Peptide Missing?

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Alejandro Cohen

Jul 9, 2021, 1:27:49 PM7/9/21
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Hi MQ people,

I'm doing a quick comparison for human LFQ data I get from .raw files (QExactive) on Proteome Discoverer and MQ (using same Fasta, raw files, and matching as much as possible remaining search parameters). I'm happy to see a good overlap in protein IDs.

HOWEVER, there is one unique peptide (NKGSSAVR) which appears on PD and not in MQ>Identification>Peptide table. However, that missing peptide IS present in MQ>Scans>MS/MS Scans table and assigned to the CORRECT Protein :-O (The exported row at the end of this email)

I suppose the MSMS scan was filtered out, and did not make it to the Identifications table. My  question is: Is there a way to know WHY it was filtered out? I'm surprised to see that Andromeda correctly assigned the PSM, but somewhere on the process did not make it to the final Identification table.

Any ideas?



Raw file Scan number Retention time Ion injection time Total ion current Collision energy Summations Base peak intensity Elapsed time Identified Matched Reverse MS/MS IDs Sequence Length Filtered peaks m/z Mass Charge Type Fragmentation Mass analyzer Parent intensity fraction Fraction of total spectrum Base peak fraction Precursor full scan number Precursor intensity Precursor apex fraction Precursor apex offset Precursor apex offset time Scan event number Modifications Modified sequence Proteins Score PEP Experiment Reporter PIF Reporter fraction Intens Comp Factor CTCD Comp RawOvFtT AGC Fill Scan index MS scan index MS scan number
210609_0986_067_S04 7463 13.462 48 4694000 30 0 722310 NaN -1 NKGSSAVR 8 126 409.727922537255 817.441292141311 2 MULTI HCD FTMS 0 0 0 7459 17621186 0.679932063846957 -1 0.0165081024169922 4 Unmodified _NKGSSAVR_ C9J9C5;C9JD95;Ct-P10914;P10914;R4GNI0;V9P921 75.243467161836 0.240107312076459 4 0.6486 1.319 165718.3 1 6393 1068 7459

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