Search for linear modification

[cxdummies]

Dear Lutz

If I understood correctly, in the default setting, the following line defines the search for BS3amidated linear peptide

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105

In the defaut BS3 crosslinker setting, there is also the MODIFICATIONS:NH2,17.026549105

From which one of these two does xiSEARCH use to find the linear modification? Does one take precedence over the other? If BS3 is quenched by an amine-based reagent other than ammonia, e.g. Tris, where should the modifiation be defined to find the corresponding monolinks?

In the Linear Peitides result table from a search using the default BS3 setting, one can find both bs3nh and bs3nh2 in the peptide sequences. bs3nh2 is not in the search setting. Could you explain what it is and why it shows up in the sequences?

Many thanks!

[grandrea]

Hey,

As far as I know, those are additive i.e. you are defining a modification on linear peptides only called bs3nh with a deltamass of 155.094619105 AND a modification on all peptides with an NH2 group that has a mass of crosslinker mass+17.026549105. The priority will be given to the one that matches better (but here @lutzfischer is the one that should answer!).

If you want to simplify the search, use only

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105

and remove the MODIFICATIONS lines from the BS3 defitinition.

If instead you want to consider more possibilities (mods on both linear and crosslinked peptides), use only

modification:variable::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105

What you are referring to is the fact that the same syntax can be put inside the crosslinker definition instead (https://github.com/Rappsilber-Laboratory/XiSearch#crosslinker-settings)
Here with modifications on linear peptides only

crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:BS3;MASS:138.06807;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);LINEARMODIFICATIONS:NH2,17.026549105

here with modifications on all peptides

  crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:BS3;MASS:138.06807;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);MODIFICATIONS:NH2,17.026549105

to define Tris as the quencher, you can define a modification for it, again as a separate modification or inside the crosslinker definition (please double check the bs3-tris mass!!)

modification:linear::SYMBOLEXT:bs3tris;MODIFIED:K,S,T,Y;DELTAMASS:259.141973

or

modification:variable::SYMBOLEXT:bs3tris;MODIFIED:K,S,T,Y;DELTAMASS:259.141973

And the same definitions can be given inside the crosslinker as well with the same syntax as above.

[cxdummies]

Thank you very much for the explanation! It's still not entirely clear to me.

Do all peptides mean the masses of both linear and crosslinked peptides?

If MODIFICATIONS are added to the crosslinker definition, any precusor mass matched to the mass of peptide1+crosslinker+modification+peptide2 will be considered as a crosslinked peptide. If we take BS3 and NH2 as an example, where would the NH2 modification be added to peptide1-BS3-peptide2? If loop, 0 is added to the MODIFICATIONS as well, shouldn't a loop link only be considered in a linear peptide?

Would it be correct to define loop link like this?
modification:linear::SYMBOLEXT:bs3loop;MODIFIED:K,S,T,Y,nterm;DELTAMASS:138.06807

If MODIFICATIONS are added to the crosslinker definition and are searched in both linear and crosslinked peptides, would matches to linear peptides show up in the Linear Peptides result table?

In the example of modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105, why is nterm not added to MOIDIFIED? I believe that nterm is interpreted as protein N-terminus not peptide N-terminus in xiSEARCH?

In the Linear Peptides result table from a search using the default BS3 setting, one can find both bs3nh and bs3nh2 in the peptide sequences. bs3nh2 is not in the search setting. Could you explain what it is and why it shows up in the sequences?

Many many thanks!

[grandrea]

Hello,

No problem- sorry I was not clear enough, it is a bit confusing in its flexibility. There are 2 kinds of modifications: variable and linear. "Variable" searches for the modification on all peptides, "Linear" only on linear peptides.

You can encode these modifications 2 ways:

1. in a line defining a modification
2. inside the crosslinker definition

If you are encoding a linear modification with 1) indeed what you write:

modification:linear::SYMBOLEXT:bs3loop;MODIFIED:K,S,T,Y,nterm;DELTAMASS:138.06807

is correct. The deltamass is the mass change relative to the original amino acid. Then the crosslinker definition should look like this

crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:BS3;MASS:138.06807;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0)

I.e. not include the modification inside the crosslinker, as they are defined separately.

If instead you use 2), then you should not have the separate line that says modification:linear and so on, but rather

crosslinker:SymetricSingleAminoAcidRestrictedCrossLinker:Name:BS3;MASS:138.06807;LINKEDAMINOACIDS:K(0),S(0.2),T(0.2),Y(0.2),nterm(0);LINEARMODIFICATIONS:NH2,17.026549105,loop,0

In this case, the modification mass is the mass to change the crosslinker by- hence a loop link is 0 (a loop link has the same mass as a crosslink) and an nh2 group is 17.02654915. this is what defines the bs3nh2 that was not in your search.

Whether you want a linear or a variable modification in 1) is defined by the choice of

modification:linear

or

modification:variable

In 2) it is defined by using the word

MODIFICATIONS

or

LINEARMODIFICATIONS

Back to your original question- you defined the modification twice (once as a separate line and once in the crosslinker) and xiSEARCH was assigning both, also because they were defined with slightly different masses. Simply choose one and you're good to go. You can edit your config by clicking "as text config" after setting things in the interface to adjust definitions as needed.

