PD-node_same error message

[adamurminsky]

Hello,

I am also having a problem running MSFrager as a PD node. I have the same error message as was posted on other topics

Usually it was caused by JRE notinstalled or only 32 bit version. I should have installed the newest version and MSFrager is also working fine via FragPipe.

I was following instructions from http://www.nesvilab.org/PD-Nodes/ . I have newest MSFrager3.5.jar and also Philosopher 4.4.0. The path to .jar file is also correct. I am using raw file or mzml. I am using closed search with defined offset masses (all highres spectra) - the same as in FragPipe. It does not work also with Percolator. In some threads you were mentioning samething about problem with path to pep.xml file, but i could not find how to resolve it ( if it is the problem).

Here are the verbose from processing step:

Time | Processing Node | Level | Message -- | -- | -- | -- 8/16 12:08 PM | (4) Percolator | Error | Percolator isn't performed for MSFragger (2): There are only 0 peptides, but there have to be at least 200. 8/16 12:08 PM | (4) Percolator | Info | The input file contains 0 PSMs, 0 decoy PSMs and 0 features. 8/16 12:08 PM | (4) Percolator | Info | Creating percolator input file with results from MSFragger (2) took 9.1 ms. 8/16 12:08 PM | (2) MSFragger | Info | Persist PepMatch--D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\temp1924\210125_21SP002_4A_500ng_10ul_real.pepXML ; 0:0:0 8/16 12:08 PM | (2) MSFragger | Info | Transform to pepMatch-- 0:0:0 8/16 12:08 PM | (2) MSFragger | Info | Parse pepXML--D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\temp1924\210125_21SP002_4A_500ng_10ul_real.pepXML ; 0:1:19 8/16 12:07 PM | (1) Spectrum Selector | Info | -- Total execution of Spectrum Selector (1) took 2 min 10 s -- 8/16 12:07 PM | (1) Spectrum Selector | Info | Sent 18000 spectra from 1 files (processing time: 47.4 s). 8/16 12:05 PM | (2) MSFragger | Info | MSFragger Running Time --0:0:30 8/16 12:05 PM | (2) MSFragger | Info | at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source) 8/16 12:05 PM | (2) MSFragger | Info | at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source) 8/16 12:05 PM | (2) MSFragger | Info | at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source) 8/16 12:05 PM | (2) MSFragger | Info | at u.(Unknown Source) 8/16 12:05 PM | (2) MSFragger | Info | at u.a(Unknown Source) 8/16 12:05 PM | (2) MSFragger | Info | at java.base/java.lang.Float.parseFloat(Float.java:476) 8/16 12:05 PM | (2) MSFragger | Info | at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122) 8/16 12:05 PM | (2) MSFragger | Info | at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054) 8/16 12:05 PM | (2) MSFragger | Info | java.lang.NumberFormatException: For input string: "494.1748 1022.3802 365.1322 876.3223 1095.3966 1021.3598 947.3230 730.2644 1312.4552 656.2276 203.0794 1378.4756 1704.6348 1702.5812 1695.6231 2204.7724 1864.6340 1647.6133 2117.7768 2715.9625 2205.7928 1444.5339 1216.4228 1298.4760 1930.6923 1241.4545 2060.7553 2263.8347 1038.3751 2350.7924 1710.5976 1694.6027 1548.5448 2352.8460 1711.6180 3009.0736 3007.0579 1872.6504 892.3172 1540.5284 1200.4279 2059.7349 2206.8132 2075.7298 2350.8303 1768.6395 2221.7877 2076.7502 2222.8081 2101.7819 1581.5550 2018.7083 2190.7932 1907.7142 1913.6770 1880.6668 2157.7830 2012.7455 2465.8937 1362.4807 1825.6610 2116.7564 2092.7451 1751.6242 1622.5816 1752.6446 2100.7615 2262.8143 1971.7189 1955.7240 1809.6661 2408.8722 1897.6821 2424.8671 3081.0947 2481.8886 1914.6974 2133.7717 1784.6344 2391.8569 1850.6927 2174.7983 1735.6293 2141.7881 2498.9039 2570.9250 2789.9993 