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Messages - plasma33

1
XCMS / Peak List Generation
Hi Guys,

I want to generate a peak list with intensities in respect to the precursor ions so that I can do the MS/MS spectrum Match Analysis. I have got a result output file from metlin which are purely MS/MS. I did the mass search with help of the CAMERA Result and and filtered the ms2 data out of it. The masses in the output file are the precursor ions. I want the peak list and intensities generated by means of xcms so that I can search on Metlin - MS/MS Spectrum Match. I know that we can do by Xcalibur and Mass Frontier but I want to do via XCMS - R.

I am sending the link for Metlin Result File. Its modified but the content are same.
http://http://www.mediafire.com/?416td277ubu75hp

Thanks in advance guys.

Cheers
plasma33
2
XCMS / Re: xcmsRaw Error
I fixed the above error by installing R 2.13. But now I am getting a new error which is "MS1 data not found".

Here is the code->
Code: [Select]
> col<-collect(xraw, rt=20)
199.99658203125 181.93 159.256652832031 106.89 116.93 114 140.894668579102 275.978149414063 235.17 141.789566040039 124.060859680176 275.977996826172 235.2 176.01350402832 118.971122741699 251.447891235352 235.22 158.002883911133 106.94 116.92 346.990142822266 504.102935791016 504.102508544922 522.200378417969 340.17 281.08 219.03 522.200256347656 340.18 281.1 219.02 141.447265625 340.16 281.06 219.01 522.200317382813 340.22 281.16 219.05 386.180145263672 165.03 327.04 120.97 340.15 281.09 219.08 416.191192626953 195.11 150.97 357.08 720.333618164063 558.29 264.16 514.3 696.285217285156 534.24 636.14 251.14 648.228515625 589.18 455.14 411.17 166.921905517578 139.062774658203 124.157600402832 105.18482208252 275.978210449219 275.978179931641 235.16 275.978088378906 235.21 107.342735290527 141.758514404297 199.029373168945 148.554931640625 188.070678710938 146.04 144.06 170.04 141.530746459961 123 199.02946472168 82.98 97.09 107 430.656799316406 235.18 150.014251708984 275.978332519531 235.19 148.018508911133 116.638687133789 141.097290039063 275.978057861328 173.029937744141 130.92 120.94 199.029388427734 225.995788574219 114.306816101074 275.978271484375 235.15 109.133369445801 158.002777099609 106.91 116.91 141.12141418457 123.06 119.140701293945 140.296264648438 122.02 141.11149597168 159.005279541016 106.87 176.013366699219 220.372833251953 496.961578369141 275.978302001953 140.088104248047 104.007209777832 141.486923217773 148.018585205078 199.302337646484 158 259.07 275.978240966797 259.05 113.462104797363 105.125312805176 275.978118896484 144.057540893555 728.997619628906 558.33 264.15 514.29 147.026275634766 104.687942504883 123.06120300293 611.158386230469 449.1 303.08 611.160339355469 449 303.13 188.110382080078 124.08 611.159362792969 449.04 303.16 188.110305786133 124.07 107.01 611.161865234375 448.98 188.110336303711 107.05 188.110366821289 124.06 107.09 188.110321044922 124.05 107.02 115.56241607666 595.166076660156 433.07 287.14 432.99 287.18 595.166015625 433.02 287.12 449.09 595.165405273438 433.05 287.1 595.165466308594 449.02 287.09 625.176635742188 463.14 317.13 625.17626953125 463.03 317.11 479.15 250.147201538086 208.14 232.17 625.176025390625 317.12 479.04 625.176147460938 463.05 317.15 647.158874511719 501.09 625.176574707031 463.04 176.794830322266 146.716934204102 118.1 176.013488769531 149.07 623.17919921875 109.459930419922 579.169738769531 124.731056213379 579.170715332031 433.06 203.109924316406 137.06 94.99 139.05 163.262969970703 579.170288085938 433.08 579.170776367188 287.07 579.170227050781 433.17 609.18115234375 463.06 609.180786132813 631.161987304688 485.11 463.07 317.23 631.164306640625 485.1 609.181030273438 317.14 609.181518554688 199.029403686523 449.107574462891 303.09 449.107818603516 303.07 287.08 431.01 449.107940673828 287.11 413.2 449.107666015625 303.1 287.06 303.11 479.119079589844 479.118194580078 317.07 230.078674316406 303.086090087891 177.02 152.99 179.03 709.252685546875 709.253112792969 709.252502441406 275.091674804688 106.97 169.04 148.95 134.006423950195 709.251708984375 793.328247070313 670.31 203.47688293457 793.3291015625 670.26 793.334106445313 