[cxdummies]

Thank you very much for the further explanation!

If I define a monolink or a loop link in a linear peptide as follows

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y,nterm;DELTAMASS:155.094619105
modification:linear::SYMBOLEXT:bs3loop;MODIFIED:K,S,T,Y,nterm;DELTAMASS:138.06807

I think it is reasonable to include the protein N-terminus as the possible modified amino acid for a monolink. My question is does xiSEARCH treat "nterm" as protein N-terminus or peptide N-terminus in this context?

Am I correct that if I add "nterm" to the defintion of a crosslinker "nterm" will be considered as protein N-terminus?

[cxdummies]

One more question if I may. In the Github document, the following is written

"Similarly, to perform a search with a lot of modifications on a peptide, the value MAX_MODIFICATION_PER_PEPTIDE (default 3) also needs to be adjusted in order to consider combinations of more than 3 modifications. Variable modifications don't count against either limit. Both of these variables reduce the search space. Increasing them leads to a computational cost in terms of memory and search time."

Am I right that this limit of default 3 maximum modifications per peptide includes fixed modifications but not variable modifications? Does this limit include the modification:linear as well? If I define linear peptide modifications for bs3nh, bs3oh and bs3loop, would this exceed the total limit of 3 modifications already?

[grandrea]

modification:linear::SYMBOLEXT:bs3loop;MODIFIED:K,S,T,Y,nterm;DELTAMASS:138.06807

these are correct provided your crosslinker definition then does not have MODIFICATIONS or LINEARMODIFICATIONS defined in it.

"Similarly, to perform a search with a lot of modifications on a peptide, the value MAX_MODIFICATION_PER_PEPTIDE (default 3) also needs to be adjusted in order to consider combinations of more than 3 modifications. Variable modifications don't count against either limit. Both of these variables reduce the search space. Increasing them leads to a computational cost in terms of memory and search time."

I am sorry, I made a typo there. FIXED modifications do not count against the limit. Meaning, for example, if you have carbamidomethylation on C, and a peptide is GKLCMKR, the Ccm will not count against the modification limit in the search.

bs3nh, bs3oh and bs3loop, would this exceed the total limit of 3 modifications already?

No- what that means is in the step of generating theoretical peptides in the search, all those mods will be included (you can define as many as you like, but that explodes your memory and search time), but theoretical peptides will be defined with at most with MAX_MODIFICATION_PER_PEPTIDE.

For example, if you define 2 mods, "a" that can go on K/S/T/Y and "b" that can go on K/L, and set MAX_MODIFICATION_PER_PEPTIDE to 3. for the peptide

AKLSTYKNR

Only theoretical peptides with up to 3 modifications will be considered. This generates a lot of combinations! Hence there is also the number MAX_PEPTIDES_PER_PEPTIDE to tweak how many different peptides are generated per peptide

[grandrea]

"nterm" is protein N terminus and xiSEARCH automatically considers the possibility of trimming of n-terminal methionine

[cxdummies]

Thank you very much for the speedy replies!

There seems to be one problem. When I defined a linear peptide modification including "nterm" like this

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y,nterm;DELTAMASS:155.094619105

all the linear peptide modifications previously detected using MODIFIED:K,S,T,Y were gone from the linear peptide result table. Only linear peptides with a protein N-terminal modification were in the table.

If I switched the modification definition back to

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105

then all those linear peptides with the a modication showed up again in the table.

I've tried a couple of different datasets. This behaviour appeared consistent. Could this problem be solved?

[grandrea]

which version of xiSEARCH are you using? I will try to reproduce this. Could you also attach your config file?

[cxdummies]

xiSEARCH_1.7.6.7 is the version I'm using. I used MODIFIED:K,S,T,Y,nterm for all the bs3 monolink and loop link linear peptide modification search.

Many thanks.

Sorry, I was searching for where to attached a file... here it is.
bs3_nterm_Mod_linear.txt

[grandrea]

could you attach it as a text file (just change the extension to .txt) so that it doesn't take the markdown formatting

[grandrea]

could you check with this configuration: one line for mods on residue, the other line on any amino acid and specifying position

modification:linear::SYMBOLEXT:bs3nh;MODIFIED:K,S,T,Y;DELTAMASS:155.094619105
modification:linear::SYMBOLEXT:bs3nhn;MODIFIED:X;DELTAMASS:155.094619105;PROTEINPOSITION:nterm

[grandrea]

We could reproduce the bug whenever "nterm" is in the definition of the modification. The workaround of defining the n-terminal modification separately as above seems to solve the issue

[cxdummies]

Thank you! Indeed, with two separate deifintions for KSTY and nterm, it seems to have solved the issue.