2432.8835 2043.7400 1996.7506 1873.6708 1606.5867 1866.6876 1857.6759 2861.0000 2158.8034 2019.7287 2028.7404 1898.7025 1565.5601 1987.7138 1403.5073 2278.8092 2716.9829 2878.0153 2279.8296 2336.8511 2643.9414 2287.8460 2580.9571 2425.8875 2644.9618 2627.9465 2448.8784 2215.8249 3372.1901 2320.8562 2407.8518 2553.9097 2459.9309 2621.9837 2246.8194 2245.7990 2069.7670 2717.9782 3594.3005 3959.4327 2393.8726 1257.4494 1663.6082 1460.5288 1954.7036 1501.5554 1549.5652 1727.6129 2571.9454 2864.0361 2142.8085 2674.9359 2110.7936 2256.8515 1419.5022 4307.5496 1589.5714 3010.1191 3229.1683 3083.1355 2937.0776 3228.1730 2569.9046 1387.5124 2475.9258 2053.7721 3048.0845 2919.0419 2966.0313 3519.2684 3517.2276 3663.2855 2313.8730 2775.0248 2701.9833 3284.1741 3374.2058 3520.2637 2539.9305 2772.9840 4028.4177 3140.1570 3405.2003 3064.0794 3521.2841 3448.2426 2434.8992 3407.2411 4247.5171 1013.3434 1856.6555 2351.8507 2366.8252 2699.9676 2862.0204 2936.0572 2935.0368 2993.0787 3008.0783 3023.0528 3097.0896 3139.1366 3153.1158 3227.1526 3226.1322 3300.1941 3388.1850 3446.2269 351... 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'deneutralloss' was not supplied. Using default value: 1 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'min_sequence_matches' was not supplied. Using default value: 2 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'restrict_deltamass_to' was not supplied. Using default value: all 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'labile_search_mode' was not supplied. Using default value: OFF 8/16 12:05 PM | (2) MSFragger | Info | Checking database... 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'data_type' was not supplied. Using default value: 0 8/16 12:05 PM | (2) MSFragger | Info | ************************************MAIN SEARCH************************************ 8/16 12:05 PM | (2) MSFragger | Info | Z:\2022zaloha\SP002_Neuro\210125_21SP002_4A_500ng_10ul_real.raw: Scans = 23251 8/16 12:05 PM | (2) MSFragger | Info | Checking spectral files... 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'diagnostic_fragments' was not supplied. Using default value: 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'Y_type_masses' was not supplied. Using default value: 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'activation_types' was not supplied. Using default value: 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'deneutralloss' was not supplied. Using default value: 1 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'min_sequence_matches' was not supplied. Using default value: 2 8/16 12:05 PM | (2) MSFragger | Info | Checking database... 8/16 12:05 PM | (2) MSFragger | Info | Parameter 'data_type' was not supplied. Using default value: 0 8/16 12:05 PM | (2) MSFragger | Info | JVM started with 50 GB memory 8/16 12:05 PM | (2) MSFragger | Info | Java Info: 18.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation 8/16 12:05 PM | (2) MSFragger | Info | System OS: Windows 10, Architecture: AMD64 8/16 12:05 PM | (2) MSFragger | Info | RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. 8/16 12:05 PM | (2) MSFragger | Info | (c) University of Michigan 8/16 12:05 PM | (2) MSFragger | Info | timsdata library version timsdata-2-8-7-1 8/16 12:05 PM | (2) MSFragger | Info | Batmass-IO version 1.25.5 8/16 12:05 PM | (2) MSFragger | Info | MSFragger version MSFragger-3.5 8/16 12:05 PM | Job Execution | Info | Processing D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\2101257_21SP002_50c_xxx_ion_series_definitions_full__done_offset_ext_folder_xxx_java_JRE_oracle-(9).msf If I need to provide anything else,let me know. Thank you

