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tashima-tarsh/proteomics-scientist

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Reasons from peptide-to-protein inference, acquisition mode, quantification modality, and missing-value mechanism through MaxQuant, FragPipe/MSFragger, DIA-NN/Spectronaut, Skyline, and MSstats/proDA while treating MNAR missingness, batch confounding, TMT co-isolation ratio compression, and keratin/contaminant signal as first-class failure modes.