Now I have 6 defined modifications (bs3nh, bs3nhn, bs3oh, bs3ohn, bs3loop, bs3loopn) instead of 3 (bs3nh, bs3oh, bs3loop), do you think I should increase the value of MAX_MODIFICATION_PER_PEPTIDE (default 3)? Or rather not, since the protein N-terminal peptide is unlikely to carry more than 3 of these different modifications?

[grandrea]

It's hard to know, that depends on the number of proteins in your database. I would start with default values and see what memory and search times come out. If your database is small, rather than increasing MAX_MODIFICATION_PER_PEPTIDE, I would increase MAX_MODIFIED_PEPTIDES_PER_PEPTIDE to for example 100, if your memory and search time allows for it. Half those mods can only occur on n-terminal peptides, so i don't think number of modifications per peptide is what is limiting you, rather how many possibilities of the different combinations to consider in site assignment.

[grandrea]

as an aside- we strongly recommend searching with multiple crosslinker and including noncovalent associations in the search

[cxdummies]

Do you mean adding unrelated crosslinkers together into the search? Is this practice more for in-cell crosslink data or also for recombinant proteins? Could you point to a publication showing the comparison to a regular single crossliner search? That would be great. Thank you.

[grandrea]

No- I mean to select "multiple crosslinkers" in the interface and select the crosslinker you used and "NonCovalent" which handles non-covalent association of peptides in the gas phase. This helps removing false positive identifications. https://github.com/Rappsilber-Laboratory/xisearch#crosslinker-selection This defines an additional crosslinker with mass 0 called "NonCovalent" (see the end of this section https://github.com/Rappsilber-Laboratory/xisearch#crosslinker-settings on how to add it to the config file).

Publication: https://pubs.acs.org/doi/10.1021/acs.analchem.8b04037 (see fig.5 for an example of why this is useful to add).

[cxdummies]

I see. Thank you very much for you help and all the speedy replies!

[cxdummies]

If I may ask again, with "NonCovalent" added, I saw an extra table "NAPS". Have these PSMs been automatically excluded from the result of the Links table?

[cxdummies]

I'm afraid I've encountered another problem. If I included crosslinker:NonCovalentBound:Name:NonCovalent additionally, the search crashed with the following error:

Search Crashed:null Peptides:DDDDK, DDDDK

What might be the problem?

[grandrea]

If I may ask again, with "NonCovalent" added, I saw an extra table "NAPS". Have these PSMs been automatically excluded from the result of the Links table?

The NAPS table reports noncovalently associated peptides and the links table your crosslinks. If you open the links table in excel, you will see the "crosslinker" column and check that no "NonCovalent" are there. MzIdentML will contain both reporting which psm is which, and xiview.org will show only crosslinkers that aren't from noncovalent association.

I'm afraid I've encountered another problem. If I included crosslinker:NonCovalentBound:Name:NonCovalent additionally, the search crashed with the following error:

Search Crashed:null Peptides:DDDDK, DDDDK

What might be the problem?

at what stage of the search? could you paste more of the log? Have you tried rerunning allocating more memory if possible?

[cxdummies]

Allocating more memory didn't help. It stopped about midway during the search. Here is the error log of the latest try.

Aug 14, 2023 2:36:27 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_27 finished (Search got stoped through config)
Aug 14, 2023 2:36:27 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_23 finished (Search got stoped through config)
Aug 14, 2023 2:36:24 PM rappsilber.ui.LoggingStatus setStatus
INFO: 68% processed (41905) 42572 read of 61021 Estimated remaining: 1minute 42seconds to 1minute 52seconds
Aug 14, 2023 2:36:22 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_29 finished (Search got stoped through config)
Aug 14, 2023 2:36:33 PM rappsilber.ui.LoggingStatus setStatus
INFO: 68% processed (41905) 42572 read of 61021 Estimated remaining: 1minute 42seconds to 1minute 52seconds
Aug 14, 2023 2:36:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_17 finished (Search got stoped through config)
Aug 14, 2023 2:36:34 PM rappsilber.ui.LoggingStatus setStatus
INFO: 69% processed (42419) 42572 read of 61021
Aug 14, 2023 2:36:34 PM rappsilber.ui.LoggingStatus setStatus
INFO: 69% processed (42419) 42572 read of 61021
Aug 14, 2023 2:36:35 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO: Search Finished (42419) 42572 read of 61021
Aug 14, 2023 2:36:35 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (42419) 42572 read of 61021 waiting for writing out results
Aug 14, 2023 2:36:35 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (42419) 42572 read of 61021 waiting for writing out results
Aug 14, 2023 2:36:36 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO:
All Results : 38135
Top Matches : 38135
Aug 14, 2023 2:36:36 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:-1 Peptides:EVEEMoxCcmK, DYD
Aug 14, 2023 2:36:36 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:-1 Peptides:EVEEMoxCcmK, DYD

[grandrea]

and the search runs otherwise through to the end without the NonCovalent line? Could you attach your current config file? Apologies for the many questions, just trying to understand.

[cxdummies]

I tried a different dataset and got the following error log if I included NAP search. Without the NonCovalent line, it always went through, also the previous one.