[huiyinc]

Hi,

According to your log file, there is an error occurs when running MSFragger node:

8/16 12:05 PM (2) MSFragger Info java.lang.NumberFormatException: For input string: "494.1748 1022.3802 365.1322 876.3223 1095.3966 1021.3598 947.3230 730.2644 1312.4552 656.2276 203.0794 1378.4756 1704.6348 1702.5812 1695.6231 2204.7724 1864.6340 1647.6133 2117.7768 2715.9625 2205.7928 1444.5339 1216.4228 1298.4760 1930.6923 1241.4545 2060.7553 2263.8347 1038.3751 2350.7924 1710.5976 1694.6027 1548.5448 2352.8460 1711.6180 3009.0736 3007.0579 1872.6504 892.3172 1540.5284 1200.4279 2059.7349 2206.8132 2075.7298 2350.8303 1768.6395 2221.7877 2076.7502 2222.8081 2101.7819 1581.5550 2018.7083 2190.7932 1907.7142 1913.6770 1880.6668 2157.7830 2012.7455 2465.8937 1362.4807 1825.6610 2116.7564 2092.7451 1751.6242 1622.5816 1752.6446 2100.7615 2262.8143 1971.7189 1955.7240 1809.6661 2408.8722 1897.6821 2424.8671 3081.0947 2481.8886 1914.6974 2133.7717 1784.6344 2391.8569 1850.6927 2174.7983 1735.6293 2141.7881 2498.9039 2570.9250 2789.9993 2432.8835 2043.7400 1996.7506 1873.6708 1606.5867 1866.6876 1857.6759 2861.0000 2158.8034 2019.7287 2028.7404 1898.7025 1565.5601 1987.7138 1403.5073 2278.8092 2716.9829 2878.0153 2279.8296 2336.8511 2643.9414 2287.8460 2580.9571 2425.8875 2644.9618 2627.9465 2448.8784 2215.8249 3372.1901 2320.8562 2407.8518 2553.9097 2459.9309 2621.9837 2246.8194 2245.7990 2069.7670 2717.9782 3594.3005 3959.4327 2393.8726 1257.4494 1663.6082 1460.5288 1954.7036 1501.5554 1549.5652 1727.6129 2571.9454 2864.0361 2142.8085 2674.9359 2110.7936 2256.8515 1419.5022 4307.5496 1589.5714 3010.1191 3229.1683 3083.1355 2937.0776 3228.1730 2569.9046 1387.5124 2475.9258 2053.7721 3048.0845 2919.0419 2966.0313 3519.2684 3517.2276 3663.2855 2313.8730 2775.0248 2701.9833 3284.1741 3374.2058 3520.2637 2539.9305 2772.9840 4028.4177 3140.1570 3405.2003 3064.0794 3521.2841 3448.2426 2434.8992 3407.2411 4247.5171 1013.3434 1856.6555 2351.8507 2366.8252 2699.9676 2862.0204 2936.0572 2935.0368 2993.0787 3008.0783 3023.0528 3097.0896 3139.1366 3153.1158 3227.1526 3226.1322 3300.1941 3388.1850 3446.2269 351...

That's why you got the error message, saying that the pepXML file can't be found. Do you have any idea what these strings mean? Are they from your parameter setting or raw (mzML) files? Thanks.

Huiyin

adamurminsky @.***> 於 2022年8月16日 下午9:20 寫道：



Hello,

I am also having a problem running MSFrager as a PD node. I have the same error message as was posted on other topics [image: image] https://user-images.githubusercontent.com/109969166/184860614-2b35b1eb-730d-4b63-94f0-ad0e89f8c37c.png

Usually it was caused by JRE notinstalled or only 32 bit version. I should have installed the newest version and MSFrager is also working fine via FragPipe.

