,] 229.9169    0
 [390,] 230.0003    0
 [391,] 230.0836    0
 [392,] 230.1669    0
 [393,] 230.2503    0
 [394,] 230.3336    0
 [395,] 230.4169    0
 [396,] 230.5003    0
 [397,] 230.5836    0
 [398,] 230.6669    0
 [399,] 230.8336    0
 [400,] 231.0003    0
 [401,] 231.0836    0
 [402,] 231.2503    0
 [403,] 231.3336    0
 [404,] 231.4169    0
 [405,] 231.5003    0
 [406,] 231.5836    0
 [407,] 231.6669    0
 [408,] 231.7503    0
 [409,] 231.9169    0
 [410,] 232.0003    0
 [411,] 232.0836    0
 [412,] 232.1669    0
 [413,] 232.2503    0
 [414,] 232.3336    0
 [415,] 232.4169    0
 [416,] 232.5003    0
 [417,] 232.5836    0
 [418,] 232.6669    0
 [419,] 232.7503    0
 [420,] 232.8336    0
 [421,] 232.9169    0
 [422,] 233.0003    0
 [423,] 233.0836    0
 [424,] 233.2503    0
 [425,] 233.3336    0
 [426,] 233.4169    0
 [427,] 233.5003    0
 [428,] 233.5836    0
 [429,] 233.6669    0
 [430,] 233.7503    0
 [431,] 233.8336    0
 [432,] 233.9169    0
 [433,] 234.0003    0
 [434,] 234.0836    0
 [435,] 234.1669    0
 [436,] 234.2503    0
 [437,] 234.3336    0
 [438,] 234.4169    0
 [439,] 234.5003    0
 [440,] 234.5836    0
 [441,] 234.6669    0
 [442,] 234.7503    0
 [443,] 234.8336    0
 [444,] 234.9169    0
 [445,] 235.0003    0
 [446,] 235.0836    0
 [447,] 235.1669    0
 [448,] 235.2503    0
 [449,] 235.3336    0
 [450,] 235.4169    0
 [451,] 235.5003    0
 [452,] 235.5836    0
 [453,] 235.6670    0
 [454,] 235.7503    0
 [455,] 235.8336    0
 [456,] 235.9170    0
 [457,] 236.0003    0
 [458,] 236.0836    0
 [459,] 236.1670    0
 [460,] 236.2503    0
 [461,] 236.3336    0
 [462,] 236.4170    0
 [463,] 236.5003    0
 [464,] 236.5836    0
 [465,] 236.6670    0
 [466,] 236.7503    0
 [467,] 236.8336    0
 [468,] 236.9170    0
 [469,] 237.0003    0
 [470,] 237.0836    0
 [471,] 237.1670    0
 [472,] 237.2503    0
 [473,] 237.3336    0
 [474,] 237.4170    0
 [475,] 237.5003    0
 [476,] 237.5836    0
 [477,] 237.6670    0
 [478,] 237.7503    0
 [479,] 237.8336    0
 [480,] 237.9170    0
 [481,] 238.0003    0
 [482,] 238.0836    0
 [483,] 238.1670    0
 [484,] 238.2503    0
 [485,] 238.3336    0
 [486,] 238.4170    0
 [487,] 238.5003    0
 [488,] 238.5836    0
 [489,] 238.6670    0
 [490,] 238.7503    0
 [491,] 238.8336    0
 [492,] 238.9170    0
 [493,] 239.0003    0
 [494,] 239.0836    0
 [495,] 239.1670    0
 [496,] 239.2503    0
 [497,] 239.3336    0
 [498,] 239.4170    0
 [499,] 239.5003    0
 [500,] 239.5836    0
 [ reached getOption("max.print") -- omitted 5302 rows ]