INFO: Search Thread Search_22 finished (Search got stoped through config)
Aug 14, 2023 5:57:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_12 finished (Search got stoped through config)
Aug 14, 2023 5:57:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_24 finished ()
Aug 14, 2023 5:57:53 PM rappsilber.ui.LoggingStatus setStatus
INFO: 74% processed (45515) 46407 read of 61021 Estimated remaining: 2minutes 45seconds to 2minutes 53seconds
Aug 14, 2023 5:57:48 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_16 finished (Search got stoped through config)
Aug 14, 2023 5:57:57 PM rappsilber.ui.LoggingStatus setStatus
INFO: 75% processed (46301) 46407 read of 61021
Aug 14, 2023 5:57:58 PM rappsilber.ui.LoggingStatus setStatus
INFO: 75% processed (46301) 46407 read of 61021
Aug 14, 2023 5:57:58 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO: Search Finished (46301) 46407 read of 61021
Aug 14, 2023 5:57:58 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (46301) 46407 read of 61021 waiting for writing out results
Aug 14, 2023 5:57:58 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (46301) 46407 read of 61021 waiting for writing out results
Aug 14, 2023 5:58:00 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO:
All Results : 41821
Top Matches : 41821
Aug 14, 2023 5:58:00 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null Peptides:DDDDK, DDDDK
Aug 14, 2023 5:58:00 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null Peptides:DDDDK, DDDDK
BS3_with_NAPsearch.txt

[lutzfischer]

can you post the full log - or email it to me? From what you send, a error occurred somewhere and as a result xisearch stopped the search. Just that the actual error is not in the part of the log you posted - need to see why that is the case -
the null in

INFO: Search Crashed:null Peptides:DDDDK, DDDDK

should have been the error reported again. I hope in the full log there is somewhere the actual error.

[cxdummies]

I've just re-run the search with apl files using the same config file. Here is the error log. Thank you.

Aug 22, 2023 5:49:24 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_10)Spectra Read 10200

Aug 22, 2023 5:49:24 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_0)Spectra Read 10200

Aug 22, 2023 5:49:24 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_29)Spectra Read 10200

Link site is < 0
DDDDK - -1
DDDDK - -1
peak_list - 15107
Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
SEVERE: (Search_32) Error while processing spectra
java.lang.ArrayIndexOutOfBoundsException

Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_19)Spectra Read 10300

Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_11)Spectra Read 10300

Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_34)Spectra Read 10300

Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_12)Spectra Read 10300

Aug 22, 2023 5:49:25 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_2)Spectra Read 10300

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_16)Spectra Read 10400

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_22)Spectra Read 10400

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_9)Spectra Read 10400

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_7)Spectra Read 10400

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_17)Spectra Read 10400

Aug 22, 2023 5:49:26 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_6)Spectra Read 10400

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_25)Spectra Read 10500

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_1)Spectra Read 10500

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_7)Spectra Read 10600

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_14)Spectra Read 10600

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_17)Spectra Read 10600

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_4)Spectra Read 10600

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_15)Spectra Read 10600

Aug 22, 2023 5:49:28 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_6)Spectra Read 10600

Aug 22, 2023 5:49:29 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_16)Spectra Read 10700

Aug 22, 2023 5:49:29 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_22)Spectra Read 10700

Aug 22, 2023 5:49:29 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_12)Spectra Read 10700

Aug 22, 2023 5:49:29 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_9)Spectra Read 10700

Aug 22, 2023 5:49:29 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_2)Spectra Read 10700

java.lang.ArrayIndexOutOfBoundsException
java.lang.ArrayIndexOutOfBoundsException
Aug 22, 2023 5:49:30 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null
Aug 22, 2023 5:49:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_29)Spectra Read 10800

Aug 22, 2023 5:49:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_34)Spectra Read 10800

Aug 22, 2023 5:49:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_19)Spectra Read 10800

Aug 22, 2023 5:49:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_11)Spectra Read 10800

Aug 22, 2023 5:49:30 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_0)Spectra Read 10800

Aug 22, 2023 5:49:31 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_23)Spectra Read 10900

Aug 22, 2023 5:49:31 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_10)Spectra Read 10900

Aug 22, 2023 5:49:31 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_20)Spectra Read 10900

Aug 22, 2023 5:49:31 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_27)Spectra Read 10900

Aug 22, 2023 5:49:31 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_33)Spectra Read 10900

Aug 22, 2023 5:49:32 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_26)Spectra Read 11000

Aug 22, 2023 5:49:32 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_13)Spectra Read 11000

Aug 22, 2023 5:49:32 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_3)Spectra Read 11000

Aug 22, 2023 5:49:32 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_8)Spectra Read 11000

Aug 22, 2023 5:49:32 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_24)Spectra Read 11000

Aug 22, 2023 5:49:33 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_30)Spectra Read 11100

Aug 22, 2023 5:49:33 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_21)Spectra Read 11100

Aug 22, 2023 5:49:33 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_31)Spectra Read 11100