[image: image] https://user-images.githubusercontent.com/109969166/184860867-b19c6f29-b2f9-4fad-8257-dcf791d3a435.png

I was following instructions from http://www.nesvilab.org/PD-Nodes/ . I have newest MSFrager3.5.jar and also Philosopher 4.4.0. The path to .jar file is also correct. I am using raw file or mzml. I am using closed search with defined offset masses (all highres spectra) - the same as in FragPipe. It does not work also with Percolator. In some threads you were mentioning samething about problem with path to pep.xml file, but i could not find how to resolve it ( if it is the problem).

Here are the verbose from processing step: Time Processing Node Level Message 8/16 12:08 PM (4) Percolator Error Percolator isn't performed for MSFragger (2): There are only 0 peptides, but there have to be at least 200. 8/16 12:08 PM (4) Percolator Info The input file contains 0 PSMs, 0 decoy PSMs and 0 features. 8/16 12:08 PM (4) Percolator Info Creating percolator input file with results from MSFragger (2) took 9.1 ms. 8/16 12:08 PM (2) MSFragger Info Persist PepMatch--D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\temp1924\210125_21SP002_4A_500ng_10ul_real.pepXML ; 0:0:0 8/16 12:08 PM (2) MSFragger Info Transform to pepMatch-- 0:0:0 8/16 12:08 PM (2) MSFragger Info Parse pepXML--D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\temp1924\210125_21SP002_4A_500ng_10ul_real.pepXML ; 0:1:19 8/16 12:07 PM (1) Spectrum Selector Info -- Total execution of Spectrum Selector (1) took 2 min 10 s -- 8/16 12:07 PM (1) Spectrum Selector Info Sent 18000 spectra from 1 files (processing time: 47.4 s). 8/16 12:05 PM (2) MSFragger Info MSFragger Running Time --0:0:30 8/16 12:05 PM (2) MSFragger Info at edu.umich.andykong.msfragger.MSFragger.main(Unknown Source) 8/16 12:05 PM (2) MSFragger Info at edu.umich.andykong.msfragger.MSFragger.b(Unknown Source) 8/16 12:05 PM (2) MSFragger Info at edu.umich.andykong.msfragger.MSFragger.a(Unknown Source) 8/16 12:05 PM (2) MSFragger Info at u.(Unknown Source) 8/16 12:05 PM (2) MSFragger Info at u.a(Unknown Source) 8/16 12:05 PM (2) MSFragger Info at java.base/java.lang.Float.parseFloat(Float.java:476) 8/16 12:05 PM (2) MSFragger Info at java.base/jdk.internal.math.FloatingDecimal.parseFloat(FloatingDecimal.java:122) 8/16 12:05 PM (2) MSFragger Info at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054) 8/16 12:05 PM (2) MSFragger Info java.lang.NumberFormatException: For input string: "494.1748 1022.3802 365.1322 876.3223 1095.3966 1021.3598 947.3230 730.2644 1312.4552 656.2276 203.0794 1378.4756 1704.6348 1702.5812 1695.6231 2204.7724 1864.6340 1647.6133 2117.7768 2715.9625 2205.7928 1444.5339 1216.4228 1298.4760 1930.6923 1241.4545 2060.7553 2263.8347 1038.3751 2350.7924 1710.5976 1694.6027 1548.5448 2352.8460 1711.6180 3009.0736 3007.0579 1872.6504 892.3172 1540.5284 1200.4279 2059.7349 2206.8132 2075.7298 2350.8303 1768.6395 2221.7877 2076.7502 2222.8081 2101.7819 1581.5550 2018.7083 2190.7932 1907.7142 1913.6770 1880.6668 2157.7830 2012.7455 2465.8937 1362.4807 1825.6610 2116.7564 2092.7451 1751.6242 1622.5816 1752.6446 2100.7615 2262.8143 1971.7189 1955.7240 1809.6661 2408.8722 1897.6821 2424.8671 3081.0947 2481.8886 1914.6974 2133.7717 1784.6344 2391.8569 1850.6927 2174.7983 1735.6293 2141.7881 2498.9039 2570.9250 2789.9993 2432.8835 2043.7400 1996.7506 1873.6708 1606.5867 1866.6876 1857.6759 2861.0000 2158.8034 2019.7287 2028.7404 1898.7025 1565.5601 1987.7138 1403.5073 2278.8092 2716.9829 2878.0153 2279.8296 2336.8511 