670.21 202.125991821289 138.09 92.99 121.02 202.1259765625 138.1 93 121.04 199.029357910156 121 202.125946044922 138.11 425.226928710938 224.13 202.125961303711 92.93 121.14 425.226806640625 224.22 249.160552978516 425.226470947266 224.18 435.128234863281 273.16 417.08 435.128265380859 273.1 425.226135253906 224.21 175.49137878418 132.03 273.12 417.23 425.226104736328 435.128356933594 273.075805664063 153 146.99 179.04 636.245361328125 435.131256103516 273.09 417.09 160.902465820313 163.617736816406 437.143829345703 437.144226074219 419.25 437.144073486328 419.09 275.091339111328 148.93 463.122924804688 419.07 275.17 275.091369628906 106.96 169.02 148.91 463.123718261719 437.144012451172 419.14 275.09 275.091400146484 148.99 795.34326171875 763.19 672.29 601.2 795.343322753906 763.27 601.29 672.24 649.285827636719 795.344909667969 763.25 601.3 672.31 109.849395751953 89.25 649.284301757813 616.15 777.332580566406 745.22 654.25 622.33 777.334594726563 745.28 654.27 622.31 745.31 654.24 622.23 777.333984375 745.32 654.21 622.22 647.269897460938 629.29 615.21 647.269775390625 629.27 615.2 647.27001953125 629.28 615.25 199.029434204102 649.2890625 630.29 616.14 605.33 398.166412353516 649.2861328125 630.25 605.24 649.285766601563 605.22 616.24 630.32 649.285034179688 605.23 616.19 630.28 419.135498046875 273.14 398.166687011719 419.134246826172 649.285400390625 605.26 616.16 526.25 398.166381835938 449.144714355469 431.07 236.11 449.144287109375 431.04 413.1 125.253143310547 398.166351318359 236.07 449.143951416016 431.06 413.09 236.11376953125 138.04 218.13 615.1689453125 391.11 615.16748046875 571.27 615.167663574219 391.12 571.14 275.97802734375 663.303161621094 663.302917480469 615.167541503906 391.13 793.236083984375 663.302856445313 539.15 793.233581542969 663.302124023438 539.17 570.160278320313 268.08 552.25 539.13 633.291870117188 510.2 460.23 633.29150390625 601.22 510.19 460.26 633.291748046875 460.22 633.291625976563 601.16 510.16 460.19 663.302429199219 630.24 663.30224609375 630.18 539.26 663.302978515625 663.304504394531 630.16 663.301208496094 539.29 649.285095214844 617.2 573.32 631.26 201.048049926758 201.15 143.085144042969 101.91 119.97 257.118133544922 242.11 235.136245727539 203.11 179.23 257.118103027344 242.17 235.136138916016 203.08 179.16 203.109939575195 137.04 139.06 94.94 257.1181640625 242.15 235.136184692383 203.1 179.25 203.110046386719 137.03 95.02 292.117980957031 207.05 111.97 250.18 314.099853515625 137.05 139.11 207.07 111.96 250.11 663.3017578125 631.16 540.2 510.13 314.099731445313 292.117950439453 111.93 671.197509765625 639.28 663.301818847656 540.26 292.118011474609 207.08 250.16 671.196899414063 671.198669433594 292.117858886719 273.075897216797 152.97 147.02 189.04 273.075775146484 147 273.075714111328 153.02 147.04 189.08 273.075744628906 152.98 189.03 179.01 303.08642578125 177.07 179 303.086242675781 177.04 303.086334228516 177.05 153.01 303.086212158203 177.06 303.087341308594 177 176.013397216797 645.291931152344 613.21 522.19 645.2919921875 613.23 490.11 643.202941894531 645.292419433594 613.22 522.16 490.22 643.201721191406 643.2021484375 671.195983886719 661.285705566406 629.24 538.24 143.805191040039 104.007194519043 176.013610839844 149.12 353.229766845703 335.27 311.18 348.274566650391 113.170204162598 631.274108886719 599.25 104.934875488281 418.649536132813 693.2568359375 693.256713867188 693.257385253906 693.257446289063 199.029510498047 220.082382202148 156.09 140.11 147.05 123.937927246094 491.266998291016 491.267150878906 473.255554199219 455.22 204.141723632813 187.09 491.267364501953 491.266632080078 501.194793701172 202.09 147.26594543457 491.267120361328 199.029327392578 176.013473510742 190.050033569336 475.271850585938 493.282470703125 493.282928466797 515.266357421875 353.23 331.23 395.21 493.285278320313 475.274566650391 221.841674804688 493.282958984375 493.283050537109 515.264282226563 331.25 353.27 395.3 510.310363769531 493.283416748047 493.283294677734 493.283081054688 509.275451660156 481.19 410.11 346.14 367.24560546875 349.21 249.12 267.17 475.272064208984 475.272644042969 493.283264160156 475.276763916016 153.658096313477 256.080017089844 