Aug 22, 2023 5:49:33 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_18)Spectra Read 11100

Aug 22, 2023 5:49:33 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_28)Spectra Read 11100

Aug 22, 2023 5:49:34 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_18)Spectra Read 11200

Aug 22, 2023 5:49:34 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_31)Spectra Read 11200

Aug 22, 2023 5:49:34 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_21)Spectra Read 11200

Aug 22, 2023 5:49:34 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_28)Spectra Read 11200

Aug 22, 2023 5:49:34 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_5)Spectra Read 11200

Aug 22, 2023 5:49:35 PM rappsilber.ui.LoggingStatus setStatus
INFO: 15% processed (10222) 11354 read of 65740 Estimated time remaining: 8minutes
Aug 22, 2023 5:49:35 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_13)Spectra Read 11300

Aug 22, 2023 5:49:35 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_3)Spectra Read 11300

Aug 22, 2023 5:49:35 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_8)Spectra Read 11300

Aug 22, 2023 5:49:35 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_30)Spectra Read 11300

Aug 22, 2023 5:49:35 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_24)Spectra Read 11300

Aug 22, 2023 5:49:36 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_20)Spectra Read 11400

Aug 22, 2023 5:49:36 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_27)Spectra Read 11400

Aug 22, 2023 5:49:36 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_26)Spectra Read 11400

Aug 22, 2023 5:49:36 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_33)Spectra Read 11400

Aug 22, 2023 5:49:36 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_10)Spectra Read 11400

Aug 22, 2023 5:49:37 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_0)Spectra Read 11500

Aug 22, 2023 5:49:37 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_11)Spectra Read 11500

Aug 22, 2023 5:49:37 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_19)Spectra Read 11500

Aug 22, 2023 5:49:37 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_23)Spectra Read 11500

Aug 22, 2023 5:49:37 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_34)Spectra Read 11500

Aug 22, 2023 5:49:38 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null
Aug 22, 2023 5:49:39 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_29)Spectra Read 11600

Aug 22, 2023 5:49:39 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_22)Spectra Read 11600

Aug 22, 2023 5:49:39 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_12)Spectra Read 11600

Aug 22, 2023 5:49:39 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_9)Spectra Read 11600

Aug 22, 2023 5:49:39 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_2)Spectra Read 11600

Aug 22, 2023 5:49:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_6)Spectra Read 11700

Aug 22, 2023 5:49:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_16)Spectra Read 11700

Aug 22, 2023 5:49:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_4)Spectra Read 11700

Aug 22, 2023 5:49:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_15)Spectra Read 11700

Aug 22, 2023 5:49:40 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_17)Spectra Read 11700

Aug 22, 2023 5:49:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_1)Spectra Read 11800

Aug 22, 2023 5:49:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_25)Spectra Read 11800

Aug 22, 2023 5:49:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_14)Spectra Read 11800

Aug 22, 2023 5:49:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_7)Spectra Read 11800

Aug 22, 2023 5:49:41 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_17)Spectra Read 11800

Aug 22, 2023 5:49:42 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_6)Spectra Read 11900

Aug 22, 2023 5:49:42 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_16)Spectra Read 11900

Aug 22, 2023 5:49:42 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_4)Spectra Read 11900

Aug 22, 2023 5:49:42 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_15)Spectra Read 11900

Aug 22, 2023 5:49:43 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_12)Spectra Read 12000

Aug 22, 2023 5:49:43 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_22)Spectra Read 12000

Aug 22, 2023 5:49:43 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_2)Spectra Read 12000

Aug 22, 2023 5:49:43 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_9)Spectra Read 12000

