Nesvilab/FragPipe

No identifications for ETCID?

Closed this issue · 4 comments

rolivella commented

Hello

I'm running FragPipe 22.0 (linux container version) for analyzing this file but I get 0 identifications for proteins and peptides if the activation type is ETCID. For the other activation methods I got identifications (CID, HCD, ETHCD) but for ETCID nothing. And I know there're a lot of ETCID spectra like for example:
Screenshot from 2024-06-07 10-34-24
Am I doing something wrong? I put the activation type like msfragger.activation_types=ECD. And here is my workflow file:
fragpipe-qc03-run4-etcid.zip. Also the log file: fragpipe_etcid.log.zip

Thanks!

dpolasky commented

Hi,
ETciD is ETD-based and should be specified as the ETD activation type, not ECD.
Best,
Dan

rolivella commented

@dpolasky ok but I how can distinguish between ETHCD and ETCID? According the code the available types are:

    public static final String ACTIVATION_TYPE_ALL = "all";
    public static final String ACTIVATION_TYPE_HCD = "HCD";
    public static final String ACTIVATION_TYPE_ETD = "ETD";
    public static final String ACTIVATION_TYPE_CID = "CID";
    public static final String ACTIVATION_TYPE_ECD = "ECD";
rolivella commented

So I understood that:

public static final String ACTIVATION_TYPE_ETD = "ETD"; --------> ETHCD
public static final String ACTIVATION_TYPE_ECD = "ECD"; --------> ETCID

dpolasky commented

ECD is election capture dissociation and ETD is election transfer dissociation - it has nothing to do with the supplemental activation.

It is not currently supported to distinguish between EThcD and ETciD in msfragger, but you can extract them to separate mzML files with MSConvert and search them separately that way.

Best,
Dan

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