197.06 234.098037719727 170.08 154.14 97.98 256.080169677734 197.13 170.1 154.09 98.01 197.1 170.09 154.11 98.02 256.080078125 197.14 473.197052001953 240.16 234.098068237305 154.1 98 473.196990966797 240.12 234.098052978516 170.11 98.09 495.297943115234 495.299224853516 495.298065185547 495.297912597656 495.298248291016 629.256225585938 597.18 489.24 458.21 143.292999267578 101.99 119.94 477.288238525391 477.287506103516 477.287933349609 517.277893066406 82.97 97.01 333.262786865234 97 105.852592468262 143.083297729492 101.93 597.303283691406 597.305114746094 597.303405761719 597.303161621094 597.302917480469 437.193237304688 407.28 453.167846679688 460.269287109375 415.15 295.13 397.22 437.193328857422 303.14 407.29 453.167358398438 432.238037109375 437.196411132813 407.31 453.170623779297 460.272705078125 415.13 295.12 397.33 162.732757568359 477.289031982422 619.284362792969 283.04 601.41 127.259956359863 526.341674804688 523.330139160156 523.330017089844 505.319793701172 523.333068847656 523.330078125 545.310852050781 425.38 677.374938964844 477.288482666016 343.295196533203 240.29 283.01 325.28 677.373901367188 505.319183349609 493.281188964844 465.18 394.08 346.15 505.318664550781 523.328918457031 505.319519042969 408.29 256.300109863281 124.600845336914 699.356140136719 537.37 694.397705078125 694.398986816406 677.370727539063 103.697074890137 108.594078063965 277.216156005859 259.19 149.11 404.207763671875 105.282562255859 186.131103515625 121.08 93.03 522.28271484375 504.13 277.216278076172 149.14 135.13 259.25 349.234710693359 331.24 277.216186523438 149.1 135.11 259.22 349.23486328125 277.216369628906 135.08 679.391479492188 293.210235595703 275.2 237.25 529.20947265625 292.16 507.227355957031 256.14 238.11 507.227661132813 256.16 238.15 529.209594726563 292.11 552.285583496094 529.217102050781 292.1 292.13 507.227844238281 256.15 199.169250488281 97.02 83.05 293.211181640625 275.18 171.04 257.2 555.425720214844 293.211151123047 275.21 171.06 257.27 315.193115234375 277.22 297.19 331.203338623047 277.24 313.16 295.17 677.40625 649.42 659.4 566.36 655.424255371094 544.29 231.11 542.35 293.212310791016 171.14 257.22 293.211059570313 171.1 257.26 315.193054199219 275.200531005859 257.21 159.12 147.08 597.303527832031 579.291442871094 557.454650878906 597.303894042969 619.285034179688 439.27 283.06 601.27 579.293701171875 439.23 601.26 283.11 579.292663574219 619.285278320313 439.29 579.292846679688 597.303588867188 619.285766601563 439.26 283.02 579.293151855469 561.25 439.25 283.05 614.329895019531 295.226837158203 277.18 249.24 614.330078125 317.208740234375 295.226623535156 249.19 259.21 614.329284667969 295.226928710938 277.23 179.18 614.329772949219 277.21 179.14 241.27 317.208618164063 614.330749511719 259.33 241.2 165.19 317.208709716797 277.216339111328 261.23 243.27 317.208648681641 277.216247558594 260.3 242.21 150.13 277.217010498047 241.24 611.432556152344 277.21630859375 241.21 611.42822265625 595.361511230469 190.049865722656 301.140838623047 245.1 342.167541503906 190.049911499023 301.141021728516 245.08 342.167663574219 190.049880981445 674.375 137.757919311523 323.374206542969 125.390182495117 297.242462158203 279.19 261.2 361.693420410156 297.242370605469 279.24 261.22 243.24 297.242431640625 279.2 261.27 243.25 297.242492675781 183.14 279.16 183.12 261.31 319.224426269531 319.224334716797 609.339233398438 142.757614135742 609.339782714844 319.224548339844 609.33935546875 373.23 604.38427734375 207.14 263.09 609.340087890625 604.385864257813 475.07 353.268585205078 261.24 609.340881347656 604.385498046875 353.268646240234 335.25 353.268768310547 261.25 311.21 502.372955322266 485.18 546.400268554688 529.24 403.23 634.454040527344 617.32 187.448944091797 590.425842285156 573.23 291.32 447.26 546.400390625 529.23 403.29 335.24 634.452026367188 617.31 291.27 353.268707275391 329.06 261.21 311.26 590.427062988281 573.2 291.31 634.453552246094 617.33 676.390502929688 722.502563476563 705.33 676.390319824219 676.390686035156 463.130004882813 463.130859375 480.157867431641 485.113616943359 480.157104492188 485.112915039063 463.130950927734 480.157501220703 485.112762451172 480.157409667969 485.112426757813 