Aug 22, 2023 5:49:43 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
SEVERE: Crashed Spectrum:Run Scan Precursor MZ Charge Intensity Elution Time
peak_list 15107 451.84039710915 3 -1.0 -1.0
IONS
MZ Intensity
141.0660 7,395.5050
141.1024 7,243.7240
143.0817 4,371.9595
143.1178 64,285.5695
147.1128 129,405.3185
148.1165 18,902.7418
155.0816 4,018.4321
156.0769 23,384.7671
156.1125 4,941.3848
157.1086 11,678.0094
157.1337 11,663.1650
158.0922 40,361.1802
158.3871 4,217.0067
159.0767 16,710.7928
167.0815 13,511.2988
167.0929 42,755.8080
167.1178 13,928.7095
167.7191 6,132.3191
169.0974 7,357.5571
171.0768 4,502.1553
171.1127 27,560.0462
173.1286 4,585.5764
175.1189 177,503.5023
176.1227 7,871.4823
178.0529 9,649.2245
179.0930 10,661.8127
181.0724 4,290.5057
181.0977 4,260.1880
183.0764 13,166.5104
183.1128 24,732.4634
185.1648 16,923.5076
187.1079 10,219.1492
187.1441 12,858.8215
188.0703 9,906.9669
193.0715 11,518.0673
193.0972 7,137.8738
195.0769 21,333.7134
195.0874 8,282.4958
195.1130 7,209.5736
197.1032 5,704.9167
197.1284 13,571.8397
197.1650 14,302.3501
200.1394 4,584.2729
201.1234 14,040.4225
205.0967 5,404.1622
207.0876 5,000.2290
210.0251 4,954.6202
212.1029 10,158.7423
213.0869 10,288.6570
213.1601 9,744.4558
215.1382 5,075.6044
216.0977 9,500.4988
218.1496 5,670.3188
219.0765 9,044.9713
221.0917 5,367.2045
221.1284 63,264.0602
222.1327 15,201.9583
224.1142 15,380.6140
225.0980 14,176.8213
226.1188 20,616.0753
226.1548 34,221.3619
227.1385 4,263.5447
227.1585 12,219.3717
229.1176 7,324.6584
229.1304 7,940.6876
232.1396 16,787.7302
234.0199 5,867.2316
235.0830 10,600.7324
239.1136 15,594.3457
240.0993 5,066.3674
240.1342 57,906.6068
241.0816 10,784.4265
242.1864 7,688.8884
244.0932 8,501.5516
244.1300 5,559.8341
244.1653 205,493.7265
245.0921 9,712.1479
245.1691 81,910.7480
246.1558 18,652.2784
246.1709 10,492.5066
249.1235 27,894.0498
249.1594 10,404.9008
252.1100 10,222.3237
257.6524 13,453.8000
258.1453 9,960.2947
260.1969 11,654.9697
261.0068 8,033.6813
262.1398 20,856.3160
266.1121 5,222.8575
266.1642 7,867.3547
271.0722 8,463.8667
271.1757 11,741.8027
278.0332 25,524.4142
279.0418 21,498.5913
284.1216 4,917.2097
287.1351 5,012.5095
288.2028 183,238.6385
289.0819 18,987.0857
289.2064 20,574.9457
293.0888 11,003.3398
293.1245 9,162.8093
294.1551 7,041.7421
302.0843 6,523.3436
304.1612 7,385.8373
305.0968 7,099.0040
306.1455 6,931.5052
310.1143 91,041.4001
311.1179 40,755.7957
312.1189 5,024.2598
317.0764 11,425.9384
318.3812 4,214.4979
319.1112 8,562.5142
321.1555 8,521.6572
323.1714 34,035.9979
331.6863 5,012.4852
333.1714 4,949.1083
338.1834 17,020.1599
351.1661 24,415.9935
358.1739 8,785.2582
358.6463 7,699.6733
362.0784 8,569.3256
368.1927 6,810.9236
369.1771 6,020.9064
375.1989 11,026.2212
376.2018 4,176.7770
377.2161 4,350.0781
386.2043 8,196.8324
386.7404 12,021.8546
387.1957 12,634.4971
387.7004 5,169.8640
388.4838 8,770.7041
389.1520 18,780.9703
394.7122 5,376.2205
397.2210 5,858.1299
397.7108 5,601.1615
399.2016 7,667.3274
401.7343 4,464.2046
403.2293 87,513.4819
404.2309 9,024.4253
406.0695 13,351.4266
406.1746 5,814.4297
406.2249 144,557.6719
406.7265 51,903.6146
407.2276 15,688.8040
408.6164 11,232.4469
409.1830 40,313.7278
410.1850 30,235.3190
413.4910 5,516.4382
416.8181 40,572.7339
417.1490 17,015.7454
417.2459 4,722.9198
417.4881 14,699.0818
418.2420 6,282.8809
419.2139 6,710.2559
422.1591 8,186.5226
422.4912 5,622.5585
422.8215 298,633.0052
423.1558 161,521.6492
423.2106 9,215.4685
423.4906 50,462.9229
423.6128 8,222.8335
424.2189 6,526.5125
426.1628 5,001.2993
426.4949 7,983.1530
429.2515 5,089.2992
432.6185 17,415.7842
433.1197 10,393.3771
434.0646 10,298.2239
434.2093 23,476.7626
434.2436 7,711.6893
435.1987 12,595.1537
437.1712 7,882.3562
441.2188 5,035.6761
442.2056 38,207.5979
442.7115 23,343.9634
442.7565 11,152.1665
443.7280 27,881.6177
445.2460 7,203.4740
445.5817 5,575.3916
446.1714 12,178.9833
446.2354 29,813.0785
446.4995 5,376.1804
451.2000 11,988.7739
451.2316 50,042.9141
451.2663 412,127.9458
451.5975 18,975.0898
451.7297 15,375.0803
451.7667 125,730.9688
451.8406 17,270.7051
452.1447 14,253.7783
452.2176 47,354.9297
452.2425 138,458.6765
452.5085 6,719.4167
452.7471 10,018.2280
473.3099 6,629.1217
476.0509 9,587.2222
487.7364 13,274.5325
488.2358 5,241.3086
490.1318 8,965.9834
514.6948 5,082.4253
515.3255 9,362.1859
516.2439 5,373.4178
528.8292 5,740.3069
531.3260 31,319.5198
532.3297 5,753.6365
536.2930 12,864.9069
538.2404 10,144.8088
541.2111 5,590.9725
541.2944 5,213.6273
542.2698 7,062.1750
557.2565 11,696.6277
564.3476 33,657.7361
564.8521 21,552.6675
565.3521 9,913.2429
574.2930 11,917.4457
586.3165 12,303.2858
598.7255 12,221.3851
601.2413 5,226.1245
603.3182 9,581.6439
605.0902 27,724.6561
606.0961 11,058.5092
615.3238 7,183.6165
631.3143 46,855.9558
632.3202 9,112.2345
637.3440 5,479.3652
643.3160 11,816.1665
644.2826 29,737.6061
644.3485 6,700.9297
645.2853 6,136.8088
648.1377 5,020.6737
652.3380 5,642.0612
653.3456 23,233.0205
657.2982 58,162.5481
658.3016 158,059.0532
659.3062 47,774.5322
659.8174 7,371.6405
660.3241 7,562.2377
662.3655 10,699.7832
665.3359 37,610.9529
666.3401 14,847.1145
670.3617 5,383.0471
672.3494 6,527.9521
673.3934 30,299.3564
674.3892 5,903.1533
683.3529 5,669.9890
692.1475 8,009.0298
693.1604 6,031.4760
714.8408 5,122.5312
727.4234 5,032.2051
729.3577 9,015.2909
732.3650 39,347.7136
733.3685 10,667.2991
736.1333 13,712.2228
747.3784 16,595.5167
788.4249 7,293.5858
811.4414 25,972.7211
812.4439 5,854.0320
954.4605 4,463.6772
993.4750 4,973.1412