2643.9414 2287.8460 2580.9571 2425.8875 2644.9618 2627.9465 2448.8784 2215.8249 3372.1901 2320.8562 2407.8518 2553.9097 2459.9309 2621.9837 2246.8194 2245.7990 2069.7670 2717.9782 3594.3005 3959.4327 2393.8726 1257.4494 1663.6082 1460.5288 1954.7036 1501.5554 1549.5652 1727.6129 2571.9454 2864.0361 2142.8085 2674.9359 2110.7936 2256.8515 1419.5022 4307.5496 1589.5714 3010.1191 3229.1683 3083.1355 2937.0776 3228.1730 2569.9046 1387.5124 2475.9258 2053.7721 3048.0845 2919.0419 2966.0313 3519.2684 3517.2276 3663.2855 2313.8730 2775.0248 2701.9833 3284.1741 3374.2058 3520.2637 2539.9305 2772.9840 4028.4177 3140.1570 3405.2003 3064.0794 3521.2841 3448.2426 2434.8992 3407.2411 4247.5171 1013.3434 1856.6555 2351.8507 2366.8252 2699.9676 2862.0204 2936.0572 2935.0368 2993.0787 3008.0783 3023.0528 3097.0896 3139.1366 3153.1158 3227.1526 3226.1322 3300.1941 3388.1850 3446.2269 351... 8/16 12:05 PM (2) MSFragger Info Parameter 'deneutralloss' was not supplied. Using default value: 1 8/16 12:05 PM (2) MSFragger Info Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000 8/16 12:05 PM (2) MSFragger Info Parameter 'min_sequence_matches' was not supplied. Using default value: 2 8/16 12:05 PM (2) MSFragger Info Parameter 'restrict_deltamass_to' was not supplied. Using default value: all 8/16 12:05 PM (2) MSFragger Info Parameter 'labile_search_mode' was not supplied. Using default value: OFF 8/16 12:05 PM (2) MSFragger Info Checking database... 8/16 12:05 PM (2) MSFragger Info Parameter 'data_type' was not supplied. Using default value: 0 8/16 12:05 PM (2) MSFragger Info MAIN SEARCH 8/16 12:05 PM (2) MSFragger Info Z:\2022zaloha\SP002_Neuro\210125_21SP002_4A_500ng_10ul_real.raw: Scans = 23251 8/16 12:05 PM (2) MSFragger Info Checking spectral files... 8/16 12:05 PM (2) MSFragger Info Parameter 'diagnostic_fragments' was not supplied. Using default value: 8/16 12:05 PM (2) MSFragger Info Parameter 'Y_type_masses' was not supplied. Using default value: 8/16 12:05 PM (2) MSFragger Info Parameter 'activation_types' was not supplied. Using default value: 8/16 12:05 PM (2) MSFragger Info Parameter 'use_all_mods_in_first_search' was not supplied. Using default value: 0 8/16 12:05 PM (2) MSFragger Info Parameter 'deneutralloss' was not supplied. Using default value: 1 8/16 12:05 PM (2) MSFragger Info Parameter 'diagnostic_intensity_filter' was not supplied. Using default value: 0.000000 8/16 12:05 PM (2) MSFragger Info Parameter 'min_sequence_matches' was not supplied. Using default value: 2 8/16 12:05 PM (2) MSFragger Info Checking database... 8/16 12:05 PM (2) MSFragger Info Parameter 'data_type' was not supplied. Using default value: 0 8/16 12:05 PM (2) MSFragger Info JVM started with 50 GB memory 8/16 12:05 PM (2) MSFragger Info Java Info: 18.0.2, Java HotSpot(TM) 64-Bit Server VM, Oracle Corporation 8/16 12:05 PM (2) MSFragger Info System OS: Windows 10, Architecture: AMD64 8/16 12:05 PM (2) MSFragger Info RawFileReader reading tool. Copyright (c) 2016 by Thermo Fisher Scientific, Inc. All rights reserved. 8/16 12:05 PM (2) MSFragger Info (c) University of Michigan 8/16 12:05 PM (2) MSFragger Info timsdata library version timsdata-2-8-7-1 8/16 12:05 PM (2) MSFragger Info Batmass-IO version 1.25.5 8/16 12:05 PM (2) MSFragger Info MSFragger version MSFragger-3.5 8/16 12:05 PM Job Execution Info Processing D:\PD_vyhodnocovanie\22SP002_neuro_PD_MSfrager_pokus\SP002_NEuro_MS_frager_pokus\2101257_21SP002_50c_xxx_ion_series_definitions_full__done_offset_ext_folder_xxx_java_JRE_oracle-(9).msf