480.157165527344 485.112640380859 445.120422363281 429 131.567886352539 141.960266113281 347.255584716797 325.273529052734 269.23 307.27 263.237213134766 245.24 163.19 149.09 347.255737304688 325.273803710938 307.25 269.21 307.263275146484 289.25 271.28 207.15 347.255859375 325.273864746094 307.26 269.15 307.26318359375 289.27 271.23 182.878707885742 142.213821411133 654.331237792969 637.16 637.306457519531 581.26 525.25 654.331909179688 637.25 637.305969238281 581.23 525.22 700.313293457031 654.331726074219 637.30517578125 652.390991210938 252.12 652.390380859375 652.392150878906 678.404907226563 130.831100463867 678.406677246094 678.406311035156 476.409210205078 678.406982421875 476.410583496094 678.405944824219 141.681350708008 142.593612670898 439.331970214844 327.24 309.29 421.36 220.390396118164 439.332153320313 327.22 309.26 421.34 554.175964355469 591.553344726563 263.26 245.25 593.11 439.331909179688 327.23 309.27 421.37 554.17578125 371.101440429688 355.04 554.175842285156 439.331726074219 309.3 421.39 371.101226806641 355.11 439.331878662109 327.25 309.25 554.17529296875 190.999771118164 203.788909912109 226.182586669922 189.024917602539 138.379318237305 191.57502746582 118.867004394531 107.290420532227 116.666229248047 114.612762451172 141.871322631836 106.174911499023 270.406951904297 439.331939697266 439.332183837891 309.28 421.41 189.079132080078 421.38 439.33203125 679.475341796875 367.27 423.28 730.541137695313 657.560852050781 375.35 393.34 256.263702392578 102 87.96 116 523.361022949219 267.05 518.406005859375 523.361083984375 211.18 518.406127929688 523.360534667969 462.357757568359 168.02 186.09 518.404724121094 628.194580078125 628.195373535156 523.360168457031 211.11 628.195129394531 628.194885253906 706.43701171875 633.150146484375 628.198425292969 633.155578613281 633.148132324219 371.1015625 355.06 633.150451660156 439.3310546875 327.26 421.33 109.250091552734 121.965446472168 101.970741271973 442.567779541016 167.775848388672 585.450744628906 567.44 493.42 413.266143798828 301.15 189.01 454.292358398438 454.292388916016 585.452087402344 567.43 493.39 413.266021728516 189.06 798.592224121094 301.17 189 287.735198974609 387.46044921875 147.25895690918 282.583404541016 702.213684082031 702.213256835938 702.213317871094 702.212707519531 702.212829589844 705.211181640625 707.170288085938 705.211730957031 131.31526184082 143.005004882813 269.582366943359 765.520751953125 764.530883789063 173.350921630859 536.165100097656 518.9 502.99 536.165710449219 502.95 502.94 536.166015625 518.88 281.11 502.92 536.165344238281 518.89 281.13 519.139404296875 519.139099121094 519.139343261719 519.139465332031 519.140319824219 155.517807006836 142.436996459961 190.434127807617 142.312622070313 275.229827880859 613.482971191406 595.53 521.51 539.55 613.482238769531 595.48 521.46 539.49 613.482116699219 595.46 521.47 539.48 613.481872558594 595.45 521.45 539.44 775.534423828125 613.481506347656 539.46 153.78059387207 211.29167175293 617.8583984375 104.615577697754 476.628143310547 142.380874633789 776.232238769531 776.233520507813 776.230346679688 776.231262207031 302.014099121094 128.981414794922 778.226501464844 394.347351074219 134.07 322.31 282.37 126.326148986816 394.34814453125 134.05 323.31 101.121589660645 141.876129150391 204.472351074219 103.911376953125 766.557800292969 208.039291381836 192.06169128418 150.98 264.955444335938 223.81 208.039337158203 184.9 166.92 305.981903076172 264.955383300781 264.954986572266 249.011657714844 199.029342651367 130.374420166016 109.95 85.97 199.029846191406 157.99 127.476104736328 199.029312133789 199.029556274414 182.01 207.159072875977 151.11 133.09 199.029968261719 157.96 181.98 225.995742797852 181.95 159.04 165.647476196289 181.9 181.96 158.96 163.617935180664 182.04 207.159133911133 151.07 133.02 182.05 199.029296875 158.98 225.995590209961 241.622253417969 225.995849609375 142.900238037109 142.672637939453 101.94 120.04 207.985214233398 184.94 166.93 179.491226196289 138.94 156.95 199.996597290039 158.002853393555 235.23 119.330146789551 
Calculating accurate mass...
Warning messages:
1: In .local(object, ...) :
  This method will be removed in the next releases