Aug 22, 2023 5:49:44 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_29)Spectra Read 12100

Aug 22, 2023 5:49:44 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_19)Spectra Read 12100

Aug 22, 2023 5:49:44 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_23)Spectra Read 12100

Aug 22, 2023 5:49:44 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_34)Spectra Read 12100

Aug 22, 2023 5:49:45 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_10)Spectra Read 12200

Aug 22, 2023 5:49:46 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_33)Spectra Read 12200

Aug 22, 2023 5:49:46 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_11)Spectra Read 12200

Aug 22, 2023 5:49:46 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_0)Spectra Read 12200

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_20)Spectra Read 12300

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_24)Spectra Read 12300

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_26)Spectra Read 12300

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_8)Spectra Read 12400

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_13)Spectra Read 12400

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_30)Spectra Read 12400

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_27)Spectra Read 12400

Aug 22, 2023 5:49:47 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_3)Spectra Read 12400

Aug 22, 2023 5:49:48 PM rappsilber.ui.LoggingStatus setStatus
INFO: 15% processed (10222) 11354 read of 65740 Estimated time remaining: 8minutes
Aug 22, 2023 5:49:49 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_21)Spectra Read 12500

Aug 22, 2023 5:49:49 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_5)Spectra Read 12500

Aug 22, 2023 5:49:49 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_28)Spectra Read 12500

Aug 22, 2023 5:49:49 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_31)Spectra Read 12500

Aug 22, 2023 5:49:50 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_28)Spectra Read 12600

Aug 22, 2023 5:49:50 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_5)Spectra Read 12600

Aug 22, 2023 5:49:50 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_31)Spectra Read 12600

Aug 22, 2023 5:49:50 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_18)Spectra Read 12600

Aug 22, 2023 5:49:51 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_30)Spectra Read 12700

Aug 22, 2023 5:49:51 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_3)Spectra Read 12700

Aug 22, 2023 5:49:51 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_21)Spectra Read 12700

Aug 22, 2023 5:49:51 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_27)Spectra Read 12700

Aug 22, 2023 5:49:52 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_26)Spectra Read 12800

Aug 22, 2023 5:49:52 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_24)Spectra Read 12800

Aug 22, 2023 5:49:52 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_13)Spectra Read 12800

Aug 22, 2023 5:49:52 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_8)Spectra Read 12800

Aug 22, 2023 5:49:53 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_20)Spectra Read 12900

Aug 22, 2023 5:49:53 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_33)Spectra Read 12900

Aug 22, 2023 5:49:53 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_0)Spectra Read 12900

Aug 22, 2023 5:49:54 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_23)Spectra Read 13000

Aug 22, 2023 5:49:54 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_10)Spectra Read 13000

Aug 22, 2023 5:49:54 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_34)Spectra Read 13000

Aug 22, 2023 5:49:54 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_11)Spectra Read 13000

Aug 22, 2023 5:49:54 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: (Search_19)Spectra Read 13000