If I need to provide anything else,let me know. Thank you

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/28, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWAZRLXF7XXCUWPYULXTVZOIR3ANCNFSM56VZ34BA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[adamurminsky]

Hello,

I think these numbers are the mass offsets that I defined in the MSFrager as node in PD in this row:

I thought that it is the same as in FragPipe.

Thank you for looking ar it,

Adam

[huiyinc]

Hi Adam,

Can you please tell me what the data you are processing? Is it a glyco dataset? Thanks.

Huiyin

adamurminsky @.***> 於 2022年10月11日 週二 晚上10:29寫道：

Hello,

I think these numbers are the mass offsets that I defined in the MSFrager as node in PD in this row:

[image: image] https://user-images.githubusercontent.com/109969166/195117706-59d72621-62d0-40a5-b37f-c8771ed345d2.png

I thought that it is the same as in FragPipe.

Thank you for looking ar it,

Adam

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-- Hui-Yin Chang, 張彙音 Assistant Professor Department of Biomedical Sciences and Engineering National Central University, Taiwan

[adamurminsky]

Hello Huiyin,

just to try whether it works I am using one .raw file or .mzml file. I also tried to analyze the data in frag pipe so here is more information about the data: https://github.com/Nesvilab/FragPipe/issues/812

But basically, it is a glyco data set. All of the spectra are measured in orbitrap so its high resolution and MS2 spectra are a combination of HCD and EThcD fragmentations. I specified the ions as b,y,c,z. But there may also be only b,y from HCD, but I don't know whether this is a problem.

Let me know if you need any information that may be helpful to resolve this problem. It would be very beneficial for our group if the MSFrager would work in PD.

Thank you,

Adam

[huiyinc]

Hi Adam,

Currently, the MSFragger-PD node does not support the analysis of glyco datasets, because we haven't implemented PTM-Shepherd in the PD node. So, I would suggest you to use FragPipe instead.

Best,

Huiyin

adamurminsky @.***> 於 2022年10月13日 下午8:15 寫道：



Hello Huiyin,

just to try whether it works I am using one .raw file or .mzml file. I also tried to analyze the data in frag pipe so here is more information about the data: Nesvilab/FragPipe#812 https://github.com/Nesvilab/FragPipe/issues/812

But basically, it is a glyco data set. All of the spectra are measured in orbitrap so its high resolution and MS2 spectra are a combination of HCD and EThcD fragmentations. I specified the ions as b,y,c,z. But there may also be only b,y from HCD, but I don't know whether this is a problem.

Let me know if you need any information that may be helpful to resolve this problem. It would be very beneficial for our group if the MSFrager would work in PD.

Thank you,

Adam

— Reply to this email directly, view it on GitHub https://github.com/Nesvilab/PD-Nodes/issues/28#issuecomment-1277516616, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALAWWA57SRWXAHGSV3E6CETWC74MRANCNFSM56VZ34BA . You are receiving this because you commented.Message ID: @.***>

[adamurminsky]

Thank you anyway for your time to look at this.

Adam