MS1 intensity from DIAmeter output

Vyacheslav Tretyachenko

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Sep 5, 2023, 12:15:28 PM9/5/23

to crux-users

Hi,

is there a way to extract exact intensity values for an identified precursors in DIAmeter? When I look in diameter.psm-features.filtered.txt I can see the log-rank values as "precursor intensity logrank M..." but not the absolute intensity. I am interested in comparison of peptideA/peptideB values across different samples.

Thank you,

Slava

Yang Lu

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Sep 5, 2023, 5:25:51 PM9/5/23

to crux-users

Thanks for your interests in DIAmeter.

There is no straightforward way to see absolute intensity values, but there is a hacking way if you are willing to compile crux.

Namely, the source code of log-rank values is at: https://github.com/crux-toolkit/crux-toolkit/blob/81a6e03402f784eff3b5ca1a21e6f638d4d21c30/src/app/DIAmeterApplication.cpp#L713

If you replace the log-rank values by the intensity values themselves and re-build crux, you should be able to get the intensity values.

Vyacheslav Tretyachenko

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Sep 6, 2023, 3:55:55 AM9/6/23

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Sound great, thank you for a tip. Unfortunately I got some issues with proteowizard during compilation. Several errors occur during the process:

/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp: In member function ‘void boost::geometry::model::d2::point_xy<CoordinateType, CoordinateSystem>::x(const CoordinateType&)’:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:69:27: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Key, class _Compare, class _Alloc> class std::set’
69 | { this->template set<0>(v); }
| ^
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:69:27: note: expected a type, got ‘0’
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:69:27: error: template argument 2 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:69:27: error: template argument 3 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp: In member function ‘void boost::geometry::model::d2::point_xy<CoordinateType, CoordinateSystem>::y(const CoordinateType&)’:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:73:27: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Key, class _Compare, class _Alloc> class std::set’
73 | { this->template set<1>(v); }
| ^
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:73:27: note: expected a type, got ‘1’
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:73:27: error: template argument 2 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xy.hpp:73:27: error: template argument 3 is invalid
In file included from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/geometries.hpp:28,
from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/io/svg/svg_mapper.hpp:43,
from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometry.hpp:127,
from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry.hpp:17,
from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/pwiz/analysis/dia_umpire/PeakCluster.hpp:40,
from /home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/pwiz/analysis/dia_umpire/DiaUmpire.cpp:45:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp: In member function ‘void boost::geometry::model::d3::point_xyz<CoordinateType, CoordinateSystem>::x(const CoordinateType&)’:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:68:27: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Key, class _Compare, class _Alloc> class std::set’
68 | { this->template set<0>(v); }
| ^
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:68:27: note: expected a type, got ‘0’
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:68:27: error: template argument 2 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:68:27: error: template argument 3 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp: In member function ‘void boost::geometry::model::d3::point_xyz<CoordinateType, CoordinateSystem>::y(const CoordinateType&)’:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:72:27: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Key, class _Compare, class _Alloc> class std::set’
72 | { this->template set<1>(v); }
| ^
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:72:27: note: expected a type, got ‘1’
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:72:27: error: template argument 2 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:72:27: error: template argument 3 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp: In member function ‘void boost::geometry::model::d3::point_xyz<CoordinateType, CoordinateSystem>::z(const CoordinateType&)’:
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:76:27: error: type/value mismatch at argument 1 in template parameter list for ‘template<class _Key, class _Compare, class _Alloc> class std::set’
76 | { this->template set<2>(v); }
| ^
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:76:27: note: expected a type, got ‘2’
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:76:27: error: template argument 2 is invalid
/home/slavat/crux-git/crux-toolkit/ext/build/src/ProteoWizard/libraries/boost_1_76_0/boost/geometry/geometries/point_xyz.hpp:76:27: error: template argument 3 is invalid

And it finally stops as this:

...failed updating 1 target...
...skipped 3 targets...
...updated 8921 targets...
At least one pwiz target failed to build.
CMake Error at /home/slavat/crux-git/crux-toolkit/ext/build_pwiz.cmake:18 (message):
ProteoWizard build failed
Call Stack (most recent call first):
/home/slavat/crux-git/crux-toolkit/ext/build_pwiz.cmake:71 (check_status)

make[2]: *** [ext/CMakeFiles/ProteoWizard.dir/build.make:86: ext/build/src/ProteoWizard-stamp/ProteoWizard-build] Error 1
make[1]: *** [CMakeFiles/Makefile2:401: ext/CMakeFiles/ProteoWizard.dir/all] Error 2
make: *** [Makefile:156: all] Error 2

Would you hint the way around it?

Dne středa 6. září 2023 v 0:25:51 UTC+3 uživatel isaac....@gmail.com napsal:

Vyacheslav Tretyachenko

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Sep 6, 2023, 4:52:38 AM9/6/23

to crux-users

...and just to be sure, you are suggesting to replace https://github.com/crux-toolkit/crux-toolkit/blob/81a6e03402f784eff3b5ca1a21e6f638d4d21c30/src/app/DIAmeterApplication.cpp#L742 with

intensity_map->insert(make_pair((*i), boost::make_tuple(intensity_m0, intensity_m1, intensity_m2))); ?

Dne středa 6. září 2023 v 10:55:55 UTC+3 uživatel Vyacheslav Tretyachenko napsal:

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