Aug 22, 2023 5:49:55 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_32 finished ()
Aug 22, 2023 5:49:55 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_29 finished (Search got stoped through config)
Aug 22, 2023 5:49:55 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_9 finished (Search got stoped through config)
Aug 22, 2023 5:49:55 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_2 finished (Search got stoped through config)
Aug 22, 2023 5:49:56 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_22 finished (Search got stoped through config)
Aug 22, 2023 5:49:56 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_12 finished (Search got stoped through config)
Aug 22, 2023 5:49:56 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_15 finished (Search got stoped through config)
Aug 22, 2023 5:49:57 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_4 finished (Search got stoped through config)
Aug 22, 2023 5:49:57 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_16 finished (Search got stoped through config)
Aug 22, 2023 5:49:57 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_6 finished (Search got stoped through config)
Aug 22, 2023 5:49:57 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_17 finished (Search got stoped through config)
Aug 22, 2023 5:49:58 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_7 finished (Search got stoped through config)
Aug 22, 2023 5:49:58 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_14 finished (Search got stoped through config)
Aug 22, 2023 5:49:58 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_25 finished (Search got stoped through config)
Aug 22, 2023 5:49:59 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_1 finished (Search got stoped through config)
Aug 22, 2023 5:50:03 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_19 finished (Search got stoped through config)
Aug 22, 2023 5:50:03 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_11 finished (Search got stoped through config)
Aug 22, 2023 5:50:03 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_34 finished (Search got stoped through config)
Aug 22, 2023 5:50:04 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_10 finished (Search got stoped through config)
Aug 22, 2023 5:50:04 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_23 finished (Search got stoped through config)
Aug 22, 2023 5:50:04 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_0 finished (Search got stoped through config)
Aug 22, 2023 5:50:05 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_20 finished (Search got stoped through config)
Aug 22, 2023 5:50:05 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_33 finished (Search got stoped through config)
Aug 22, 2023 5:50:05 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_8 finished (Search got stoped through config)
Aug 22, 2023 5:50:06 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_13 finished (Search got stoped through config)
Aug 22, 2023 5:50:06 PM rappsilber.ui.LoggingStatus setStatus
INFO: 19% processed (12535) 13114 read of 65740 Estimated time remaining: 8minutes
Aug 22, 2023 5:50:06 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_24 finished (Search got stoped through config)
Aug 22, 2023 5:50:06 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_26 finished (Search got stoped through config)
Aug 22, 2023 5:50:07 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_27 finished (Search got stoped through config)
Aug 22, 2023 5:50:07 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_21 finished (Search got stoped through config)
Aug 22, 2023 5:50:07 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_3 finished (Search got stoped through config)
Aug 22, 2023 5:50:08 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_30 finished (Search got stoped through config)
Aug 22, 2023 5:50:08 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_18 finished (Search got stoped through config)
Aug 22, 2023 5:50:08 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_31 finished (Search got stoped through config)
Aug 22, 2023 5:50:09 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_5 finished (Search got stoped through config)
Aug 22, 2023 5:50:09 PM rappsilber.applications.SimpleXiProcessMultipleCandidates process
INFO: Search Thread Search_28 finished (Search got stoped through config)
Aug 22, 2023 5:50:12 PM rappsilber.ui.LoggingStatus setStatus
INFO: 19% processed (12535) 13114 read of 65740 Estimated time remaining: 8minutes
Aug 22, 2023 5:50:16 PM rappsilber.ui.LoggingStatus setStatus
INFO: 19% processed (13024) 13114 read of 65740
Aug 22, 2023 5:50:17 PM rappsilber.ui.LoggingStatus setStatus
INFO: 19% processed (13024) 13114 read of 65740
Aug 22, 2023 5:50:18 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO: Search Finished (13024) 13114 read of 65740
Aug 22, 2023 5:50:18 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (13024) 13114 read of 65740 waiting for writing out results
Aug 22, 2023 5:50:19 PM rappsilber.ui.LoggingStatus setStatus
INFO: Finished (13024) 13114 read of 65740 waiting for writing out results
Aug 22, 2023 5:50:19 PM rappsilber.applications.SimpleXiProcess waitEnd
INFO:
All Results : 11267
Top Matches : 11267
Aug 22, 2023 5:50:19 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null Peptides:EVEEMoxCcmK, DYD
Aug 22, 2023 5:50:20 PM rappsilber.ui.LoggingStatus setStatus
INFO: Search Crashed:null Peptides:EVEEMoxCcmK, DYD

[grandrea]

hello,
Could you repeat your search with .mgf files insead of .apl? Apl files also provide spectra with unknown precursor charge state. Could be that that is part of the problem

[cxdummies]

I only used the sil0.apl files and I can confirm that every spectrum in there has a known precursor charge state.

In the NAP paper, I tried to find an answer to why QE produced a higher proportion of NAP peptides compared to Velos or even to Lumos which uses a quad similar to QE's as an ion filter. I could not find it. Maybe I missed it in the paper. Could you comment on this?

[lutzfischer]

I am not aware that there is any official reason given for that behaviour.

But the reason for more NAPs in QE products MIGHT be down to how the ions get forwarded into the machine. The "lens" (is named somewhat differently in different machines) is different and might lead to peptides not as easily (in relative terms) disassociate for QE than in others. But that is only an very untested hypothesis. When we looked at crosslink identifications from an early qexactive instrument - without considering non-covalent peptides at the time - we had an surprising number of overlength and in fact made us in turn aware of the problem of non-covalent associated peptides.