2: In .local(object, ...) :
  This method will be removed in the next releases

> col
An "xcmsFragments" object with 1354  collected mass spectra

Mass range: 82.97-798.5922 m/z
Collision Energy range: 35 35 V
Memory usage: 0.622 MB
> met<-searchMetlin(col, file="try", MS1data = FALSE)
Error in searchMetlin(col, file = "try", MS1data = FALSE) : object 'MS1data' not found

Thanks in advance guys.

Cheers
plasma33
3
XCMS / xcmsRaw Error
Hi guys,

I am getting an error which is [unable to find an inherited method for function "collect", for signature "xcmsRaw"]. Can anyone give me a fix for the suggested error.

Here is the code from R->
Code: [Select]
R version 2.14.2 (2012-02-29)
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: i386-pc-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(xcms)
> xraw <- xcmsRaw("C:/Users/vnai039/Downloads/XCMS Results/Mutant Aux/Mutant-aux-1.mzXML", includeMSn=TRUE)
> xraw
An "xcmsRaw" object with 759 mass spectra

Time range: 0.4-2997.6 seconds (0-50 minutes)
Mass range: 121.0017-999.9907 m/z
Intensity range: 777.266-43677300 

MSn data on  2113  mass(es)
        with  2322  MSn spectra
Profile method: bin 
Profile step: 1 m/z (880 grid points from 121 to 1000 m/z)

Memory usage: 17.4 MB
> col<-collect(xraw, rt=20)
Error in function (classes, fdef, mtable)  : 
  unable to find an inherited method for function "collect", for signature "xcmsRaw"

Thanks in advance.

Cheers
plasma33
5
XCMS / xcmsSet Feature Detection Details
Hi guys,

I need complete details of xcmsSet Feature Detection. I need information like what different sorts of methods are used and what all other features do the xcmsSet have etc.

Feature detection More Details plz->

    method : centWave
    ppm 30
    snthr 6
    peakwidth 10 60
    mzdiff 0.01
    prefilter peaks 3
    prefilter intensity 100

Is there any manual that provides some info.

Thanks in advance.

Cheers
plasma33
7
XCMS / Re: Calculate Intensity/Abundance
Thanks for your reply. I am sorry for being precise. Actually there's no intensity column in the diff report that we get from XCMS. I want to do a compound search in databases such as Metlin, MMCD, HMDB and MassBank but they ask for inputs such as m/z and intensity or retention time and intensity. How am I suppose to calculate intensity from XCMS. Hope I explained it well this time. Waiting for your reply.

Cheers
Vijay
8
XCMS / Calculate Intensity/Abundance
Hi Guys,

How am I suppose to calculate intensity/abundance? Is it calculated from m/z and retention time? Can someone please help me.

Cheers
plasma33
10
metaXCMS / Re: Raw Data Alignment Error
But XCMS online provides results that can be downloaded and which are compatabile with meta-XCMS. Like XCMS provides data in .csv and .tsv format which are easily read by meta-XCMS. Its only the raw data that are not recognized/assigned by meta-XCMS. But will do go through the paper which you have provided.

Thanks
11
metaXCMS / Re: Raw Data Alignment Error
I did XCMS online and downloaded the results. And the raw data are in the same folder while I was doing XCMS online. Now results are in separate folders as I wanted to compare 3 sets. So 3 different folders for 3 results. And raw data are in different folder. But its in the same folder while I was doing XCMS online.

Thanks
12
metaXCMS / Raw Data Alignment Error
Hi Ralf,

I am getting error while performing "Raw Data Alignment". I am providing a screenshot of the error I am getting. Please suggest as in what should I do?


Cheers
Plasma33
13
Other metabolomics resources / LC-MS Raw Data
Hi Guys,

I am actually looking to download raw data from the Internet. I am actually looking for LC-MS data for E. Coli. It would be preferred if I we get raw data for metabolites i.e. for small molecules. I am not looking for raw data of any peptide or protein. Also is there any repository for LC-MS data based on metabolites? Thanks guys in advance.

Cheers
Plasma33